7YMZ

Cryo-EM structure of MERS-CoV spike protein, intermediate conformation

PDB DOI: https://doi.org/10.2210/pdb7YMZ/pdb
EM Map EMD-33948: 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: 4.39 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: 464.65 kDa
Atom Count: 27,891
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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, F, I, J, L D, F, I, J, L, N, P, Q, U, V, W, X	2		N-Glycosylation	Interactions Focus chain D Focus chain F Focus chain I Focus chain J Focus chain L Focus chain N Focus chain P Focus chain Q Focus chain U Focus chain V Focus chain W Focus chain X Interactions & Density Focus chain D Focus chain F Focus chain I Focus chain J Focus chain L Focus chain N Focus chain P Focus chain Q Focus chain U Focus chain V Focus chain W Focus chain X
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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, M, R	5		N-Glycosylation	Interactions Focus chain E Focus chain M Focus chain R Interactions & Density Focus chain E Focus chain M Focus chain R
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, K, O, S G, H, K, O, S, T	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain K Focus chain O Focus chain S Focus chain T Interactions & Density Focus chain G Focus chain H Focus chain K Focus chain O Focus chain S Focus chain T
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 C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain Y [auth A] 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 C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain Y [auth A] 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 C], HA [auth C], IA [auth C], JA [auth C], Y [auth A], 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 C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain Y [auth A] 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 C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain Y [auth A] Focus chain Z [auth A]