6Q05

MERS-CoV S structure in complex with sialyl-lewisX

PDB DOI: https://doi.org/10.2210/pdb6Q05/pdb
EM Map EMD-20543: 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
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(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 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.

Macromolecule Content

Total Structure Weight: 476.46 kDa
Atom Count: 28,977
Modelled Residue Count: 3,477
Deposited Residue Count: 4,077
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	1,359	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 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, DA [auth d], H, O, S, D, DA [auth d], H, O, S, Z	4		N-Glycosylation	Interactions Focus chain D Focus chain DA [auth d] Focus chain H Focus chain O Focus chain S Focus chain Z Interactions & Density Focus chain D Focus chain DA [auth d] Focus chain H Focus chain O Focus chain S Focus chain Z
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	Interactions Focus chain AA [auth a] Focus chain E Focus chain EA [auth e] Focus chain FA [auth f] Focus chain I Focus chain IA [auth i] Focus chain J Focus chain M Focus chain P Focus chain T Focus chain U Focus chain X Interactions & Density Focus chain AA [auth a] Focus chain E Focus chain EA [auth e] Focus chain FA [auth f] Focus chain I Focus chain IA [auth i] Focus chain J Focus chain M Focus chain P Focus chain T Focus chain U Focus chain X
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	Interactions Focus chain BA [auth b] Focus chain F Focus chain Q Interactions & Density Focus chain BA [auth b] Focus chain F Focus chain Q
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	Interactions Focus chain CA [auth c] Focus chain G Focus chain R Interactions & Density Focus chain CA [auth c] Focus chain G Focus chain R
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	Interactions Focus chain GA [auth g] Focus chain HA [auth h] Focus chain K Focus chain L Focus chain V Focus chain W Interactions & Density Focus chain GA [auth g] Focus chain HA [auth h] Focus chain K Focus chain L Focus chain V Focus chain W
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	JA [auth j], N, Y	4		N/A	Interactions Focus chain JA [auth j] Focus chain N Focus chain Y Interactions & Density Focus chain JA [auth j] Focus chain N Focus chain Y
Glycosylation Resources
GlyTouCan: G00054MO GlyCosmos: G00054MO GlyGen: G00054MO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FOL (Subject of Investigation/LOI) Query on FOL Download Ideal Coordinates CCD File SDF format, chain HB [auth C] SDF format, chain RA [auth A] SDF format, chain ZA [auth B] MOL2 format, chain HB [auth C] MOL2 format, chain RA [auth A] MOL2 format, chain ZA [auth B]	HB [auth C], RA [auth A], ZA [auth B]	FOLIC ACID C₁₉ H₁₉ N₇ O₆ OVBPIULPVIDEAO-LBPRGKRZSA-N		Interactions Focus chain HB [auth C] Focus chain RA [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain HB [auth C] Focus chain RA [auth A] Focus chain ZA [auth B]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain GB [auth C] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain MA [auth A] SDF format, chain NA [auth A] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain QA [auth A] SDF format, chain SA [auth B] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain VA [auth B] SDF format, chain WA [auth B] SDF format, chain XA [auth B] SDF format, chain YA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain YA [auth B]	AB [auth C] BB [auth C] CB [auth C] DB [auth C] EB [auth C] AB [auth C], BB [auth C], CB [auth C], DB [auth C], EB [auth C], FB [auth C], GB [auth C], KA [auth A], LA [auth A], MA [auth A], NA [auth A], OA [auth A], PA [auth A], QA [auth A], SA [auth B], TA [auth B], UA [auth B], VA [auth B], WA [auth B], XA [auth B], YA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 7
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900121 Query on PRD_900121	JA [auth N], N [auth Y], Y [auth j]	Sialyl-Lewis X antigen, beta anomer	Oligosaccharide / Antigen		Interactions Focus chain JA [auth j] Focus chain N Focus chain Y Interactions & Density Focus chain JA [auth j] Focus chain N Focus chain Y

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Rosetta
RECONSTRUCTION	RELION	3.0

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-12-11

Deposition Author(s):

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