6Q06
MERS-CoV S structure in complex with 2,3-sialyl-N-acetyl-lactosamine
- PDB DOI: https://doi.org/10.2210/pdb6Q06/pdb
- EM Map EMD-20544: EMDB EMDataResource
- Classification: VIRAL PROTEIN
- Organism(s): Human betacoronavirus 2c EMC/2012
- Expression System: Homo sapiens
- Mutation(s): Yes 
- Deposited: 2019-08-01 Released: 2019-12-11 
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 2.70 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 | 1,359 | Human betacoronavirus 2c EMC/2012 | Mutation(s): 4  | ||
UniProt | |||||
Find proteins for K0BRG7 (Human betacoronavirus 2c EMC/2012) Explore K0BRG7  Go to UniProtKB:  K0BRG7 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | K0BRG7 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D, DA [auth d], H, O, S, D, DA [auth d], H, O, S, Z | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | AA [auth a], E, EA [auth e], FA [auth f], I, AA [auth a], E, EA [auth e], FA [auth f], I, IA [auth i], J, M, P, T, U, X | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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 | BA [auth b], F, Q | 7 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G89619KY GlyCosmos:  G89619KY GlyGen:  G89619KY |
Entity ID: 5 | |||||
---|---|---|---|---|---|
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 | CA [auth c], G, R | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 6 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
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 | GA [auth g], HA [auth h], K, L, V, GA [auth g], HA [auth h], K, L, V, W | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
FOL (Subject of Investigation/LOI) Query on FOL | HB [auth C], RA [auth A], ZA [auth B] | FOLIC ACID C19 H19 N7 O6 OVBPIULPVIDEAO-LBPRGKRZSA-N | |||
NAG (Subject of Investigation/LOI) Query on NAG | AB [auth C] BB [auth C] CB [auth C] DB [auth C] EB [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 2.70 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
Task | Software Package | Version |
---|---|---|
MODEL REFINEMENT | Rosetta | |
RECONSTRUCTION | RELION | 3.0 |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-12-11  Deposition Author(s): Park, Y.J., Walls, A.C., Wang, Z., Sauer, M., Li, W., Tortorici, M.A., Bosch, B.J., DiMaio, F.D., Veesler, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | 120553 |
Revision History (Full details and data files)
- Version 1.0: 2019-12-11
Type: Initial release - Version 1.1: 2019-12-18
Changes: Database references - Version 1.2: 2020-01-08
Changes: Author supporting evidence - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary