6E39

Capsid protein of PCV2 with 2-O-sulfo-alpha-L-idopyranuronic acid and N,O6-DISULFO-GLUCOSAMINE

PDB DOI: https://doi.org/10.2210/pdb6E39/pdb
EM Map EMD-8975: EMDB EMDataResource

Classification: VIRUS LIKE PARTICLE
Organism(s): Porcine circovirus 2
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2018-07-13 Released: 2018-12-26
Deposition Author(s): Khayat, R., Dhindwal, S.
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 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 1,674.58 kDa
Atom Count: 93,036
Modelled Residue Count: 11,340
Deposited Residue Count: 13,980
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein of PCV2	A [auth A1] AA [auth AR] AB [auth Ar] B [auth A2] BA [auth AS] A [auth A1], AA [auth AR], AB [auth Ar], B [auth A2], BA [auth AS], BB [auth As], C [auth A3], CA [auth AT], CB [auth At], D [auth A4], DA [auth AU], DB [auth Au], E [auth A5], EA [auth AV], EB [auth Av], F [auth A6], FA [auth AW], FB [auth Aw], G [auth A7], GA [auth AX], GB [auth Ax], H [auth A8], HA [auth AY], HB [auth Ay], I [auth A9], IA [auth AZ], J [auth AA], JA [auth Aa], K [auth AB], KA [auth Ab], L [auth AC], LA [auth Ac], M [auth AD], MA [auth Ad], N [auth AE], NA [auth Ae], O [auth AF], OA [auth Af], P [auth AG], PA [auth Ag], Q [auth AH], QA [auth Ah], R [auth AI], RA [auth Ai], S [auth AJ], SA [auth Aj], T [auth AK], TA [auth Ak], U [auth AL], UA [auth Al], V [auth AM], VA [auth Am], W [auth AN], WA [auth An], X [auth AO], XA [auth Ao], Y [auth AP], YA [auth Ap], Z [auth AQ], ZA [auth Aq]	233	Porcine circovirus 2	Mutation(s): 0 Gene Names: cap, Cap, cp, ORF2, PCV2_gp3
UniProt
Find proteins for Q805N7 (Porcine circovirus 2) Explore Q805N7 Go to UniProtKB: Q805N7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q805N7
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid	IB [auth A]	2		N/A	Interactions Focus chain IB [auth A] Interactions & Density Focus chain IB [auth A]
Glycosylation Resources
GlyTouCan: G29057GU GlyCosmos: G29057GU GlyGen: G29057GU

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	PHENIX	1.13
RECONSTRUCTION	FREALIGN	9.11

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-12-26

Deposition Author(s):

Khayat, R.

Dhindwal, S.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5SC1AI114843

Revision History (Full details and data files)

Version 1.0: 2018-12-26
Type: Initial release
Version 1.1: 2019-07-10
Changes: Data collection, Database references
Version 1.2: 2019-12-18
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-03-13
Changes: Data collection, Database references, Structure summary

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Help and Resources

6E39

Capsid protein of PCV2 with 2-O-sulfo-alpha-L-idopyranuronic acid and N,O6-DISULFO-GLUCOSAMINE

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)