6C26
The Cryo-EM structure of a eukaryotic oligosaccharyl transferase complex
- PDB DOI: https://doi.org/10.2210/pdb6C26/pdb
- EM Map EMD-7336: EMDB EMDataResource
- Classification: TRANSFERASE
- Organism(s): Saccharomyces cerevisiae S288C
- Mutation(s): No 
- Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc
- Deposited: 2018-01-06 Released: 2018-01-31 
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.50 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
wwPDB Validation   3D Report Full Report
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 | 718 | Saccharomyces cerevisiae S288C | Mutation(s): 0  EC: 2.4.99.18 Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P39007 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P39007  Go to UniProtKB:  P39007 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P39007 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 | B [auth 1] | 476 | Saccharomyces cerevisiae S288C | Mutation(s): 0  EC: 2.4.99.18 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for P41543 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41543  Go to UniProtKB:  P41543 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P41543 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5 | C [auth 5] | 86 | Saccharomyces cerevisiae S288C | Mutation(s): 0  EC: 2.4.99.18 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for Q92316 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q92316  Go to UniProtKB:  Q92316 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q92316 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4 | D [auth 4] | 36 | Saccharomyces cerevisiae S288C | Mutation(s): 0  EC: 2.4.99.18 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for Q99380 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q99380  Go to UniProtKB:  Q99380 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q99380 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2 | E [auth 2] | 130 | Saccharomyces cerevisiae S288C | Mutation(s): 0  EC: 2.4.99.18 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for P46964 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P46964  Go to UniProtKB:  P46964 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P46964 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 6 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3 | F [auth 3] | 350 | Saccharomyces cerevisiae S288C | Mutation(s): 0  EC: 2.4.99.18 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for P48439 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P48439  Go to UniProtKB:  P48439 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P48439 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 7 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1 | G [auth C] | 286 | Saccharomyces cerevisiae S288C | Mutation(s): 0  EC: 2.4.99.18 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for Q02795 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02795  Go to UniProtKB:  Q02795 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q02795 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 8 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 | H [auth B] | 430 | Saccharomyces cerevisiae S288C | Mutation(s): 0  EC: 2.4.99.18 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for P33767 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33767  Go to UniProtKB:  P33767 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P33767 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 9 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-[beta-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 | I [auth D] | 7 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G50777HT GlyCosmos:  G50777HT GlyGen:  G50777HT |
Entity ID: 10 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | J [auth E] | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
EGY Query on EGY | K [auth A] L [auth A] M [auth A] N [auth 1] O [auth 1] | (4R,7R)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(undecanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphadocosan-1-aminium C33 H67 N O8 P GGHWXDCJHDYMKO-WJOKGBTCSA-O | |||
NAG Query on NAG | S [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.50 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
Task | Software Package | Version |
---|---|---|
RECONSTRUCTION | Coot | |
RECONSTRUCTION | UCSF Chimera | |
MODEL REFINEMENT | PHENIX | |
MODEL REFINEMENT | Coot |
Entry History & Funding Information
Deposition Data
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM111742 |
Revision History (Full details and data files)
- Version 1.0: 2018-01-31
Type: Initial release - Version 1.1: 2018-02-14
Changes: Author supporting evidence - Version 1.2: 2018-03-07
Changes: Database references - Version 1.3: 2018-03-28
Changes: Data collection, Database references - Version 1.4: 2019-12-18
Changes: Author supporting evidence, Other - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary