7B6T | pdb_00007b6t

Sheep Polyomavirus VP1 in complex with 10 mM globo-N-tetraose

PDB DOI: https://doi.org/10.2210/pdb7B6T/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: 1.70 Å
R-Value Free:
0.165 (Depositor), 0.170 (DCC)
R-Value Work:
0.143 (Depositor), 0.149 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7B6T

This is version 1.3 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: 312.31 kDa
Atom Count: 24,010
Modeled Residue Count: 2,645
Deposited Residue Count: 2,760
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose	K [auth AaA], M [auth CaC], O [auth FaF], P [auth HaH]	3		N/A	Interactions Focus chain K [auth AaA] Focus chain M [auth CaC] Focus chain O [auth FaF] Focus chain P [auth HaH] Interactions & Density Focus chain K [auth AaA] Focus chain M [auth CaC] Focus chain O [auth FaF] Focus chain P [auth HaH]
Glycosylation Resources
GlyTouCan: G30239EK GlyCosmos: G30239EK GlyGen: G30239EK

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose	L [auth BaB], N [auth DaD], Q [auth JaJ]	2		N/A	Interactions Focus chain L [auth BaB] Focus chain N [auth DaD] Focus chain Q [auth JaJ] Interactions & Density Focus chain L [auth BaB] Focus chain N [auth DaD] Focus chain Q [auth JaJ]
Glycosylation Resources
GlyTouCan: G71661JQ GlyCosmos: G71661JQ GlyGen: G71661JQ

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain W [auth BBB] SDF format, chain X [auth BBB] SDF format, chain V [auth BBB] MOL2 format, chain W [auth BBB] MOL2 format, chain X [auth BBB] MOL2 format, chain V [auth BBB] mmCIF format, chain W [auth BBB] mmCIF format, chain X [auth BBB] mmCIF format, chain V [auth BBB]	V [auth BBB], W [auth BBB], X [auth BBB]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain V [auth BBB] Focus chain W [auth BBB] Focus chain X [auth BBB] Interactions & Density Focus chain V [auth BBB] Focus chain W [auth BBB] Focus chain X [auth BBB]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain NA [auth EEE] SDF format, chain WA [auth GGG] SDF format, chain GB [auth III] MOL2 format, chain NA [auth EEE] MOL2 format, chain WA [auth GGG] MOL2 format, chain GB [auth III] mmCIF format, chain NA [auth EEE] mmCIF format, chain WA [auth GGG] mmCIF format, chain GB [auth III]	GB [auth III], NA [auth EEE], WA [auth GGG]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain GB [auth III] Focus chain NA [auth EEE] Focus chain WA [auth GGG] Interactions & Density Focus chain GB [auth III] Focus chain NA [auth EEE] Focus chain WA [auth GGG]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain BA [auth CCC] SDF format, chain EA [auth CCC] SDF format, chain IA [auth DDD] SDF format, chain LA [auth EEE] SDF format, chain R [auth AAA] SDF format, chain SA [auth FFF] MOL2 format, chain BA [auth CCC] MOL2 format, chain EA [auth CCC] MOL2 format, chain IA [auth DDD] MOL2 format, chain LA [auth EEE] MOL2 format, chain R [auth AAA] MOL2 format, chain SA [auth FFF] mmCIF format, chain BA [auth CCC] mmCIF format, chain EA [auth CCC] mmCIF format, chain IA [auth DDD] mmCIF format, chain LA [auth EEE] mmCIF format, chain R [auth AAA] mmCIF format, chain SA [auth FFF]	BA [auth CCC] EA [auth CCC] IA [auth DDD] LA [auth EEE] R [auth AAA] BA [auth CCC], EA [auth CCC], IA [auth DDD], LA [auth EEE], R [auth AAA], SA [auth FFF]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth CCC] Focus chain EA [auth CCC] Focus chain IA [auth DDD] Focus chain LA [auth EEE] Focus chain R [auth AAA] Focus chain SA [auth FFF] Interactions & Density Focus chain BA [auth CCC] Focus chain EA [auth CCC] Focus chain IA [auth DDD] Focus chain LA [auth EEE] Focus chain R [auth AAA] Focus chain SA [auth FFF]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AB [auth HHH] SDF format, chain BB [auth HHH] SDF format, chain FA [auth CCC] SDF format, chain FB [auth III] SDF format, chain MB [auth JJJ] SDF format, chain NB [auth JJJ] SDF format, chain QA [auth FFF] SDF format, chain TA [auth FFF] SDF format, chain Y [auth BBB] SDF format, chain ZA [auth HHH] SDF format, chain U [auth BBB] SDF format, chain RA [auth FFF] SDF format, chain MA [auth EEE] SDF format, chain IB [auth III] SDF format, chain HB [auth III] SDF format, chain DA [auth CCC] SDF format, chain CB [auth HHH] SDF format, chain CA [auth CCC] MOL2 format, chain AB [auth HHH] MOL2 format, chain BB [auth HHH] MOL2 format, chain FA [auth CCC] MOL2 format, chain FB [auth III] MOL2 format, chain MB [auth JJJ] MOL2 format, chain NB [auth JJJ] MOL2 format, chain QA [auth FFF] MOL2 format, chain TA [auth FFF] MOL2 format, chain Y [auth BBB] MOL2 format, chain ZA [auth HHH] MOL2 format, chain U [auth BBB] MOL2 format, chain RA [auth FFF] MOL2 format, chain MA [auth EEE] MOL2 format, chain IB [auth III] MOL2 format, chain HB [auth III] MOL2 format, chain DA [auth CCC] MOL2 format, chain CB [auth HHH] MOL2 format, chain CA [auth CCC] mmCIF format, chain AB [auth HHH] mmCIF format, chain BB [auth HHH] mmCIF format, chain FA [auth CCC] mmCIF format, chain FB [auth III] mmCIF format, chain MB [auth JJJ] mmCIF format, chain NB [auth JJJ] mmCIF format, chain QA [auth FFF] mmCIF format, chain TA [auth FFF] mmCIF format, chain Y [auth BBB] mmCIF format, chain ZA [auth HHH] mmCIF format, chain U [auth BBB] mmCIF format, chain RA [auth FFF] mmCIF format, chain MA [auth EEE] mmCIF format, chain IB [auth III] mmCIF format, chain HB [auth III] mmCIF format, chain DA [auth CCC] mmCIF format, chain CB [auth HHH] mmCIF format, chain CA [auth CCC]	AB [auth HHH] BB [auth HHH] CA [auth CCC] CB [auth HHH] DA [auth CCC] AB [auth HHH], BB [auth HHH], CA [auth CCC], CB [auth HHH], DA [auth CCC], FA [auth CCC], FB [auth III], HB [auth III], IB [auth III], MA [auth EEE], MB [auth JJJ], NB [auth JJJ], QA [auth FFF], RA [auth FFF], TA [auth FFF], U [auth BBB], Y [auth BBB], ZA [auth HHH]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth HHH] Focus chain BB [auth HHH] Focus chain CA [auth CCC] Focus chain CB [auth HHH] Focus chain DA [auth CCC] Focus chain FA [auth CCC] Focus chain FB [auth III] Focus chain HB [auth III] Focus chain IB [auth III] Focus chain MA [auth EEE] Focus chain MB [auth JJJ] Focus chain NB [auth JJJ] Focus chain QA [auth FFF] Focus chain RA [auth FFF] Focus chain TA [auth FFF] Focus chain U [auth BBB] Focus chain Y [auth BBB] Focus chain ZA [auth HHH] Interactions & Density Focus chain AB [auth HHH] Focus chain BB [auth HHH] Focus chain CA [auth CCC] Focus chain CB [auth HHH] Focus chain DA [auth CCC] Focus chain FA [auth CCC] Focus chain FB [auth III] Focus chain HB [auth III] Focus chain IB [auth III] Focus chain MA [auth EEE] Focus chain MB [auth JJJ] Focus chain NB [auth JJJ] Focus chain QA [auth FFF] Focus chain RA [auth FFF] Focus chain TA [auth FFF] Focus chain U [auth BBB] Focus chain Y [auth BBB] Focus chain ZA [auth HHH]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain AA [auth BBB] SDF format, chain EB [auth HHH] SDF format, chain PA [auth EEE] SDF format, chain VA [auth FFF] SDF format, chain T [auth AAA] SDF format, chain PB [auth JJJ] SDF format, chain LB [auth III] SDF format, chain KA [auth DDD] SDF format, chain HA [auth CCC] MOL2 format, chain AA [auth BBB] MOL2 format, chain EB [auth HHH] MOL2 format, chain PA [auth EEE] MOL2 format, chain VA [auth FFF] MOL2 format, chain T [auth AAA] MOL2 format, chain PB [auth JJJ] MOL2 format, chain LB [auth III] MOL2 format, chain KA [auth DDD] MOL2 format, chain HA [auth CCC] mmCIF format, chain AA [auth BBB] mmCIF format, chain EB [auth HHH] mmCIF format, chain PA [auth EEE] mmCIF format, chain VA [auth FFF] mmCIF format, chain T [auth AAA] mmCIF format, chain PB [auth JJJ] mmCIF format, chain LB [auth III] mmCIF format, chain KA [auth DDD] mmCIF format, chain HA [auth CCC]	AA [auth BBB] EB [auth HHH] HA [auth CCC] KA [auth DDD] LB [auth III] AA [auth BBB], EB [auth HHH], HA [auth CCC], KA [auth DDD], LB [auth III], PA [auth EEE], PB [auth JJJ], T [auth AAA], VA [auth FFF]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth BBB] Focus chain EB [auth HHH] Focus chain HA [auth CCC] Focus chain KA [auth DDD] Focus chain LB [auth III] Focus chain PA [auth EEE] Focus chain PB [auth JJJ] Focus chain T [auth AAA] Focus chain VA [auth FFF] Interactions & Density Focus chain AA [auth BBB] Focus chain EB [auth HHH] Focus chain HA [auth CCC] Focus chain KA [auth DDD] Focus chain LB [auth III] Focus chain PA [auth EEE] Focus chain PB [auth JJJ] Focus chain T [auth AAA] Focus chain VA [auth FFF]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain JA [auth DDD] SDF format, chain OB [auth JJJ] SDF format, chain UA [auth FFF] SDF format, chain Z [auth BBB] SDF format, chain YA [auth GGG] SDF format, chain XA [auth GGG] SDF format, chain S [auth AAA] SDF format, chain OA [auth EEE] SDF format, chain KB [auth III] SDF format, chain JB [auth III] SDF format, chain GA [auth CCC] SDF format, chain DB [auth HHH] MOL2 format, chain JA [auth DDD] MOL2 format, chain OB [auth JJJ] MOL2 format, chain UA [auth FFF] MOL2 format, chain Z [auth BBB] MOL2 format, chain YA [auth GGG] MOL2 format, chain XA [auth GGG] MOL2 format, chain S [auth AAA] MOL2 format, chain OA [auth EEE] MOL2 format, chain KB [auth III] MOL2 format, chain JB [auth III] MOL2 format, chain GA [auth CCC] MOL2 format, chain DB [auth HHH] mmCIF format, chain JA [auth DDD] mmCIF format, chain OB [auth JJJ] mmCIF format, chain UA [auth FFF] mmCIF format, chain Z [auth BBB] mmCIF format, chain YA [auth GGG] mmCIF format, chain XA [auth GGG] mmCIF format, chain S [auth AAA] mmCIF format, chain OA [auth EEE] mmCIF format, chain KB [auth III] mmCIF format, chain JB [auth III] mmCIF format, chain GA [auth CCC] mmCIF format, chain DB [auth HHH]	DB [auth HHH] GA [auth CCC] JA [auth DDD] JB [auth III] KB [auth III] DB [auth HHH], GA [auth CCC], JA [auth DDD], JB [auth III], KB [auth III], OA [auth EEE], OB [auth JJJ], S [auth AAA], UA [auth FFF], XA [auth GGG], YA [auth GGG], Z [auth BBB]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DB [auth HHH] Focus chain GA [auth CCC] Focus chain JA [auth DDD] Focus chain JB [auth III] Focus chain KB [auth III] Focus chain OA [auth EEE] Focus chain OB [auth JJJ] Focus chain S [auth AAA] Focus chain UA [auth FFF] Focus chain XA [auth GGG] Focus chain YA [auth GGG] Focus chain Z [auth BBB] Interactions & Density Focus chain DB [auth HHH] Focus chain GA [auth CCC] Focus chain JA [auth DDD] Focus chain JB [auth III] Focus chain KB [auth III] Focus chain OA [auth EEE] Focus chain OB [auth JJJ] Focus chain S [auth AAA] Focus chain UA [auth FFF] Focus chain XA [auth GGG] Focus chain YA [auth GGG] Focus chain Z [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.165 (Depositor), 0.170 (DCC)
R-Value Work: 0.143 (Depositor), 0.149 (DCC)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.274	α = 90
b = 130.274	β = 90
c = 222.145	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: 2022-10-05
Changes: Derived calculations
Version 1.2: 2023-04-19
Changes: Database references
Version 1.3: 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.