4X14

JC Mad-1 polyomavirus VP1 in complex with GM1 oligosaccharide

PDB DOI: https://doi.org/10.2210/pdb4X14/pdb

Classification: VIRAL PROTEIN
Organism(s): JC polyomavirus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-11-24 Released: 2015-04-22
Deposition Author(s): Stroh, L.J., Stehle, T.
Funding Organization(s): National Institutes of Health

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.211
R-Value Work: 0.187
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 154.8 kDa
Atom Count: 10,914
Modelled Residue Count: 1,286
Deposited Residue Count: 1,360
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein VP1	A, B, C, D, E	272	JC polyomavirus	Mutation(s): 0
UniProt
Find proteins for P03089 (JC polyomavirus) Explore P03089 Go to UniProtKB: P03089
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03089
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose	F	4		N/A	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G50886AE GlyCosmos: G50886AE GlyGen: G50886AE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	G, H	5		N/A	Interactions Focus chain G Focus chain H Interactions & Density Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G48558GR GlyCosmos: G48558GR GlyGen: G48558GR

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain Z [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D]	DA [auth E], I [auth A], P [auth B], U [auth C], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain I [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain DA [auth E] Focus chain I [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain Z [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain GA [auth E] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C]	AA [auth D] BA [auth D] EA [auth E] FA [auth E] GA [auth E] AA [auth D], BA [auth D], EA [auth E], FA [auth E], GA [auth E], J [auth A], K [auth A], L [auth A], M [auth A], Q [auth B], R [auth B], S [auth B], V [auth C], W [auth C], X [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]
K Query on K Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain T [auth B] SDF format, chain Y [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth C]	CA [auth D], N [auth A], O [auth A], T [auth B], Y [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain T [auth B] Focus chain Y [auth C] Interactions & Density Focus chain CA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain T [auth B] Focus chain Y [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.211
R-Value Work: 0.187
R-Value Observed: 0.188
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.45	α = 90
b = 95.59	β = 110.17
c = 129.67	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2015-04-22

Deposition Author(s):

Stroh, L.J.

Stehle, T.

Funding Organization	Location	Grant Number
National Institutes of Health	United States	--

Revision History (Full details and data files)

Version 1.0: 2015-04-22
Type: Initial release
Version 1.1: 2015-05-27
Changes: Database references
Version 1.2: 2018-01-31
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary