7B6S | pdb_00007b6s

Sheep Polyomavirus VP1 in complex with 10 mM Forssman antigen pentaose

PDB DOI: https://doi.org/10.2210/pdb7B6S/pdb

Classification: VIRAL PROTEIN
Organism(s): Sheep polyomavirus 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-12-08 Released: 2022-09-21
Deposition Author(s): Rustmeier, N.H., Stehle, T.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.176 (Depositor), 0.180 (DCC)
R-Value Work:
0.149 (Depositor), 0.154 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7B6S

This is version 1.2 of the entry. See complete history.

Literature

A novel and highly specific Forssman antigen-binding protein from sheep polyomavirus

Rustmeier, N.H., Silva, L.M., Di Maio, A., Mueller, J.C., Herrmann, A., Feizi, T., Liu, Y., Stehle, T.

(2023) bioRxiv

DOI: https://doi.org/10.1101/2023.04.10.536218

Macromolecule Content

Total Structure Weight: 316.57 kDa
Atom Count: 23,447
Modeled Residue Count: 2,642
Deposited Residue Count: 2,760
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A [auth AAA] B [auth BBB] C [auth CCC] D [auth DDD] E [auth EEE] A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD], E [auth EEE], F [auth FFF], G [auth GGG], H [auth HHH], I [auth III], J [auth JJJ]	276	Sheep polyomavirus 1	Mutation(s): 0
UniProt
Find proteins for A0ACD6B8T1 (Sheep polyomavirus 1) Explore A0ACD6B8T1 Go to UniProtKB: A0ACD6B8T1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B8T1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose	K [auth AaA], L [auth BaB], N [auth DaD], P [auth FbF], R [auth HaH], K [auth AaA], L [auth BaB], N [auth DaD], P [auth FbF], R [auth HaH], S [auth IaI]	4		N/A	Interactions Focus chain K [auth AaA] Focus chain L [auth BaB] Focus chain N [auth DaD] Focus chain P [auth FbF] Focus chain R [auth HaH] Focus chain S [auth IaI] Interactions & Density Focus chain K [auth AaA] Focus chain L [auth BaB] Focus chain N [auth DaD] Focus chain P [auth FbF] Focus chain R [auth HaH] Focus chain S [auth IaI]
Glycosylation Resources
GlyTouCan: G88796WA GlyCosmos: G88796WA GlyGen: G88796WA

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	M [auth CaC], O [auth EaE], Q [auth GaG], T [auth JaJ]	5		N/A	Interactions Focus chain M [auth CaC] Focus chain O [auth EaE] Focus chain Q [auth GaG] Focus chain T [auth JaJ] Interactions & Density Focus chain M [auth CaC] Focus chain O [auth EaE] Focus chain Q [auth GaG] Focus chain T [auth JaJ]
Glycosylation Resources
GlyTouCan: G80062GG GlyCosmos: G80062GG GlyGen: G80062GG

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain IA [auth FFF] SDF format, chain NA [auth GGG] SDF format, chain WA [auth III] MOL2 format, chain IA [auth FFF] MOL2 format, chain NA [auth GGG] MOL2 format, chain WA [auth III] mmCIF format, chain IA [auth FFF] mmCIF format, chain NA [auth GGG] mmCIF format, chain WA [auth III]	IA [auth FFF], NA [auth GGG], WA [auth III]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain IA [auth FFF] Focus chain NA [auth GGG] Focus chain WA [auth III] Interactions & Density Focus chain IA [auth FFF] Focus chain NA [auth GGG] Focus chain WA [auth III]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain BA [auth DDD] SDF format, chain JA [auth FFF] SDF format, chain KA [auth FFF] SDF format, chain QA [auth HHH] SDF format, chain U [auth AAA] SDF format, chain YA [auth JJJ] SDF format, chain W [auth BBB] SDF format, chain UA [auth III] SDF format, chain PA [auth HHH] MOL2 format, chain BA [auth DDD] MOL2 format, chain JA [auth FFF] MOL2 format, chain KA [auth FFF] MOL2 format, chain QA [auth HHH] MOL2 format, chain U [auth AAA] MOL2 format, chain YA [auth JJJ] MOL2 format, chain W [auth BBB] MOL2 format, chain UA [auth III] MOL2 format, chain PA [auth HHH] mmCIF format, chain BA [auth DDD] mmCIF format, chain JA [auth FFF] mmCIF format, chain KA [auth FFF] mmCIF format, chain QA [auth HHH] mmCIF format, chain U [auth AAA] mmCIF format, chain YA [auth JJJ] mmCIF format, chain W [auth BBB] mmCIF format, chain UA [auth III] mmCIF format, chain PA [auth HHH]	BA [auth DDD] JA [auth FFF] KA [auth FFF] PA [auth HHH] QA [auth HHH] BA [auth DDD], JA [auth FFF], KA [auth FFF], PA [auth HHH], QA [auth HHH], U [auth AAA], UA [auth III], W [auth BBB], YA [auth JJJ]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain BA [auth DDD] Focus chain JA [auth FFF] Focus chain KA [auth FFF] Focus chain PA [auth HHH] Focus chain QA [auth HHH] Focus chain U [auth AAA] Focus chain UA [auth III] Focus chain W [auth BBB] Focus chain YA [auth JJJ] Interactions & Density Focus chain BA [auth DDD] Focus chain JA [auth FFF] Focus chain KA [auth FFF] Focus chain PA [auth HHH] Focus chain QA [auth HHH] Focus chain U [auth AAA] Focus chain UA [auth III] Focus chain W [auth BBB] Focus chain YA [auth JJJ]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain GA [auth EEE] SDF format, chain MA [auth GGG] SDF format, chain RA [auth HHH] SDF format, chain VA [auth III] SDF format, chain Z [auth CCC] MOL2 format, chain GA [auth EEE] MOL2 format, chain MA [auth GGG] MOL2 format, chain RA [auth HHH] MOL2 format, chain VA [auth III] MOL2 format, chain Z [auth CCC] mmCIF format, chain GA [auth EEE] mmCIF format, chain MA [auth GGG] mmCIF format, chain RA [auth HHH] mmCIF format, chain VA [auth III] mmCIF format, chain Z [auth CCC]	GA [auth EEE], MA [auth GGG], RA [auth HHH], VA [auth III], Z [auth CCC]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain GA [auth EEE] Focus chain MA [auth GGG] Focus chain RA [auth HHH] Focus chain VA [auth III] Focus chain Z [auth CCC] Interactions & Density Focus chain GA [auth EEE] Focus chain MA [auth GGG] Focus chain RA [auth HHH] Focus chain VA [auth III] Focus chain Z [auth CCC]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain CA [auth DDD] SDF format, chain DA [auth DDD] SDF format, chain FA [auth EEE] SDF format, chain Y [auth CCC] SDF format, chain ZA [auth JJJ] SDF format, chain SA [auth HHH] MOL2 format, chain CA [auth DDD] MOL2 format, chain DA [auth DDD] MOL2 format, chain FA [auth EEE] MOL2 format, chain Y [auth CCC] MOL2 format, chain ZA [auth JJJ] MOL2 format, chain SA [auth HHH] mmCIF format, chain CA [auth DDD] mmCIF format, chain DA [auth DDD] mmCIF format, chain FA [auth EEE] mmCIF format, chain Y [auth CCC] mmCIF format, chain ZA [auth JJJ] mmCIF format, chain SA [auth HHH]	CA [auth DDD] DA [auth DDD] FA [auth EEE] SA [auth HHH] Y [auth CCC] CA [auth DDD], DA [auth DDD], FA [auth EEE], SA [auth HHH], Y [auth CCC], ZA [auth JJJ]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth DDD] Focus chain DA [auth DDD] Focus chain FA [auth EEE] Focus chain SA [auth HHH] Focus chain Y [auth CCC] Focus chain ZA [auth JJJ] Interactions & Density Focus chain CA [auth DDD] Focus chain DA [auth DDD] Focus chain FA [auth EEE] Focus chain SA [auth HHH] Focus chain Y [auth CCC] Focus chain ZA [auth JJJ]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AB [auth JJJ] SDF format, chain EA [auth DDD] SDF format, chain HA [auth EEE] SDF format, chain LA [auth FFF] SDF format, chain OA [auth GGG] SDF format, chain TA [auth HHH] SDF format, chain V [auth AAA] SDF format, chain X [auth BBB] SDF format, chain XA [auth III] SDF format, chain AA [auth CCC] MOL2 format, chain AB [auth JJJ] MOL2 format, chain EA [auth DDD] MOL2 format, chain HA [auth EEE] MOL2 format, chain LA [auth FFF] MOL2 format, chain OA [auth GGG] MOL2 format, chain TA [auth HHH] MOL2 format, chain V [auth AAA] MOL2 format, chain X [auth BBB] MOL2 format, chain XA [auth III] MOL2 format, chain AA [auth CCC] mmCIF format, chain AB [auth JJJ] mmCIF format, chain EA [auth DDD] mmCIF format, chain HA [auth EEE] mmCIF format, chain LA [auth FFF] mmCIF format, chain OA [auth GGG] mmCIF format, chain TA [auth HHH] mmCIF format, chain V [auth AAA] mmCIF format, chain X [auth BBB] mmCIF format, chain XA [auth III] mmCIF format, chain AA [auth CCC]	AA [auth CCC] AB [auth JJJ] EA [auth DDD] HA [auth EEE] LA [auth FFF] AA [auth CCC], AB [auth JJJ], EA [auth DDD], HA [auth EEE], LA [auth FFF], OA [auth GGG], TA [auth HHH], V [auth AAA], X [auth BBB], XA [auth III]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth CCC] Focus chain AB [auth JJJ] Focus chain EA [auth DDD] Focus chain HA [auth EEE] Focus chain LA [auth FFF] Focus chain OA [auth GGG] Focus chain TA [auth HHH] Focus chain V [auth AAA] Focus chain X [auth BBB] Focus chain XA [auth III] Interactions & Density Focus chain AA [auth CCC] Focus chain AB [auth JJJ] Focus chain EA [auth DDD] Focus chain HA [auth EEE] Focus chain LA [auth FFF] Focus chain OA [auth GGG] Focus chain TA [auth HHH] Focus chain V [auth AAA] Focus chain X [auth BBB] Focus chain XA [auth III]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.176 (Depositor), 0.180 (DCC)
R-Value Work: 0.149 (Depositor), 0.154 (DCC)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.494	α = 90
b = 130.494	β = 90
c = 222.435	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-09-21

Deposition Author(s):

Rustmeier, N.H.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	FOR2327

Revision History (Full details and data files)

Version 1.0: 2022-09-21
Type: Initial release
Version 1.1: 2023-04-19
Changes: Database references
Version 1.2: 2024-02-07
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.