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- PDB-6y5x: Structure of apo New Jersey Polyomavirus VP1 -

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Basic information

Entry
Database: PDB / ID: 6y5x
TitleStructure of apo New Jersey Polyomavirus VP1
ComponentsVP1
KeywordsVIRAL PROTEIN / Major Capsid Protein / Polyomavirus
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / metal ion 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
Biological speciesNew Jersey polyomavirus-2013
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsStroh, L.J. / Rustmeier, N.H. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2327 Germany
CitationJournal: Mbio / Year: 2020
Title: Structural Basis and Evolution of Glycan Receptor Specificities within the Polyomavirus Family.
Authors: Stroh, L.J. / Rustmeier, N.H. / Blaum, B.S. / Botsch, J. / Rossler, P. / Wedekink, F. / Lipkin, W.I. / Mishra, N. / Stehle, T.
History
DepositionFeb 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 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: VP1
B: VP1
C: VP1
D: VP1
E: VP1
F: VP1
G: VP1
H: VP1
I: VP1
J: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,57945
Polymers340,96610
Non-polymers2,61335
Water17,078948
1
A: VP1
B: VP1
C: VP1
D: VP1
E: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,89424
Polymers170,4835
Non-polymers1,41119
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26290 Å2
ΔGint-184 kcal/mol
Surface area48610 Å2
MethodPISA
2
F: VP1
G: VP1
H: VP1
I: VP1
J: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,68521
Polymers170,4835
Non-polymers1,20216
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25340 Å2
ΔGint-173 kcal/mol
Surface area49150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.480, 151.760, 130.910
Angle α, β, γ (deg.)90.00, 106.85, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
VP1


Mass: 34096.566 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) New Jersey polyomavirus-2013 / Gene: VP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta 2 / References: UniProt: A0A024B5J2
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 948 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Succinic acid, PEG 3350

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Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2014
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.3→48.31 Å / Num. obs: 143717 / % possible obs: 99.93 % / Redundancy: 5.78 % / Biso Wilson estimate: 24.66 Å2 / CC1/2: 0.983 / Rrim(I) all: 0.254 / Net I/σ(I): 6.66
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.58 / Num. unique obs: 14225 / CC1/2: 0.645 / Rrim(I) all: 1.027 / % possible all: 99.96

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FMG

4fmg


Resolution: 2.3→48.309 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.26
RfactorNum. reflection% reflectionSelection details
Rfree0.2432 7152 5 %Random selection
Rwork0.2016 ---
obs0.2037 143007 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→48.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21138 0 165 948 22251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221756
X-RAY DIFFRACTIONf_angle_d0.52829537
X-RAY DIFFRACTIONf_dihedral_angle_d3.90913613
X-RAY DIFFRACTIONf_chiral_restr0.0433223
X-RAY DIFFRACTIONf_plane_restr0.0043888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.32492370.28884498X-RAY DIFFRACTION100
2.3261-2.35340.3382370.27994496X-RAY DIFFRACTION100
2.3534-2.38210.3532370.28154515X-RAY DIFFRACTION100
2.3821-2.41230.30722380.27434519X-RAY DIFFRACTION100
2.4123-2.4440.34082390.26444524X-RAY DIFFRACTION100
2.444-2.47750.30052370.264514X-RAY DIFFRACTION100
2.4775-2.51290.32262350.26214469X-RAY DIFFRACTION100
2.5129-2.55040.31042400.25744558X-RAY DIFFRACTION100
2.5504-2.59030.31872380.25434514X-RAY DIFFRACTION100
2.5903-2.63270.28992390.25254538X-RAY DIFFRACTION100
2.6327-2.67810.30182380.24384523X-RAY DIFFRACTION100
2.6781-2.72680.29342370.25274496X-RAY DIFFRACTION100
2.7268-2.77930.28382370.23764516X-RAY DIFFRACTION100
2.7793-2.8360.28352370.22964492X-RAY DIFFRACTION100
2.836-2.89760.30662390.23634542X-RAY DIFFRACTION100
2.8976-2.9650.28532380.23084520X-RAY DIFFRACTION100
2.965-3.03920.30062380.23114516X-RAY DIFFRACTION100
3.0392-3.12130.27222400.22064556X-RAY DIFFRACTION100
3.1213-3.21320.24292370.20574505X-RAY DIFFRACTION100
3.2132-3.31690.26642380.19944536X-RAY DIFFRACTION100
3.3169-3.43540.23862390.19174535X-RAY DIFFRACTION100
3.4354-3.57290.25422370.18654507X-RAY DIFFRACTION100
3.5729-3.73540.22122400.18494547X-RAY DIFFRACTION100
3.7354-3.93230.20782390.16744543X-RAY DIFFRACTION100
3.9323-4.17850.16152390.14984537X-RAY DIFFRACTION100
4.1785-4.50090.15952390.13984547X-RAY DIFFRACTION100
4.5009-4.95350.1742390.1454533X-RAY DIFFRACTION100
4.9535-5.66930.19362400.16194568X-RAY DIFFRACTION100
5.6693-7.1390.20192410.1744572X-RAY DIFFRACTION100
7.139-48.3090.17582430.16874619X-RAY DIFFRACTION100

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