8RJB | pdb_00008rjb

Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-RAMP4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.69 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural analysis of the dynamic ribosome-translocon complex.

Lewis, A.J.O.Zhong, F.Keenan, R.J.Hegde, R.S.

(2024) Elife 13

  • DOI: https://doi.org/10.7554/eLife.95814
  • Primary Citation of Related Structures:  
    8RJB, 8RJC, 8RJD

  • PubMed Abstract: 

    The protein translocon at the endoplasmic reticulum comprises the Sec61 translocation channel and numerous accessory factors that collectively facilitate the biogenesis of secretory and membrane proteins. Here, we leveraged recent advances in cryo-electron microscopy (cryo-EM) and structure prediction to derive insights into several novel configurations of the ribosome-translocon complex. We show how a transmembrane domain (TMD) in a looped configuration passes through the Sec61 lateral gate during membrane insertion; how a nascent chain can bind and constrain the conformation of ribosomal protein uL22; and how the translocon-associated protein (TRAP) complex can adjust its position during different stages of protein biogenesis. Most unexpectedly, we find that a large proportion of translocon complexes contains RAMP4 intercalated into Sec61's lateral gate, widening Sec61's central pore and contributing to its hydrophilic interior. These structures lead to mechanistic hypotheses for translocon function and highlight a remarkably plastic machinery whose conformations and composition adjust dynamically to its diverse range of substrates.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit alpha isoform 1A [auth 1]476Canis lupus familiarisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit betaB [auth 2]96Canis lupus familiarisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit gammaC [auth 3]68Canis lupus familiarisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Stress-associated endoplasmic reticulum proteinD [auth 4]66Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for A0A8I3PRN4 (Canis lupus familiaris)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L8E [auth A]257Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent chainF [auth B]229Bos taurusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4G [auth C]425Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L18_c domain-containing proteinH [auth D]297Oryctolagus cuniculusMutation(s): 0 
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Find proteins for P19949 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6I [auth E]291Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal Protein uL30J [auth F]247Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aK [auth G]319Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9L [auth H]192Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SWI6 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10M [auth I]214Oryctolagus cuniculusMutation(s): 0 
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Find proteins for B7NZQ2 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11N [auth J]178Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13P [auth L]211Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TKB3 (Oryctolagus cuniculus)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14Q [auth M]218Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SZ12 (Oryctolagus cuniculus)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15R [auth N]204Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T0C1 (Oryctolagus cuniculus)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13S [auth O]203Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TVS8 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
uL22T [auth P]184Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SCJ6 (Oryctolagus cuniculus)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26U [auth Q]187Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TFE0 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L19V [auth R]196Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aW [auth S]176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21X [auth T]160Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L22Y [auth U]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23Z [auth V]140Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24AA [auth W]157Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L23eN domain-containing proteinBA [auth X]156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26CA [auth Y]145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27DA [auth Z]136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aEA [auth a]148Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29FA [auth b]226Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL30GA [auth c]115OryctolagusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31HA [auth d]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L32IA [auth e]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aJA [auth f]110Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34KA [auth g]116Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35LA [auth h]123Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36MA [auth i]105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37NA [auth j]97Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38OA [auth k]70Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39-likePA [auth l]51Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
eL40QA [auth m]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41RA [auth n]25Oryctolagus cuniculusMutation(s): 0 
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Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36a-likeSA [auth o]106Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T040 (Oryctolagus cuniculus)
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aTA [auth p]92Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Go to UniProtKB:  G1SY53
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UniProt GroupG1SY53
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28VA [auth r]137Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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UniProt GroupG1U7L1
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L3YA [auth w]403Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TL06 (Oryctolagus cuniculus)
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UniProt GroupG1TL06
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Entity ID: 15
MoleculeChains LengthOrganismImage
28S rRNAO [auth K]3,543Oryctolagus cuniculus
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Entity ID: 47
MoleculeChains LengthOrganismImage
P-site tRNAUA [auth q]76Sus scrofa
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Entity ID: 49
MoleculeChains LengthOrganismImage
5S rRNAWA [auth u]120Oryctolagus cuniculus
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Entity ID: 50
MoleculeChains LengthOrganismImage
5.8S rRNAXA [auth v]156Oryctolagus cuniculus
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AJ [auth o],
BJ [auth p],
WI [auth g],
YI [auth j],
ZI [auth m]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth K]
AC [auth K]
AD [auth K]
AE [auth K]
AF [auth K]
AB [auth K],
AC [auth K],
AD [auth K],
AE [auth K],
AF [auth K],
AG [auth K],
AH [auth K],
AI [auth K],
BB [auth K],
BC [auth K],
BD [auth K],
BE [auth K],
BF [auth K],
BG [auth K],
BH [auth K],
BI [auth K],
CB [auth K],
CC [auth K],
CD [auth K],
CE [auth K],
CF [auth K],
CG [auth K],
CH [auth K],
CI [auth K],
CJ [auth u],
DB [auth K],
DC [auth K],
DD [auth K],
DE [auth K],
DF [auth K],
DG [auth K],
DH [auth K],
DI [auth K],
DJ [auth u],
EB [auth K],
EC [auth K],
ED [auth K],
EE [auth K],
EF [auth K],
EG [auth K],
EH [auth K],
EI [auth K],
EJ [auth u],
FB [auth K],
FC [auth K],
FD [auth K],
FE [auth K],
FF [auth K],
FG [auth K],
FH [auth K],
FI [auth K],
FJ [auth u],
GB [auth K],
GC [auth K],
GD [auth K],
GE [auth K],
GF [auth K],
GG [auth K],
GH [auth K],
GI [auth K],
GJ [auth u],
HB [auth K],
HC [auth K],
HD [auth K],
HE [auth K],
HF [auth K],
HG [auth K],
HH [auth K],
HI [auth K],
HJ [auth u],
IB [auth K],
IC [auth K],
ID [auth K],
IE [auth K],
IF [auth K],
IG [auth K],
IH [auth K],
II [auth K],
IJ [auth u],
JB [auth K],
JC [auth K],
JD [auth K],
JE [auth K],
JF [auth K],
JG [auth K],
JH [auth K],
JI [auth K],
JJ [auth v],
KB [auth K],
KC [auth K],
KD [auth K],
KE [auth K],
KF [auth K],
KG [auth K],
KH [auth K],
KI [auth K],
KJ [auth v],
LB [auth K],
LC [auth K],
LD [auth K],
LE [auth K],
LF [auth K],
LG [auth K],
LH [auth K],
LI [auth K],
LJ [auth v],
MB [auth K],
MC [auth K],
MD [auth K],
ME [auth K],
MF [auth K],
MG [auth K],
MH [auth K],
MI [auth K],
MJ [auth v],
NB [auth K],
NC [auth K],
ND [auth K],
NE [auth K],
NF [auth K],
NG [auth K],
NH [auth K],
NI [auth K],
NJ [auth v],
OB [auth K],
OC [auth K],
OD [auth K],
OE [auth K],
OF [auth K],
OG [auth K],
OH [auth K],
OI [auth K],
PB [auth K],
PC [auth K],
PD [auth K],
PE [auth K],
PF [auth K],
PG [auth K],
PH [auth K],
PI [auth K],
QB [auth K],
QC [auth K],
QD [auth K],
QE [auth K],
QF [auth K],
QG [auth K],
QH [auth K],
QI [auth K],
RB [auth K],
RC [auth K],
RD [auth K],
RE [auth K],
RF [auth K],
RG [auth K],
RH [auth K],
RI [auth K],
SB [auth K],
SC [auth K],
SD [auth K],
SE [auth K],
SF [auth K],
SG [auth K],
SH [auth K],
SI [auth K],
TB [auth K],
TC [auth K],
TD [auth K],
TE [auth K],
TF [auth K],
TG [auth K],
TH [auth K],
TI [auth K],
UB [auth K],
UC [auth K],
UD [auth K],
UE [auth K],
UF [auth K],
UG [auth K],
UH [auth K],
UI [auth V],
VB [auth K],
VC [auth K],
VD [auth K],
VE [auth K],
VF [auth K],
VG [auth K],
VH [auth K],
VI [auth a],
WB [auth K],
WC [auth K],
WD [auth K],
WE [auth K],
WF [auth K],
WG [auth K],
WH [auth K],
XB [auth K],
XC [auth K],
XD [auth K],
XE [auth K],
XF [auth K],
XG [auth K],
XH [auth K],
XI [auth g],
YB [auth K],
YC [auth K],
YD [auth K],
YE [auth K],
YF [auth K],
YG [auth K],
YH [auth K],
ZA [auth I],
ZB [auth K],
ZC [auth K],
ZD [auth K],
ZE [auth K],
ZF [auth K],
ZG [auth K],
ZH [auth K]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.69 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_A022_1007
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM130051
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM086487

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-24
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Data collection, Database references