7YMV

Cryo-EM structure of MERS-CoV spike protein, Two RBD-up conformation 1

PDB DOI: https://doi.org/10.2210/pdb7YMV/pdb
EM Map EMD-33943: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Human betacoronavirus 2c EMC/2012
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2022-07-29 Released: 2023-08-09
Deposition Author(s): Hsu, S.T.D., Chang, N.E., Weng, Z.W., Yang, T.J., Draczkowski, P.
Funding Organization(s): Academia Sinica (Taiwan)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 6.74 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

GlycoSHIELD: a versatile pipeline to assess glycan impact on protein structures

Gecht, M., von Bulow, S., Penet, C., Hummer, G., Hanus, C., Sikora, M.

To be published.

Macromolecule Content

Total Structure Weight: 467.39 kDa
Atom Count: 28,075
Modelled Residue Count: 3,498
Deposited Residue Count: 4,107
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,369	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 Annotations Expand
Reference Sequence

Oligosaccharides

Help

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, F, N, X	4		N-Glycosylation	Interactions Focus chain D Focus chain F Focus chain N Focus chain X Interactions & Density Focus chain D Focus chain F Focus chain N Focus chain X
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 3
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	E	5		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, J, L, M G, H, J, L, M, R, S, U	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain J Focus chain L Focus chain M Focus chain R Focus chain S Focus chain U Interactions & Density Focus chain G Focus chain H Focus chain J Focus chain L Focus chain M Focus chain R Focus chain S Focus chain U
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I, P	3		N-Glycosylation	Interactions Focus chain I Focus chain P Interactions & Density Focus chain I Focus chain P
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 6
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	K, O, Q, T, V K, O, Q, T, V, W	3		N-Glycosylation	Interactions Focus chain K Focus chain O Focus chain Q Focus chain T Focus chain V Focus chain W Interactions & Density Focus chain K Focus chain O Focus chain Q Focus chain T Focus chain V Focus chain W
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	Y	2		N-Glycosylation	Interactions Focus chain Y Interactions & Density Focus chain Y
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain Z [auth A]	AA [auth A] BA [auth A] CA [auth B] DA [auth B] EA [auth B] AA [auth A], BA [auth A], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth C], KA [auth C], LA [auth C], MA [auth C], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain Z [auth A]