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- PDB-3bwr: SV40 VP1 pentamer in complex with GM1 oligosaccharide -

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Basic information

Entry
Database: PDB / ID: 3bwr
TitleSV40 VP1 pentamer in complex with GM1 oligosaccharide
ComponentsCapsid protein VP1
KeywordsVIRAL PROTEIN / SV40 / GM1 / viral receptor / viral attachment / ganglioside / VP1 / polyomaviruses / Capsid protein / Late protein / Nucleus / Virion
Function / homology
Function and homology information


capsomere / caveolin-mediated endocytosis of virus by host cell / viral capsid assembly / T=7 icosahedral viral capsid / host cell endoplasmic reticulum / molecular adaptor activity / virion attachment to host cell / host cell nucleus / structural molecule activity / identical protein binding
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
Major capsid protein VP1
Similarity search - Component
Biological speciesSimian virus 40
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsNeu, U. / Stehle, T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structural basis of GM1 ganglioside recognition by simian virus 40.
Authors: Neu, U. / Woellner, K. / Gauglitz, G. / Stehle, T.
History
DepositionJan 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Other
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_ref_seq_dif / 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_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,04114
Polymers148,6725
Non-polymers3,3699
Water15,403855
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.764, 93.087, 118.882
Angle α, β, γ (deg.)90.00, 105.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Capsid protein VP1


Mass: 29734.420 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 40 / Genus: Polyomavirus / Gene: VP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03087
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha- ...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


Type: oligosaccharide / Mass: 998.885 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-4-2/a4-b1_b3-c2_b4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 855 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsAUTHORS STATE THAT ALTHOUGH MODELED AS BETA, O1 OF GLC302 EXHIBITS INTERCHANGING ALPHA AND BETA ...AUTHORS STATE THAT ALTHOUGH MODELED AS BETA, O1 OF GLC302 EXHIBITS INTERCHANGING ALPHA AND BETA CONFORMATIONS IN SOLUTION

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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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: RESERVOIR: 0.1 M TRIS, PH 8.5, 24% PEG3350. DROP: RESERVOIR MIXED 4:1 WITH 30% ETHYLENE GLYCOL. THIS WAS MIXED 1:1 WITH VP1 (11 MG/ML), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 29, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 68387 / % possible obs: 89.8 % / Redundancy: 8.7 % / Biso Wilson estimate: 33.9 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.2
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4050 / % possible all: 53.8

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Processing

Software
NameVersionClassification
REFMAC5.4.0013refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SVA

1sva


Resolution: 2.25→29.76 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.883 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: some of the residues from Gly30 to Asp42 were disordered in several chains and were not modeled. The side chain of Asp42 of chain E was modeled as Ala due to missing density.
RfactorNum. reflection% reflectionSelection details
Rfree0.23318 6868 10 %RANDOM
Rwork0.18743 ---
obs0.19206 68387 89.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.589 Å2
Baniso -1Baniso -2Baniso -3
1--2.26 Å20 Å2-2.6 Å2
2--2.29 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10160 0 228 855 11243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02210681
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8141.98414567
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.51451331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47425.879461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.741151741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6411530
X-RAY DIFFRACTIONr_chiral_restr0.0030.021692
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028005
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.2610
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21388
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2219
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.320.26
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.082106598
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3141510739
X-RAY DIFFRACTIONr_scbond_it2.728104081
X-RAY DIFFRACTIONr_scangle_it4.006153815
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 290 -
Rwork0.242 2580 -
obs-4050 51.8 %

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