6VV5

Cryo-EM structure of porcine epidemic diarrhea virus (PEDV) spike protein

PDB DOI: https://doi.org/10.2210/pdb6VV5/pdb
EM Map EMD-21391: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Porcine epidemic diarrhea virus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2020-02-17 Released: 2020-02-26
Deposition Author(s): Kirchdoerfer, R.N., Ward, A.B.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 3.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 466.5 kDa
Atom Count: 26,838
Modelled Residue Count: 3,291
Deposited Residue Count: 4,068
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,356	Porcine epidemic diarrhea virus	Mutation(s): 0
UniProt
Find proteins for S5RJN4 (Porcine epidemic diarrhea virus) Explore S5RJN4 Go to UniProtKB: S5RJN4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	S5RJN4
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]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, N, X	8		N-Glycosylation	Interactions Focus chain D Focus chain N Focus chain X Interactions & Density Focus chain D Focus chain N Focus chain X
Glycosylation Resources
GlyTouCan: G59621EZ GlyCosmos: G59621EZ GlyGen: G59621EZ

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], CA [auth c], DA [auth d], E, EA [auth e], AA [auth a], CA [auth c], DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], I, J, K, L, M, O, P, Q, S, T, U, V, W, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain E Focus chain EA [auth e] Focus chain F Focus chain FA [auth f] Focus chain G Focus chain GA [auth g] Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain O Focus chain P Focus chain Q Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain E Focus chain EA [auth e] Focus chain F Focus chain FA [auth f] Focus chain G Focus chain GA [auth g] Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain O Focus chain P Focus chain Q Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
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	BA [auth b], H, R	3		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain H Focus chain R Interactions & Density Focus chain BA [auth b] Focus chain H Focus chain R
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PAM Query on PAM Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain MA [auth A] SDF format, chain NA [auth A] SDF format, chain TA [auth B] SDF format, chain UA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B]	AB [auth C] BB [auth C] MA [auth A] NA [auth A] TA [auth B] AB [auth C], BB [auth C], MA [auth A], NA [auth A], TA [auth B], UA [auth B]	PALMITOLEIC ACID C₁₆ H₃₀ O₂ SECPZKHBENQXJG-FPLPWBNLSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain TA [auth B] Focus chain UA [auth B] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain TA [auth B] Focus chain UA [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C]	HA [auth A] IA [auth A] JA [auth A] KA [auth A] LA [auth A] HA [auth A], IA [auth A], JA [auth A], KA [auth A], LA [auth A], OA [auth B], PA [auth B], QA [auth B], RA [auth B], SA [auth B], VA [auth C], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Rosetta	3.10
MODEL REFINEMENT	PHENIX	1.17rc2-3619
RECONSTRUCTION	RELION	3.0

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-02-26

Deposition Author(s):

Kirchdoerfer, R.N.

Ward, A.B.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI123498
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI127521

Revision History (Full details and data files)

Version 1.0: 2020-02-26
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 3.0: 2020-11-04
Changes: Advisory, Atomic model, Data collection, Derived calculations, Experimental preparation, Structure summary
Version 3.1: 2021-01-20
Changes: Database references
Version 3.2: 2021-04-14
Changes: Database references

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Help and Resources

6VV5

Cryo-EM structure of porcine epidemic diarrhea virus (PEDV) spike protein

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)