6FTI

Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the Programmed 80S Ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

Structural basis for coupling protein transport and N-glycosylation at the mammalian endoplasmic reticulum.

Braunger, K.Pfeffer, S.Shrimal, S.Gilmore, R.Berninghausen, O.Mandon, E.C.Becker, T.Forster, F.Beckmann, R.

(2018) Science 360: 215-219

  • DOI: https://doi.org/10.1126/science.aar7899
  • Primary Citation of Related Structures:  
    6FTG, 6FTI, 6FTJ

  • PubMed Abstract: 

    Protein synthesis, transport, and N-glycosylation are coupled at the mammalian endoplasmic reticulum by complex formation of a ribosome, the Sec61 protein-conducting channel, and oligosaccharyltransferase (OST). Here we used different cryo-electron microscopy approaches to determine structures of native and solubilized ribosome-Sec61-OST complexes. A molecular model for the catalytic OST subunit STT3A (staurosporine and temperature sensitive 3A) revealed how it is integrated into the OST and how STT3-paralog specificity for translocon-associated OST is achieved. The OST subunit DC2 was placed at the interface between Sec61 and STT3A, where it acts as a versatile module for recruitment of STT3A-containing OST to the ribosome-Sec61 complex. This detailed structural view on the molecular architecture of the cotranslational machinery for N-glycosylation provides the basis for a mechanistic understanding of glycoprotein biogenesis at the endoplasmic reticulum.


  • Organizational Affiliation

    Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, 81377 Munich, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
uL2244Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
uL3394Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L4362Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SVW5 (Oryctolagus cuniculus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5292Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SYJ6 (Oryctolagus cuniculus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6248Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TG04 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
uL30225Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SV32 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
eL8241Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1STW0 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
uL6190Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L10 (Predicted)213Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for B7NZQ2 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L11169Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
eL13K [auth L]210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L14L [auth M]138Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for U3KNW6 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15M [auth N]203Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T0C1 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
uL13N [auth O]199Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
uL22O [auth P]153Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TVT6 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
uL14P [auth Q]187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
eL19Q [auth R]180Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
eL20R [auth S]175Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
eL21S [auth T]159Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
eL22T [auth U]99Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
uL14U [auth V]131Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24V [auth W]63Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
uL23W [auth X]119Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26X [auth Y]134Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27Y [auth Z]135Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
uL15Z [auth a]147Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SNY0 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29AA [auth b]75Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TN82 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
eL30BA [auth c]94Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
eL31CA [auth d]107Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SHG0 (Oryctolagus cuniculus)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
eL32DA [auth e]128Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TUN8 (Oryctolagus cuniculus)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
eL33EA [auth f]109Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SF08 (Oryctolagus cuniculus)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
eL34FA [auth g]114Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1U945 (Oryctolagus cuniculus)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
uL29GA [auth h]122Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SIT5 (Oryctolagus cuniculus)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36HA [auth i]102Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TTQ5 (Oryctolagus cuniculus)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37IA [auth j]86Oryctolagus cuniculusMutation(s): 0 
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Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
eL38JA [auth k]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
eL39KA [auth l]50Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SYU7 (Oryctolagus cuniculus)
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
eL40LA [auth m]52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60s ribosomal protein l41MA [auth n]23Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
eL42NA [auth o]104Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T040 (Oryctolagus cuniculus)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37aOA [auth p]91Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
eL28PA [auth r]136Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0QA [auth s]198Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L12RA [auth t]163Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit alpha isoform 1WA [auth x]461Canis lupus familiarisMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit gammaXA [auth y]62Canis lupus familiarisMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit betaYA [auth z]29Canis lupus familiarisMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1,RPN1ZA [auth 1]162Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for E2RQ08 (Canis lupus familiaris)
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
TMEM258AB [auth 2]60Canis lupus familiarisMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Oligosaccharyltransferase complex subunit OSTCBB [auth 3]120Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for P86218 (Canis lupus familiaris)
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UniProt GroupP86218
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4CB [auth 4]34Canis lupus familiarisMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3ADB [auth 5]705Canis lupus familiarisMutation(s): 0 
EC: 2.4.99.18
UniProt
Find proteins for F1PJP5 (Canis lupus familiaris)
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UniProt GroupF1PJP5
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
DAD1EB [auth 6]109Canis lupus familiarisMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
OST48FB [auth 7]25Canis lupus familiarisMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
RPN1GB [auth 8]80Canis lupus familiarisMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Unidentified TMHB [auth 0]24Canis lupus familiarisMutation(s): 0 
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Entity ID: 45
MoleculeChains LengthOrganismImage
p-Site tRNASA [auth q]76Oryctolagus cuniculus
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Entity ID: 46
MoleculeChains LengthOrganismImage
28S rRNATA [auth u]3,662Oryctolagus cuniculus
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Entity ID: 47
MoleculeChains LengthOrganismImage
5S ribosomal RNAUA [auth v]120Oryctolagus cuniculus
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Entity ID: 48
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAVA [auth w]156Oryctolagus cuniculus
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Oligosaccharides

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Entity ID: 61
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseIB [auth K]8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G83582BK
GlyCosmos:  G83582BK
GlyGen:  G83582BK
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9UB
Query on 9UB

Download Ideal Coordinates CCD File 
RH [auth 5][(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl]oxy-phosphinic acid
C29 H51 N O11 P2
ZBWKCDFMHFZRQG-MJTKDKBSSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
PB [auth g],
RB [auth j],
SB [auth m],
TB [auth o],
UB [auth p]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth u]
AD [auth u]
AE [auth u]
AF [auth u]
AG [auth u]
AC [auth u],
AD [auth u],
AE [auth u],
AF [auth u],
AG [auth u],
AH [auth u],
BC [auth u],
BD [auth u],
BE [auth u],
BF [auth u],
BG [auth u],
BH [auth u],
CC [auth u],
CD [auth u],
CE [auth u],
CF [auth u],
CG [auth u],
CH [auth u],
DC [auth u],
DD [auth u],
DE [auth u],
DF [auth u],
DG [auth u],
DH [auth u],
EC [auth u],
ED [auth u],
EE [auth u],
EF [auth u],
EG [auth u],
EH [auth u],
FC [auth u],
FD [auth u],
FE [auth u],
FF [auth u],
FG [auth u],
FH [auth u],
GC [auth u],
GD [auth u],
GE [auth u],
GF [auth u],
GG [auth u],
GH [auth u],
HC [auth u],
HD [auth u],
HE [auth u],
HF [auth u],
HG [auth u],
HH [auth u],
IC [auth u],
ID [auth u],
IE [auth u],
IF [auth u],
IG [auth u],
IH [auth u],
JB [auth B],
JC [auth u],
JD [auth u],
JE [auth u],
JF [auth u],
JG [auth u],
JH [auth u],
KB [auth I],
KC [auth u],
KD [auth u],
KE [auth u],
KF [auth u],
KG [auth u],
KH [auth v],
LB [auth P],
LC [auth u],
LD [auth u],
LE [auth u],
LF [auth u],
LG [auth u],
LH [auth v],
MB [auth V],
MC [auth u],
MD [auth u],
ME [auth u],
MF [auth u],
MG [auth u],
MH [auth v],
NB [auth a],
NC [auth u],
ND [auth u],
NE [auth u],
NF [auth u],
NG [auth u],
NH [auth v],
OB [auth e],
OC [auth u],
OD [auth u],
OE [auth u],
OF [auth u],
OG [auth u],
OH [auth v],
PC [auth u],
PD [auth u],
PE [auth u],
PF [auth u],
PG [auth u],
PH [auth w],
QB [auth g],
QC [auth u],
QD [auth u],
QE [auth u],
QF [auth u],
QG [auth u],
QH [auth w],
RC [auth u],
RD [auth u],
RE [auth u],
RF [auth u],
RG [auth u],
SC [auth u],
SD [auth u],
SE [auth u],
SF [auth u],
SG [auth u],
TC [auth u],
TD [auth u],
TE [auth u],
TF [auth u],
TG [auth u],
UC [auth u],
UD [auth u],
UE [auth u],
UF [auth u],
UG [auth u],
VB [auth u],
VC [auth u],
VD [auth u],
VE [auth u],
VF [auth u],
VG [auth u],
WB [auth u],
WC [auth u],
WD [auth u],
WE [auth u],
WF [auth u],
WG [auth u],
XB [auth u],
XC [auth u],
XD [auth u],
XE [auth u],
XF [auth u],
XG [auth u],
YB [auth u],
YC [auth u],
YD [auth u],
YE [auth u],
YF [auth u],
YG [auth u],
ZB [auth u],
ZC [auth u],
ZD [auth u],
ZE [auth u],
ZF [auth u],
ZG [auth u]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyGRK1721
European Research CouncilGermanyCRYOTRANSLATION
German Research FoundationGermanySFB646
Center for Integrated Protein Science MunichGermany--
Boehringer Ingelheim FondsGermanyPhD Fellowship

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 2.0: 2018-04-04
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations
  • Version 2.1: 2018-04-25
    Changes: Data collection, Database references
  • Version 2.2: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 2.3: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 2.4: 2019-12-11
    Changes: Other
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary