4U60

Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with GM1 oligosaccharide

PDB DOI: https://doi.org/10.2210/pdb4U60/pdb

Classification: VIRAL PROTEIN
Organism(s): Trichodysplasia spinulosa-associated polyomavirus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-07-26 Released: 2015-08-05
Deposition Author(s): Stroh, L.J., Stehle, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.180
R-Value Work: 0.158
R-Value Observed: 0.159

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 159.77 kDa
Atom Count: 12,573
Modelled Residue Count: 1,346
Deposited Residue Count: 1,400
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Structural protein VP1	A, B, C, D, E	280	Trichodysplasia spinulosa-associated polyomavirus	Mutation(s): 0 Gene Names: VP1
UniProt
Find proteins for E2ESL7 (Trichodysplasia spinulosa-associated polyomavirus) Explore E2ESL7 Go to UniProtKB: E2ESL7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E2ESL7
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-[2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)]beta-D-galactopyranose	F, G	3		N/A	Interactions Focus chain F Focus chain G Interactions & Density Focus chain F Focus chain G
Glycosylation Resources
GlyTouCan: G45058HZ GlyCosmos: G45058HZ GlyGen: G45058HZ

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	H, I	5		N/A	Interactions Focus chain H Focus chain I Interactions & Density Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G48558GR GlyCosmos: G48558GR GlyGen: G48558GR

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIA Query on SIA Download Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B]	P [auth B]	N-acetyl-alpha-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain W [auth E] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain W [auth E]	J [auth A] K [auth A] M [auth B] N [auth B] Q [auth C] J [auth A], K [auth A], M [auth B], N [auth B], Q [auth C], R [auth C], T [auth D], U [auth D], W [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain X [auth E] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain X [auth E]	L [auth A], O [auth B], S [auth C], V [auth D], X [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain X [auth E] Interactions & Density Focus chain L [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain X [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.180
R-Value Work: 0.158
R-Value Observed: 0.159
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.99	α = 90
b = 152.05	β = 90
c = 67.97	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
XDS	data reduction
Coot	model building
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-08-05

Deposition Author(s):

Stroh, L.J.

Stehle, T.

Revision History (Full details and data files)

Version 1.0: 2015-08-05
Type: Initial release
Version 1.1: 2015-09-02
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

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Help and Resources

4U60

Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with GM1 oligosaccharide

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources