SMTL ID : 9ygy.1

Structure of a GRP94 folding intermediate engaged with a CCDC134- and FKBP11-bound secretory translocon

Coordinates
PDB Format
Method
ELECTRON MICROSCOPY
Oligo State
hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer
Ligands
1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
1 x NDG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)
1 x ELU: phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate(Non-covalent)
Links
RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP
Citation
Yamsek, M. et al., Structural basis of regulated N-glycosylation at the secretory translocon. Nature (2025)
Release Date
2025-11-19
Peptides
Translocon-associated protein subunit alpha: A
Translocon-associated protein subunit beta: B
Translocon-associated protein subunit gamma: C
Translocon-associated protein subunit delta: D
Peptidyl-prolyl cis-trans isomerase FKBP11: E
Coiled-coil domain-containing protein 134: F
Protein transport protein Sec61 subunit alpha isoform 1: G
Protein transport protein Sec61 subunit beta: H
Protein transport protein Sec61 subunit gamma: I
Stress-associated endoplasmic reticulum protein 1: J
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A: K
Oligosaccharyltransferase complex subunit OSTC: L
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4: M
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TMEM258: N
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1: O
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit KCP2: P
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit: Q
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1: R
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2: S
Endoplasmin: T
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
5
B
6
C
7
D
8
E
A
F
B
G
D
H
E
I
F
J
G
K
I
L
J
M
K2
N
L2
O
M2
P
N
Q
N2
R
O2
S
P2
T
y3
Membrane
We predict this structure to be a membrane protein.

Translocon-associated protein subunit alpha

Translocon-associated protein subunit beta

Translocon-associated protein subunit gamma

Translocon-associated protein subunit delta

Peptidyl-prolyl cis-trans isomerase FKBP11

Coiled-coil domain-containing protein 134

Protein transport protein Sec61 subunit alpha isoform 1

Protein transport protein Sec61 subunit beta

Protein transport protein Sec61 subunit gamma

Stress-associated endoplasmic reticulum protein 1

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A

Oligosaccharyltransferase complex subunit OSTC

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TMEM258

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit KCP2

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2

Endoplasmin

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