9YGY | pdb_00009ygy

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

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2025-09-29 Released: 2025-11-19 
  • Deposition Author(s): Yamsek, M., Jha, R., Keenan, R.J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of regulated N-glycosylation at the secretory translocon.

Yamsek, M.Ma, M.Jha, R.Wan, Y.Li, Q.Zhong, F.DeLong, K.Ji, Z.Rohatgi, R.Keenan, R.J.

(2025) Nature 

  • DOI: https://doi.org/10.1038/s41586-025-09756-8
  • Primary Citation of Related Structures:  
    9N9J, 9YGY

  • PubMed Abstract: 

    Most human secretory pathway proteins are N-glycosylated by oligosaccharyltransferase (OST) complexes as they enter the endoplasmic reticulum (ER) 1-3 . Recent work revealed a substrate-assisted mechanism by which N-glycosylation of the chaperone glucose-regulated protein 94 (GRP94) is regulated to control cell surface receptor signalling 4 . Here we report the structure of a natively isolated GRP94 folding intermediate tethered to a specialized CCDC134-bound translocon. Together with functional analysis, the data reveal how a conserved N-terminal extension in GRP94 inhibits OST-A and how structural rearrangements within the translocon shield the tethered nascent chain from inappropriate OST-B glycosylation. These interactions depend on a hydrophobic CCDC134 groove, which recognizes a non-native conformation of nascent GRP94. Our results define a mechanism of regulated N-glycosylation and illustrate how the nascent chain remodels the translocon to facilitate its own biogenesis.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit alphaA [auth 5]286Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124783 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit betaB [auth 6]183Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163479 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit gammaC [auth 7]185Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114850 
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UniProt GroupQ9UNL2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit deltaD [auth 8]173Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000180879 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP11E [auth A]201Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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GTEx:  ENSG00000134285 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 134F [auth B]229Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100147 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit alpha isoform 1G [auth D]476Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000058262 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit betaH [auth E]96Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106803 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit gammaI [auth F]68Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132432 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Stress-associated endoplasmic reticulum protein 1J [auth G]66Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000120742 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3AK [auth I]705Homo sapiensMutation(s): 0 
EC: 2.4.99.18
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GTEx:  ENSG00000134910 
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Glycosylation
Glycosylation Sites: 2Go to GlyGen: P46977-1
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Oligosaccharyltransferase complex subunit OSTCL [auth J]149Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198856 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4M [auth K2]37Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000228474 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TMEM258N [auth L2]79Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134825 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1O [auth M2]113Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000129562 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit KCP2P [auth N]136Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163463 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunitQ [auth N2]456Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000244038 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1R [auth O2]607Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163902 
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UniProt GroupP04843
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P04843-1
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2S [auth P2]631Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118705 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
EndoplasminT [auth y3]846Homo sapiensMutation(s): 0 
EC: 3.6.4
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GTEx:  ENSG00000166598 
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Oligosaccharides

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Entity ID: 21
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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-glucopyranoseU [auth K]8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G80966KZ
GlyCosmos:  G80966KZ
GlyGen:  G80966KZ
Entity ID: 22
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseV [auth C]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 23
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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-glucopyranoseW [auth H]8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81980VO
GlyCosmos:  G81980VO
GlyGen:  G81980VO
Entity ID: 24
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranoseX [auth L]2N/A
Glycosylation Resources
GlyTouCan:  G05026ZL
GlyCosmos:  G05026ZL
GlyGen:  G05026ZL
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ELU (Subject of Investigation/LOI)
Query on ELU

Download Ideal Coordinates CCD File 
Y [auth I]phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate
C20 H38 O7 P2
SJMIVFIDXGVUHA-WKWVIOPWSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419+SVN
RECONSTRUCTIONRELION5.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM145374

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Data collection, Database references
  • Version 1.2: 2025-12-10
    Changes: Data collection, Database references