6MTE

Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structures of translationally inactive mammalian ribosomes.

Brown, A.Baird, M.R.Yip, M.C.Murray, J.Shao, S.

(2018) Elife 7

  • DOI: 10.7554/eLife.40486
  • Primary Citation of Related Structures:  
    6MTE, 6MTB, 6MTD, 6MTC

  • PubMed Abstract: 
  • The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. Here, we use electron cryomicroscopy to analyze inactive ribosomes isolated from mammalian reticulocytes, the penultimate stage of red blood cell differentiation ...

    The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. Here, we use electron cryomicroscopy to analyze inactive ribosomes isolated from mammalian reticulocytes, the penultimate stage of red blood cell differentiation. We identify two types of ribosomes that are translationally repressed by protein interactions. The first comprises ribosomes sequestered with elongation factor 2 (eEF2) by SERPINE mRNA binding protein 1 (SERBP1) occupying the ribosomal mRNA entrance channel. The second type are translationally repressed by a novel ribosome-binding protein, interferon-related developmental regulator 2 (IFRD2), which spans the P and E sites and inserts a C-terminal helix into the mRNA exit channel to preclude translation. IFRD2 binds ribosomes with a tRNA occupying a noncanonical binding site, the 'Z site', on the ribosome. These structures provide functional insights into how ribosomal interactions may suppress translation to regulate gene expression.


    Organizational Affiliation

    Department of Cell Biology, Harvard Medical School, Boston, United States.



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Entity ID: 4
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uL2D [auth A]248Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
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uL3E [auth B]394Oryctolagus cuniculusMutation(s): 0 
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uL4F [auth C]362Oryctolagus cuniculusMutation(s): 0 
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uL18G [auth D]293Oryctolagus cuniculusMutation(s): 0 
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eL6H [auth E]291Oryctolagus cuniculusMutation(s): 0 
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uL30I [auth F]225Oryctolagus cuniculusMutation(s): 0 
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eL8J [auth G]319Oryctolagus cuniculusMutation(s): 0 
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uL6K [auth H]190Oryctolagus cuniculusMutation(s): 0 
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uL16L [auth I]214Oryctolagus cuniculusMutation(s): 0 
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uL5M [auth J]170Oryctolagus cuniculusMutation(s): 0 
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eL14O [auth M]138Oryctolagus cuniculusMutation(s): 0 
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uL13Q [auth O]199Oryctolagus cuniculusMutation(s): 0 
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uL22R [auth P]153Oryctolagus cuniculusMutation(s): 0 
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eL21V [auth T]159Oryctolagus cuniculusMutation(s): 0 
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uL15CA [auth a]147Oryctolagus cuniculusMutation(s): 0 
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eL30EA [auth c]98Oryctolagus cuniculusMutation(s): 0 
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uL29JA [auth h]122Oryctolagus cuniculusMutation(s): 0 
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eL36KA [auth i]102Oryctolagus cuniculusMutation(s): 0 
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eL37LA [auth j]86Oryctolagus cuniculusMutation(s): 0 
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eL39NA [auth l]50Oryctolagus cuniculusMutation(s): 0 
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eL42QA [auth o]103Oryctolagus cuniculusMutation(s): 0 
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eL43RA [auth p]91Oryctolagus cuniculusMutation(s): 0 
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SERBP1WA [auth w]55Oryctolagus cuniculusMutation(s): 0 
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eS1ZA [auth BB]213Oryctolagus cuniculusMutation(s): 0 
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uS3BB [auth DD]228Oryctolagus cuniculusMutation(s): 0 
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eS10IB [auth KK]96Oryctolagus cuniculusMutation(s): 0 
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uS15LB [auth NN]149Oryctolagus cuniculusMutation(s): 0 
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uS19NB [auth PP]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
uS10SB [auth UU]100Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
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eS21TB [auth VV]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
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uS8UB [auth WW]129Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 74
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uS12VB [auth XX]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
eS24WB [auth YY]124Oryctolagus cuniculusMutation(s): 0 
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NIH Common Fund Data Resources
PHAROS:  P62847
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
eS25XB [auth ZZ]75Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
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eS26YB [auth aa]101Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
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eS27ZB [auth bb]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
eS28AC [auth cc]62Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
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Entity ID: 80
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uS14BC [auth dd]55Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 81
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eS30CC [auth ee]55Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
eS31DC [auth ff]68Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
RACK1EC [auth gg]313Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
28S rRNAA [auth 5]3597Oryctolagus cuniculus
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Entity ID: 2
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5S rRNAB [auth 7]120Oryctolagus cuniculus
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5.8S rRNAC [auth 8]151Oryctolagus cuniculus
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Entity ID: 50
MoleculeChainsLengthOrganismImage
18S rRNAXA [auth 9]1698Oryctolagus cuniculus
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
UK [auth v]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

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OK [auth g], QK [auth j], RK [auth m], SK [auth o], TK [auth p], WN [auth KK], YN [auth aa], ZN [auth ff]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AD [auth 5] , AE [auth 5] , AF [auth 5] , AG [auth 5] , AH [auth 5] , AI [auth 5] , AJ [auth 5] , AK [auth 7] , 
AD [auth 5],  AE [auth 5],  AF [auth 5],  AG [auth 5],  AH [auth 5],  AI [auth 5],  AJ [auth 5],  AK [auth 7],  AL [auth 9],  AM [auth 9],  AN [auth 9],  BD [auth 5],  BE [auth 5],  BF [auth 5],  BG [auth 5],  BH [auth 5],  BI [auth 5],  BJ [auth 5],  BK [auth 7],  BL [auth 9],  BM [auth 9],  BN [auth 9],  CD [auth 5],  CE [auth 5],  CF [auth 5],  CG [auth 5],  CH [auth 5],  CI [auth 5],  CJ [auth 5],  CK [auth 7],  CL [auth 9],  CM [auth 9],  CN [auth 9],  DD [auth 5],  DE [auth 5],  DF [auth 5],  DG [auth 5],  DH [auth 5],  DI [auth 5],  DJ [auth 5],  DK [auth 7],  DL [auth 9],  DM [auth 9],  DN [auth 9],  ED [auth 5],  EE [auth 5],  EF [auth 5],  EG [auth 5],  EH [auth 5],  EI [auth 5],  EJ [auth 5],  EK [auth 8],  EL [auth 9],  EM [auth 9],  EN [auth 9],  FC [auth 5],  FD [auth 5],  FE [auth 5],  FF [auth 5],  FG [auth 5],  FH [auth 5],  FI [auth 5],  FJ [auth 5],  FK [auth 8],  FL [auth 9],  FM [auth 9],  FN [auth 9],  GC [auth 5],  GD [auth 5],  GE [auth 5],  GF [auth 5],  GG [auth 5],  GH [auth 5],  GI [auth 5],  GJ [auth 5],  GK [auth 8],  GL [auth 9],  GM [auth 9],  GN [auth 9],  HC [auth 5],  HD [auth 5],  HE [auth 5],  HF [auth 5],  HG [auth 5],  HH [auth 5],  HI [auth 5],  HJ [auth 5],  HK [auth 8],  HL [auth 9],  HM [auth 9],  HN [auth 9],  IC [auth 5],  ID [auth 5],  IE [auth 5],  IF [auth 5],  IG [auth 5],  IH [auth 5],  II [auth 5],  IJ [auth 5],  IK [auth 8],  IL [auth 9],  IM [auth 9],  IN [auth 9],  JC [auth 5],  JD [auth 5],  JE [auth 5],  JF [auth 5],  JG [auth 5],  JH [auth 5],  JI [auth 5],  JJ [auth 5],  JK [auth 8],  JL [auth 9],  JM [auth 9],  JN [auth 9],  KC [auth 5],  KD [auth 5],  KE [auth 5],  KF [auth 5],  KG [auth 5],  KH [auth 5],  KI [auth 5],  KJ [auth 5],  KK [auth A],  KL [auth 9],  KM [auth 9],  KN [auth 9],  LC [auth 5],  LD [auth 5],  LE [auth 5],  LF [auth 5],  LG [auth 5],  LH [auth 5],  LI [auth 5],  LJ [auth 5],  LK [auth P],  LL [auth 9],  LM [auth 9],  LN [auth 9],  MC [auth 5],  MD [auth 5],  ME [auth 5],  MF [auth 5],  MG [auth 5],  MH [auth 5],  MI [auth 5],  MJ [auth 5],  MK [auth V],  ML [auth 9],  MM [auth 9],  MN [auth 9],  NC [auth 5],  ND [auth 5],  NE [auth 5],  NF [auth 5],  NG [auth 5],  NH [auth 5],  NI [auth 5],  NJ [auth 5],  NK [auth a],  NL [auth 9],  NM [auth 9],  NN [auth 9],  OC [auth 5],  OD [auth 5],  OE [auth 5],  OF [auth 5],  OG [auth 5],  OH [auth 5],  OI [auth 5],  OJ [auth 5],  OL [auth 9],  OM [auth 9],  ON [auth 9],  PC [auth 5],  PD [auth 5],  PE [auth 5],  PF [auth 5],  PG [auth 5],  PH [auth 5],  PI [auth 5],  PJ [auth 5],  PK [auth j],  PL [auth 9],  PM [auth 9],  PN [auth 9],  QC [auth 5],  QD [auth 5],  QE [auth 5],  QF [auth 5],  QG [auth 5],  QH [auth 5],  QI [auth 5],  QJ [auth 5],  QL [auth 9],  QM [auth 9],  QN [auth 9],  RC [auth 5],  RD [auth 5],  RE [auth 5],  RF [auth 5],  RG [auth 5],  RH [auth 5],  RI [auth 5],  RJ [auth 5],  RL [auth 9],  RM [auth 9],  RN [auth 9],  SC [auth 5],  SD [auth 5],  SE [auth 5],  SF [auth 5],  SG [auth 5],  SH [auth 5],  SI [auth 5],  SJ [auth 5],  SL [auth 9],  SM [auth 9],  SN [auth 9],  TC [auth 5],  TD [auth 5],  TE [auth 5],  TF [auth 5],  TG [auth 5],  TH [auth 5],  TI [auth 5],  TJ [auth 5],  TL [auth 9],  TM [auth 9],  TN [auth 9],  UC [auth 5],  UD [auth 5],  UE [auth 5],  UF [auth 5],  UG [auth 5],  UH [auth 5],  UI [auth 5],  UJ [auth 5],  UL [auth 9],  UM [auth 9],  UN [auth 9],  VC [auth 5],  VD [auth 5],  VE [auth 5],  VF [auth 5],  VG [auth 5],  VH [auth 5],  VI [auth 5],  VJ [auth 5],  VK [auth v],  VL [auth 9],  VM [auth 9],  VN [auth 9],  WC [auth 5],  WD [auth 5],  WE [auth 5],  WF [auth 5],  WG [auth 5],  WH [auth 5],  WI [auth 5],  WJ [auth 5],  WK [auth 9],  WL [auth 9],  WM [auth 9],  XC [auth 5],  XD [auth 5],  XE [auth 5],  XF [auth 5],  XG [auth 5],  XH [auth 5],  XI [auth 5],  XJ [auth 7],  XK [auth 9],  XL [auth 9],  XM [auth 9],  XN [auth TT],  YC [auth 5],  YD [auth 5],  YE [auth 5],  YF [auth 5],  YG [auth 5],  YH [auth 5],  YI [auth 5],  YJ [auth 7],  YK [auth 9],  YL [auth 9],  YM [auth 9],  ZC [auth 5],  ZD [auth 5],  ZE [auth 5],  ZF [auth 5],  ZG [auth 5],  ZH [auth 5],  ZI [auth 5],  ZJ [auth 7],  ZK [auth 9],  ZL [auth 9],  ZM [auth 9]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MLZ
Query on MLZ
F [auth C]L-PEPTIDE LINKINGC7 H16 N2 O2LYS
DDE
Query on DDE
VA [auth v]L-PEPTIDE LINKINGC13 H24 N5 O3HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 2.0: 2019-05-15
    Changes: Atomic model, Data collection, Derived calculations, Polymer sequence