7TM3

Structure of the rabbit 80S ribosome stalled on a 2-TMD Rhodopsin intermediate in complex with the multipass translocon


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism of an intramembrane chaperone for multipass membrane proteins.

Smalinskaite, L.Kim, M.K.Lewis, A.J.O.Keenan, R.J.Hegde, R.S.

(2022) Nature 611: 161-166

  • DOI: https://doi.org/10.1038/s41586-022-05336-2
  • Primary Citation of Related Structures:  
    7TM3, 7TUT

  • PubMed Abstract: 

    Multipass membrane proteins play numerous roles in biology and include receptors, transporters, ion channels and enzymes 1,2 . How multipass proteins are co-translationally inserted and folded at the endoplasmic reticulum is not well understood 2 . The prevailing model posits that each transmembrane domain (TMD) of a multipass protein successively passes into the lipid bilayer through a front-side lateral gate of the Sec61 protein translocation channel 3-9 . The PAT complex, an intramembrane chaperone comprising Asterix and CCDC47, engages early TMDs of multipass proteins to promote their biogenesis by an unknown mechanism 10 . Here, biochemical and structural analysis of intermediates during multipass protein biogenesis showed that the nascent chain is not engaged with Sec61, which is occluded and latched closed by CCDC47. Instead, Asterix binds to and redirects the substrate to a location behind Sec61, where the PAT complex contributes to a multipass translocon surrounding a semi-enclosed, lipid-filled cavity 11 . Detection of multiple TMDs in this cavity after their emergence from the ribosome suggests that multipass proteins insert and fold behind Sec61. Accordingly, biogenesis of several multipass proteins was unimpeded by inhibitors of the Sec61 lateral gate. These findings elucidate the mechanism of an intramembrane chaperone and suggest a new framework for multipass membrane protein biogenesis at the endoplasmic reticulum.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cell Biology Division, Cambridge, UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
uL2257Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent chain229Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
uL4425Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
uL18297Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
eL6291Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
uL30247Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
eL8319Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
uL6192Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
uL16214Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uL5178Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
eL13K [auth L]211Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TPV0 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
eL14L [auth M]218Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SZ12 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
eL15M [auth N]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
uL13N [auth O]203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
uL22O [auth P]184Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
eL18P [auth Q]188Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
eL19Q [auth R]196Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
eL20R [auth S]176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
eL21S [auth T]160Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
eL22T [auth U]128Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TSG1 (Oryctolagus cuniculus)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
uL14U [auth V]140Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
eL24V [auth W]157Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
uL23W [auth X]156Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
uL24X [auth Y]145Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
eL27Y [auth Z]136Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
uL15Z [auth a]148Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
eL29AA [auth b]226Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
eL30BA [auth c]115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
eL31CA [auth d]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
eL32DA [auth e]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
eL33EA [auth f]110Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
eL34FA [auth g]116Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
uL29GA [auth h]123Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
eL36HA [auth i]105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
eL37IA [auth j]97Oryctolagus 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]70Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
eL39KA [auth l]51Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
eL40LA [auth m]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
eL41MA [auth n]25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
eL42NA [auth o]106Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T040 (Oryctolagus cuniculus)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
eL43OA [auth p]92Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
eL28QA [auth r]137Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
uL3TA [auth w]403Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit alpha isoform 1UA [auth 1]476Canis lupusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit betaVA [auth 2]96Canis lupusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 gammaWA [auth 3]68Canis lupusMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain containing 47XA [auth 4]483Canis lupusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
PAT complex subunit AsterixYA [auth 5]106Canis lupusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
NicalinZA [auth 7]563Canis lupusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A8C0S144 (Canis lupus familiaris)
Explore A0A8C0S144 
Go to UniProtKB:  A0A8C0S144
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UniProt GroupA0A8C0S144
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein 147AB [auth 6]224Canis lupusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A8C0RUW0 (Canis lupus familiaris)
Explore A0A8C0RUW0 
Go to UniProtKB:  A0A8C0RUW0
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UniProt GroupA0A8C0RUW0
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Entity ID: 42
MoleculeChains LengthOrganismImage
P-site tRNAPA [auth q]77Oryctolagus cuniculus
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Entity ID: 44
MoleculeChains LengthOrganismImage
5S ribosomal RNARA [auth u]120Oryctolagus cuniculus
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Entity ID: 45
MoleculeChains LengthOrganismImage
5.8S ribosomal RNASA [auth v]156Oryctolagus cuniculus
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Entity ID: 54
MoleculeChains LengthOrganismImage
28S ribosomal RNABB [auth K]3,543Oryctolagus 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 
GB [auth g],
IB [auth j],
KB [auth m],
LB [auth o],
MB [auth p]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth K]
AD [auth K]
AE [auth K]
AF [auth K]
AG [auth K]
AC [auth K],
AD [auth K],
AE [auth K],
AF [auth K],
AG [auth K],
AH [auth K],
AI [auth K],
AJ [auth K],
BC [auth K],
BD [auth K],
BE [auth K],
BF [auth K],
BG [auth K],
BH [auth K],
BI [auth K],
BJ [auth K],
CB [auth P],
CC [auth K],
CD [auth K],
CE [auth K],
CF [auth K],
CG [auth K],
CH [auth K],
CI [auth K],
CJ [auth K],
DB [auth P],
DC [auth K],
DD [auth K],
DE [auth K],
DF [auth K],
DG [auth K],
DH [auth K],
DI [auth K],
DJ [auth K],
EB [auth V],
EC [auth K],
ED [auth K],
EE [auth K],
EF [auth K],
EG [auth K],
EH [auth K],
EI [auth K],
EJ [auth K],
FB [auth a],
FC [auth K],
FD [auth K],
FE [auth K],
FF [auth K],
FG [auth K],
FH [auth K],
FI [auth K],
FJ [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 K],
HB [auth g],
HC [auth K],
HD [auth K],
HE [auth K],
HF [auth K],
HG [auth K],
HH [auth K],
HI [auth K],
HJ [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 K],
JB [auth j],
JC [auth K],
JD [auth K],
JE [auth K],
JF [auth K],
JG [auth K],
JH [auth K],
JI [auth K],
JJ [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 K],
LC [auth K],
LD [auth K],
LE [auth K],
LF [auth K],
LG [auth K],
LH [auth K],
LI [auth K],
LJ [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 K],
NB [auth u],
NC [auth K],
ND [auth K],
NE [auth K],
NF [auth K],
NG [auth K],
NH [auth K],
NI [auth K],
NJ [auth K],
OB [auth u],
OC [auth K],
OD [auth K],
OE [auth K],
OF [auth K],
OG [auth K],
OH [auth K],
OI [auth K],
OJ [auth K],
PB [auth u],
PC [auth K],
PD [auth K],
PE [auth K],
PF [auth K],
PG [auth K],
PH [auth K],
PI [auth K],
PJ [auth K],
QB [auth u],
QC [auth K],
QD [auth K],
QE [auth K],
QF [auth K],
QG [auth K],
QH [auth K],
QI [auth K],
QJ [auth K],
RB [auth u],
RC [auth K],
RD [auth K],
RE [auth K],
RF [auth K],
RG [auth K],
RH [auth K],
RI [auth K],
RJ [auth K],
SB [auth u],
SC [auth K],
SD [auth K],
SE [auth K],
SF [auth K],
SG [auth K],
SH [auth K],
SI [auth K],
SJ [auth K],
TB [auth u],
TC [auth K],
TD [auth K],
TE [auth K],
TF [auth K],
TG [auth K],
TH [auth K],
TI [auth K],
UB [auth v],
UC [auth K],
UD [auth K],
UE [auth K],
UF [auth K],
UG [auth K],
UH [auth K],
UI [auth K],
VB [auth v],
VC [auth K],
VD [auth K],
VE [auth K],
VF [auth K],
VG [auth K],
VH [auth K],
VI [auth K],
WB [auth v],
WC [auth K],
WD [auth K],
WE [auth K],
WF [auth K],
WG [auth K],
WH [auth K],
WI [auth K],
XB [auth v],
XC [auth K],
XD [auth K],
XE [auth K],
XF [auth K],
XG [auth K],
XH [auth K],
XI [auth K],
YB [auth v],
YC [auth K],
YD [auth K],
YE [auth K],
YF [auth K],
YG [auth K],
YH [auth K],
YI [auth K],
ZB [auth v],
ZC [auth K],
ZD [auth K],
ZE [auth K],
ZF [auth K],
ZG [auth K],
ZH [auth K],
ZI [auth K]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2-4158

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United StatesMC_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: 2022-10-19
    Type: Initial release
  • Version 1.1: 2022-11-02
    Changes: Database references
  • Version 1.2: 2022-11-09
    Changes: Data collection, Structure summary
  • Version 1.3: 2022-11-16
    Changes: Database references