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- PDB-1vps: POLYOMAVIRUS VP1 PENTAMER COMPLEXED WITH A DISIALYLATED HEXASACCHARIDE -

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Basic information

Entry
Database: PDB / ID: 1vps
TitlePOLYOMAVIRUS VP1 PENTAMER COMPLEXED WITH A DISIALYLATED HEXASACCHARIDE
ComponentsPOLYOMAVIRUS VP1 PENTAMER
KeywordsVIRAL PROTEIN / VIRUS COAT PROTEIN / OLIGOSACCHARIDE BINDING / VIRUS ASSEMBLY / SIALIC ACID
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / T=7 icosahedral viral capsid / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Capsid protein VP1,Polyomavirus / Polyomavirus Vp1; Chain A / Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMurine polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStehle, T. / Harrison, S.C.
Citation
Journal: Embo J. / Year: 1997
Title: High-resolution structure of a polyomavirus VP1-oligosaccharide complex: implications for assembly and receptor binding.
Authors: Stehle, T. / Harrison, S.C.
#1: Journal: Structure / Year: 1996
Title: The Structure of Simian Virus 40 Refined at 3.1 A Resolution
Authors: Stehle, T. / Gamblin, S.J. / Yan, Y. / Harrison, S.C.
#2: Journal: Structure / Year: 1996
Title: Crystal Structures of Murine Polyomavirus in Complex with Straight-Chain and Branched-Chain Sialyloligosaccharide Receptor Fragments
Authors: Stehle, T. / Harrison, S.C.
#3: Journal: Nature / Year: 1994
Title: Structure of Murine Polyomavirus Complexed with an Oligosaccharide Receptor Fragment
Authors: Stehle, T. / Yan, Y. / Benjamin, T.L. / Harrison, S.C.
History
DepositionMar 7, 1997Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POLYOMAVIRUS VP1 PENTAMER
B: POLYOMAVIRUS VP1 PENTAMER
C: POLYOMAVIRUS VP1 PENTAMER
D: POLYOMAVIRUS VP1 PENTAMER
E: POLYOMAVIRUS VP1 PENTAMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,26510
Polymers160,4365
Non-polymers4,8295
Water38,3182127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29440 Å2
ΔGint-96 kcal/mol
Surface area55100 Å2
MethodPISA
2
A: POLYOMAVIRUS VP1 PENTAMER
B: POLYOMAVIRUS VP1 PENTAMER
C: POLYOMAVIRUS VP1 PENTAMER
D: POLYOMAVIRUS VP1 PENTAMER
E: POLYOMAVIRUS VP1 PENTAMER
hetero molecules

A: POLYOMAVIRUS VP1 PENTAMER
B: POLYOMAVIRUS VP1 PENTAMER
C: POLYOMAVIRUS VP1 PENTAMER
D: POLYOMAVIRUS VP1 PENTAMER
E: POLYOMAVIRUS VP1 PENTAMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,53120
Polymers320,87210
Non-polymers9,65910
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_674x-y+1,-y+2,-z-1/31
Buried area61590 Å2
ΔGint-212 kcal/mol
Surface area107500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.500, 221.500, 99.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsTHE COORDINATE SET CONSISTS OF FIVE VP1 MOLECULES (A VP1 PENTAMER) THAT ARE EACH COMPLEXED WITH A DISIALYLATED OLIGOSACCHARIDE.

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Components

#1: Protein
POLYOMAVIRUS VP1 PENTAMER


Mass: 32087.213 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine polyomavirus / Genus: Polyomavirus / Production host: Escherichia coli (E. coli) / References: UniProt: P49302
#2: Polysaccharide
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 965.858 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3[DNeup5Aca2-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-3/a3-b1_a6-d2_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}[(6+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2127 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.4 Å3/Da / Density % sol: 65 %
Crystal growpH: 8
Details: DROP: 1.0 M AMMONIUM PHOSPHATE PH 8.0 2.5 & ETHANOL 8-10 MG/ML PROTEIN RESERVOIR: 2.0 M AMMONIUM PHOSPHATE PH 8.0 5 % ETHANOL
Crystal
*PLUS
Density % sol: 65 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.0 Mammonium phosphate1drop
22.5 %ethanol1drop
38-10 mg/mlprotein1drop
42.0 Mammonium phosphate1reservoir
55 %ethanol1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Feb 1, 1996 / Details: MIRROR
RadiationMonochromator: WIGGLER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 188556 / % possible obs: 85.6 % / Observed criterion σ(I): 0 / Rsym value: 0.058 / Net I/σ(I): 14.5
Reflection shellResolution: 1.9→2 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.232 / % possible all: 56.5
Reflection
*PLUS
Rmerge(I) obs: 0.058

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNCOMPLEXED VP1 PENTAMER (PDB ENTRY 1VPN)

1vpn


Resolution: 1.9→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.205 -2 %RANDOM
Rwork0.177 ---
obs0.177 188556 85.6 %-
Displacement parametersBiso mean: 29.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å / Luzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11134 0 330 2127 13591
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.35
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: UNRESTRAINED
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM3.CHOTOPH3.CHO

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