4POS

Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'-sialyllactosamine

• PDB DOI: https://doi.org/10.2210/pdb4POS/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human polyomavirus 9
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-02-26 Released: 2014-04-09 
• Deposition Author(s): Khan, Z.M., Stehle, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.213 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 310.51 kDa 
• Atom Count: 23,830 
• Modelled Residue Count: 2,709 
• Deposited Residue Count: 2,780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A, B, C, D, E, F, G, H, I, J	278	Human polyomavirus 9	Mutation(s): 0  Gene Names: gp3, vp1
UniProt
Find proteins for E9NQ90 (Human polyomavirus 9) Explore E9NQ90  Go to UniProtKB:  E9NQ90

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K, L, M, N, O, P, Q, R, S	3		N/A
Glycosylation Resources
GlyTouCan:  G00065MO GlyCosmos:  G00065MO GlyGen:  G00065MO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	AB [auth G], CA [auth B], DA [auth B], DB [auth H], EA [auth B], EB [auth H], FA [auth B], FB [auth H], GB [auth H], IA [auth C], JB [auth I], KB [auth I], LA [auth D], LB [auth I], MA [auth D], MB [auth I], PA [auth E], PB [auth J], QA [auth E], TA [auth F], U [auth A], UA [auth F], V [auth A], VA [auth F], W [auth A], WA [auth F], X [auth A], Y [auth A], Z [auth A], ZA [auth G]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA	AA [auth A], BB [auth G], GA [auth B], HB [auth H], JA [auth C], NA [auth D], NB [auth I], QB [auth J], RA [auth E], XA [auth F]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
CA	BA [auth B], CB [auth H], HA [auth C], IB [auth I], KA [auth D], OA [auth E], OB [auth J], SA [auth F], T [auth A], YA [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900067	K, L, M, N, O, P, Q, R, S	3'-sialyl-N-acetyllactosamine	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.213 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.91	α = 90
b = 180.63	β = 90
c = 199.42	γ = 90

Software Package:

Software Name	Purpose
RemDAq	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-09 
Deposition Author(s): Khan, Z.M., Stehle, T.

Revision History  

• Version 1.0: 2014-04-09
  Type: Initial release
  
• Version 1.1: 2014-11-26
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-20
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary