7TUT

Structure of the rabbit 80S ribosome stalled on a 4-TMD Rhodopsin intermediate in complex with the multipass translocon


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.88 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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Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
uL4B [auth C]413Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SVW5 (Oryctolagus cuniculus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
uL18C [auth D]297Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
eL6D [auth E]291Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SKF7 (Oryctolagus cuniculus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
uL30E [auth F]247Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TUB1 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
eL8F [auth G]319Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1STW0 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
uL6G [auth H]192Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SWI6 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
uL16H [auth I]214Oryctolagus cuniculusMutation(s): 0 
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Find proteins for B7NZQ2 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
uL5I [auth J]178Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
eL13J [auth L]211Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TPV0 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
eL14K [auth M]218Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SZ12 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
eL15L [auth N]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
uL13M [auth O]203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
uL22N [auth P]184Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
eL18O [auth Q]188Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
eL19P [auth R]196Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
eL20Q [auth S]176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
eL21R [auth T]160Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
eL22S [auth U]128Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TSG1 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
uL14T [auth V]140Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
eL24U [auth W]157Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
eL23V [auth X]156Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
uL24W [auth Y]145Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
eL27X [auth Z]136Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
uL15Y [auth a]148Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
eL29Z [auth b]226Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
eL30AA [auth c]115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
eL31BA [auth d]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
eL32CA [auth e]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
eL33DA [auth f]110Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
eL34EA [auth g]116Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
eL35FA [auth h]123Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
eL36GA [auth i]105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
eL37HA [auth j]97Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
eL38IA [auth k]70Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
eL39JA [auth l]51Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
eL40KA [auth m]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
eL41LA [auth n]25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
eL42MA [auth o]106Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
eL43NA [auth p]92Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
eL28PA [auth r]137Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
uL3SA [auth w]403Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent chainTA [auth B]273Oryctolagus 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)
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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: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium load-activated calcium channelBB [auth 8]188Canis lupusMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Obligate partner of TMCO1 insertaseDB [auth 9]129Canis lupusMutation(s): 0 
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Entity ID: 41
MoleculeChains LengthOrganismImage
P-site tRNAOA [auth q]77Oryctolagus cuniculus
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Entity ID: 43
MoleculeChains LengthOrganismImage
5S ribosomal RNAQA [auth u]120Oryctolagus cuniculus
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Entity ID: 44
MoleculeChains LengthOrganismImage
5.8S ribosomal RNARA [auth v]156Oryctolagus cuniculus
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Entity ID: 55
MoleculeChains LengthOrganismImage
28S ribosomal RNACB [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 
MB [auth g],
NB [auth j],
OB [auth m],
PB [auth o],
QB [auth p]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth v]
AD [auth K]
AE [auth K]
AF [auth K]
AG [auth K]
AC [auth v],
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],
CC [auth K],
CD [auth K],
CE [auth K],
CF [auth K],
CG [auth K],
CH [auth K],
CI [auth K],
CJ [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 K],
EB [auth C],
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 D],
FC [auth K],
FD [auth K],
FE [auth K],
FF [auth K],
FG [auth K],
FH [auth K],
FI [auth K],
FJ [auth K],
GB [auth I],
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 I],
HC [auth K],
HD [auth K],
HE [auth K],
HF [auth K],
HG [auth K],
HH [auth K],
HI [auth K],
HJ [auth K],
IB [auth J],
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 P],
JC [auth K],
JD [auth K],
JE [auth K],
JF [auth K],
JG [auth K],
JH [auth K],
JI [auth K],
JJ [auth K],
KB [auth V],
KC [auth K],
KD [auth K],
KE [auth K],
KF [auth K],
KG [auth K],
KH [auth K],
KI [auth K],
KJ [auth K],
LB [auth a],
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],
NC [auth K],
ND [auth K],
NE [auth K],
NF [auth K],
NG [auth K],
NH [auth K],
NI [auth K],
NJ [auth K],
OC [auth K],
OD [auth K],
OE [auth K],
OF [auth K],
OG [auth K],
OH [auth K],
OI [auth K],
OJ [auth K],
PC [auth K],
PD [auth K],
PE [auth K],
PF [auth K],
PG [auth K],
PH [auth K],
PI [auth K],
PJ [auth K],
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],
TJ [auth K],
UB [auth u],
UC [auth K],
UD [auth K],
UE [auth K],
UF [auth K],
UG [auth K],
UH [auth K],
UI [auth K],
UJ [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: 3.88 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: 2022-11-16
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2024-06-12
    Changes: Data collection