6U7H
Cryo-EM structure of the HCoV-229E spike glycoprotein
- PDB DOI: https://doi.org/10.2210/pdb6U7H/pdb
- EM Map EMD-20668: EMDB EMDataResource
- Classification: VIRAL PROTEIN
- Organism(s): Human coronavirus 229E
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2019-09-02 Released: 2019-11-13 
- Funding Organization(s): Canadian Institutes of Health Research (CIHR)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.10 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 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
spike glycoprotein | 1,159 | Human coronavirus 229E | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for P15423 (Human coronavirus 229E) Explore P15423  Go to UniProtKB:  P15423 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P15423 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-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 | D, I, N | 7 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G07617FP GlyCosmos:  G07617FP GlyGen:  G07617FP |
Entity ID: 3 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E, F, H, J, K E, F, H, J, K, M, O, P, R | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 4 | |||||
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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 | G, L, Q | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | AA [auth A] BA [auth A] CA [auth A] DA [auth B] EA [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: 3.10 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
Task | Software Package | Version |
---|---|---|
RECONSTRUCTION | cryoSPARC | 2.90 |
MODEL REFINEMENT | PHENIX | 1.16RC1-3535 |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-11-13  Deposition Author(s): Li, Z., Benlekbir, S., Rubinstein, J.L., Rini, J.M.
Funding Organization | Location | Grant Number |
---|---|---|
Canadian Institutes of Health Research (CIHR) | Canada | -- |
Revision History (Full details and data files)
- Version 1.0: 2019-11-13
Type: Initial release - Version 1.1: 2020-01-15
Changes: Author supporting evidence - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary