4V6M

Structure of the ribosome-SecYE complex in the membrane environment


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.6 of the entry. See complete history


Literature

Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.

Frauenfeld, J.Gumbart, J.Sluis, E.O.Funes, S.Gartmann, M.Beatrix, B.Mielke, T.Berninghausen, O.Becker, T.Schulten, K.Beckmann, R.

(2011) Nat Struct Mol Biol 18: 614-621

  • DOI: https://doi.org/10.1038/nsmb.2026
  • Primary Citation of Related Structures:  
    4V6M

  • PubMed Abstract: 

    The ubiquitous SecY-Sec61 complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers. Several structures of mostly detergent-solubilized Sec complexes have been reported. Here we present a single-particle cryo-EM structure of the SecYEG complex in a membrane environment, bound to a translating ribosome, at subnanometer resolution. Using the SecYEG complex reconstituted in a so-called Nanodisc, we could trace the nascent polypeptide chain from the peptidyltransferase center into the membrane. The reconstruction allowed for the identification of ribosome-lipid interactions. The rRNA helix 59 (H59) directly contacts the lipid surface and appears to modulate the membrane in immediate vicinity to the proposed lateral gate of the protein-conducting channel (PCC). On the basis of our map and molecular dynamics simulations, we present a model of a signal anchor-gated PCC in the membrane.


  • Organizational Affiliation

    Gene Center, Department for Biochemistry, University of Munich, Munich, Germany.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division protein FtsQD [auth AZ]98Escherichia coli O157:H7Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Apolipoprotein A-IE [auth A0],
F [auth A1]
200Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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PHAROS:  P02647
GTEx:  ENSG00000118137 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2G [auth AB]240Escherichia coli K-12Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3H [auth AC]232Escherichia coli K-12Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4I [auth AD]205Escherichia coli K-12Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5J [auth AE]166Escherichia coli K-12Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6K [auth AF]135Escherichia coli K-12Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7L [auth AG]178Escherichia coli K-12Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8M [auth AH]129Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9N [auth AI]129Escherichia coli K-12Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10O [auth AJ]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11P [auth AK]128Escherichia coli K-12Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12Q [auth AL]123Escherichia coli K-12Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13R [auth AM]117Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14S [auth AN]100Escherichia coli K-12Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15T [auth AO]88Escherichia coli K-12Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16U [auth AP]82Escherichia coli K-12Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17V [auth AQ]83Escherichia coli K-12Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18W [auth AR]74Escherichia coli K-12Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19X [auth AS]91Escherichia coli K-12Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20Y [auth AT]86Escherichia coli K-12Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21Z [auth AU]70Escherichia coli K-12Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Preprotein translocase secY subunitCA [auth BA]435Escherichia coli 536Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Preprotein translocase secE subunitDA [auth BB]116Escherichia coli 536Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1EA [auth B5]234Escherichia coli K-12Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2FA [auth B6]272Escherichia coli K-12Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3GA [auth BD]209Escherichia coli K-12Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4HA [auth BE]201Escherichia coli K-12Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5IA [auth BF]178Escherichia coli K-12Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6JA [auth BG]176Escherichia coli K-12Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9KA [auth BH]149Escherichia coli K-12Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11LA [auth BI]141Escherichia coli K-12Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13MA [auth BJ]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14NA [auth BK]123Escherichia coli K-12Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15OA [auth BL]144Escherichia coli K-12Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16PA [auth BM]136Escherichia coli K-12Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17QA [auth BN]127Escherichia coli K-12Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18RA [auth BO]117Escherichia coli K-12Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19SA [auth BP]114Escherichia coli K-12Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20TA [auth BQ]117Escherichia coli K-12Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21UA [auth BR]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22VA [auth BS]110Escherichia coli K-12Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23WA [auth BT]100Escherichia coli K-12Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24XA [auth BU]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25YA [auth BV]94Escherichia coli K-12Mutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27ZA [auth BW]84Escherichia coli K-12Mutation(s): 0 
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Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28AB [auth BX]77Escherichia coli K-12Mutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29BB [auth BY]63Escherichia coli K-12Mutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30CB [auth BZ]58Escherichia coli K-12Mutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32DB [auth B0]56Escherichia coli K-12Mutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33EB [auth B1]54Escherichia coli K-12Mutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34FB [auth B2]46Escherichia coli K-12Mutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35GB [auth B3]64Escherichia coli K-12Mutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36HB [auth B4]38Escherichia coli K-12Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S RIBOSOMAL RNAA [auth AA]1,542Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
mRNAB [auth AX]11Escherichia coli
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Entity ID: 3
MoleculeChains LengthOrganismImage
FtsQ nascent chainC [auth AV]77Escherichia coli DH1
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Entity ID: 26
MoleculeChains LengthOrganismImage
5S RIBOSOMAL RNAAA [auth B7]120Escherichia coli DH1
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Entity ID: 27
MoleculeChains LengthOrganismImage
23S RIBOSOMAL RNABA [auth B8]2,904Escherichia coli DH1
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGV
Query on PGV

Download Ideal Coordinates CCD File 
AF [auth BA]
AG [auth BB]
CE [auth B8]
FC [auth A0]
FD [auth A1]
AF [auth BA],
AG [auth BB],
CE [auth B8],
FC [auth A0],
FD [auth A1],
FE [auth BA],
FG [auth BB],
GC [auth A0],
JD [auth A1],
JE [auth BA],
JG [auth BB],
MB [auth AZ],
MD [auth A1],
NC [auth A0],
OB [auth AZ],
OF [auth BA],
PC [auth A0],
QC [auth A0],
QE [auth BA],
SB [auth A0],
SF [auth BA],
TB [auth A0],
TC [auth A0],
TE [auth BA],
UB [auth A0],
UC [auth A0],
UE [auth BA],
VF [auth BB],
WF [auth BB],
XC [auth A1],
XF [auth BB],
ZF [auth BB]
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
PEV
Query on PEV

Download Ideal Coordinates CCD File 
AC [auth A0]
AD [auth A1]
AE [auth B8]
BC [auth A0]
BD [auth A1]
AC [auth A0],
AD [auth A1],
AE [auth B8],
BC [auth A0],
BD [auth A1],
BE [auth B8],
BF [auth BA],
BG [auth BB],
CC [auth A0],
CD [auth A1],
CF [auth BA],
CG [auth BB],
DC [auth A0],
DD [auth A1],
DE [auth B8],
DF [auth BA],
DG [auth BB],
EC [auth A0],
ED [auth A1],
EE [auth B8],
EF [auth BA],
EG [auth BB],
FF [auth BA],
GD [auth A1],
GE [auth BA],
GF [auth BA],
GG [auth BB],
HC [auth A0],
HD [auth A1],
HE [auth BA],
HF [auth BA],
HG [auth BB],
IB [auth AZ],
IC [auth A0],
ID [auth A1],
IE [auth BA],
IF [auth BA],
IG [auth BB],
JB [auth AZ],
JC [auth A0],
JF [auth BA],
KB [auth AZ],
KC [auth A0],
KD [auth A1],
KE [auth BA],
KF [auth BA],
KG [auth BB],
LB [auth AZ],
LC [auth A0],
LD [auth A1],
LE [auth BA],
LF [auth BA],
MC [auth A0],
ME [auth BA],
MF [auth BA],
NB [auth AZ],
ND [auth A1],
NE [auth BA],
NF [auth BA],
OC [auth A0],
OD [auth A1],
OE [auth BA],
PB [auth A0],
PD [auth A1],
PE [auth BA],
PF [auth BA],
QB [auth A0],
QD [auth A1],
QF [auth BA],
RB [auth A0],
RC [auth A0],
RD [auth A1],
RE [auth BA],
RF [auth BA],
SC [auth A0],
SD [auth A1],
SE [auth BA],
TD [auth A1],
TF [auth BB],
UD [auth A1],
UF [auth BB],
VB [auth A0],
VC [auth A1],
VD [auth A1],
VE [auth BA],
WB [auth A0],
WC [auth A1],
WD [auth A1],
WE [auth BA],
XB [auth A0],
XD [auth A1],
XE [auth BA],
YB [auth A0],
YC [auth A1],
YD [auth B8],
YE [auth BA],
YF [auth BB],
ZB [auth A0],
ZC [auth A1],
ZD [auth B8],
ZE [auth BA]
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C39 H78 N O8 P
RPJZYOHZALDGKI-QNGWXLTQSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPIDER

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-08-20
    Changes: Database references, Structure summary
  • Version 1.2: 2014-12-10
    Changes: Other
  • Version 1.3: 2015-04-01
    Changes: Other
  • Version 1.4: 2018-07-18
    Changes: Data collection
  • Version 1.5: 2019-12-18
    Changes: Database references, Other
  • Version 1.6: 2024-02-28
    Changes: Data collection, Database references, Structure summary