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- PDB-4pcg: Structure of Human Polyomavirus 6 (HPyV6) VP1 pentamer -

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Basic information

Entry
Database: PDB / ID: 4pcg
TitleStructure of Human Polyomavirus 6 (HPyV6) VP1 pentamer
ComponentsVP1
KeywordsVIRAL PROTEIN / major viral capsid protein / jelly-roll topology / attachment to host-cell receptors
Function / homology
Function and homology information


viral process / viral capsid / host cell nucleus / structural molecule activity / nucleus
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
THIOCYANATE ION / VP1
Similarity search - Component
Biological speciesPolyomavirus HPyV6
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStroh, L.J. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
Baden-Wuerttemberg-Stiftung Germany
CitationJournal: J.Virol. / Year: 2014
Title: Structure analysis of the major capsid proteins of human polyomaviruses 6 and 7 reveals an obstructed sialic Acid binding site.
Authors: Stroh, L.J. / Neu, U. / Blaum, B.S. / Buch, M.H. / Garcea, R.L. / Stehle, T.
History
DepositionApr 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 27, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / refine_hist / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Mar 27, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)149,38825
Polymers148,4725
Non-polymers91620
Water19,2761070
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23620 Å2
ΔGint-264 kcal/mol
Surface area46530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.900, 89.440, 125.270
Angle α, β, γ (deg.)90.00, 131.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-411-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALPHEPHEAA24 - 469 - 31
21VALVALPHEPHEBB24 - 469 - 31
31VALVALPHEPHECC24 - 469 - 31
41VALVALPHEPHEDD24 - 469 - 31
51VALVALPHEPHEEE24 - 469 - 31
12ARGARGLEULEUAA58 - 7843 - 63
22ARGARGLEULEUBB58 - 7843 - 63
32ARGARGLEULEUCC58 - 7843 - 63
42ARGARGLEULEUDD58 - 7843 - 63
52ARGARGLEULEUEE58 - 7843 - 63
13GLUGLUARGARGAA99 - 12084 - 105
23GLUGLUARGARGBB99 - 12084 - 105
33GLUGLUARGARGCC99 - 12084 - 105
43GLUGLUARGARGDD99 - 12084 - 105
53GLUGLUARGARGEE99 - 12084 - 105
14PROPROILEILEAA125 - 175110 - 160
24PROPROILEILEBB125 - 175110 - 160
34PROPROILEILECC125 - 175110 - 160
44PROPROILEILEDD125 - 175110 - 160
54PROPROILEILEEE125 - 175110 - 160
15GLUGLUGLUGLUAA190 - 200175 - 185
25GLUGLUGLUGLUBB190 - 200175 - 185
35GLUGLUGLUGLUCC190 - 200175 - 185
45GLUGLUGLUGLUDD190 - 200175 - 185
55GLUGLUGLUGLUEE190 - 200175 - 185
16PHEPHELEULEUAA205 - 237190 - 222
26PHEPHELEULEUBB205 - 237190 - 222
36PHEPHELEULEUCC205 - 237190 - 222
46PHEPHELEULEUDD205 - 237190 - 222
56PHEPHELEULEUEE205 - 237190 - 222
17SERSERGLNGLNAA247 - 286232 - 271
27SERSERGLNGLNBB247 - 286232 - 271
37SERSERGLNGLNCC247 - 286232 - 271
47SERSERGLNGLNDD247 - 286232 - 271
57SERSERGLNGLNEE247 - 286232 - 271

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.682603, 0.64505, 0.343458), (-0.645909, 0.312693, 0.696437), (0.34184, -0.697233, 0.630089)1.16661, -1.67599, -1.31439
3given(0.158287, 0.400509, 0.902517), (-0.399093, -0.8101, 0.429492), (0.903144, -0.428172, 0.031612)0.52166, -4.00547, -0.48658
4given(0.161781, -0.393979, 0.904769), (0.399381, -0.812266, -0.425112), (0.902398, 0.430122, 0.025938)-1.24185, -3.55711, 1.32191
5given(0.682478, -0.644383, 0.344956), (0.644838, 0.308642, -0.699231), (0.344105, 0.69965, 0.626164)-1.5269, -1.05961, 1.59904

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Components

#1: Protein
VP1


Mass: 29694.391 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polyomavirus HPyV6 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: D6QWI0
#2: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: CNS
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1070 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris pH 8.5, 200 mM NaSCN, 13.3% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2011
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 140450 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 28.9 Å2 / Net I/σ(I): 14.8
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.8 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PHENIXrefinement
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Human Polyomavirus 7 (HPyV7) VP1 pentamer

Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.219 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17438 7049 5 %RANDOM
Rwork0.14794 ---
obs0.14926 133401 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.642 Å2
Refinement stepCycle: 1 / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10042 0 46 1070 11158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0210464
X-RAY DIFFRACTIONr_bond_other_d0.0010.029717
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.96114301
X-RAY DIFFRACTIONr_angle_other_deg0.757322369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03851386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73823.792443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.382151570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1171569
X-RAY DIFFRACTIONr_chiral_restr0.0830.21614
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112140
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022411
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4595.2035386
X-RAY DIFFRACTIONr_mcbond_other2.3545.1735372
X-RAY DIFFRACTIONr_mcangle_it2.9656.7276717
X-RAY DIFFRACTIONr_mcangle_other2.9666.7296718
X-RAY DIFFRACTIONr_scbond_it4.0676.5715078
X-RAY DIFFRACTIONr_scbond_other3.9676.555065
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2428.1367538
X-RAY DIFFRACTIONr_long_range_B_refined7.71614.72212040
X-RAY DIFFRACTIONr_long_range_B_other7.67613.87211509
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1157medium positional0.060.5
B1157medium positional0.080.5
C1157medium positional0.080.5
D1157medium positional0.060.5
E1157medium positional0.080.5
A1705loose positional0.275
B1705loose positional0.245
C1705loose positional0.355
D1705loose positional0.385
E1705loose positional0.355
A1157medium thermal1.42
B1157medium thermal1.212
C1157medium thermal1.22
D1157medium thermal1.292
E1157medium thermal1.712
A1705loose thermal2.0410
B1705loose thermal1.7510
C1705loose thermal1.7310
D1705loose thermal1.910
E1705loose thermal2.110
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 510 -
Rwork0.245 9490 -
obs--96.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.25140.25541.20381.25630.263.26420.0218-0.34940.11860.2256-0.0056-0.0464-0.1085-0.1563-0.01630.07260.0123-0.00430.0872-0.01830.05359.73923.557748.6147
20.72440.0125-0.12971.35050.45781.35080.02160.03420.0934-0.07130.0210.0126-0.1402-0.0594-0.04270.02290.0216-0.00490.08750.00010.02958.44956.170935.9022
32.7314-0.42031.53481.5417-0.31432.62510.0895-0.3145-0.25520.210.0393-0.03870.248-0.097-0.12880.0873-0.009-0.00530.10120.01290.040218.3452-28.586438.882
40.8519-0.0663-0.05610.9594-0.28891.5730.00520.02730.00480.01710.01070.0789-0.0169-0.0605-0.01590.0146-0.0074-0.01170.0525-0.00270.021613.677-19.133231.9816
53.1986-0.28231.32751.3295-0.43632.28650.12480.0857-0.3535-0.002-0.047-0.18170.24540.2142-0.07790.08890.0358-0.00070.1417-0.01640.079341.9279-24.716211.9828
61.239-0.18660.02711.3384-0.4941.0475-0.02950.0922-0.0931-0.0328-0.01320.01490.09550.00770.04270.03440.0243-0.0010.1188-0.02880.01431.4507-20.679113.3593
72.9155-0.17931.18641.2272-0.22042.1636-0.05710.11810.1050.0408-0.0085-0.2566-0.12170.32730.06560.0597-0.0197-0.00250.18430.06510.085247.179710.17647.8707
81.2916-0.2089-0.24761.18880.03320.79720.0090.13850.0217-0.0948-0.0224-0.0589-0.01020.03940.01340.0489-0.0055-0.00660.1630.04980.020336.91713.17785.6765
91.96170.3471-0.35390.9808-0.1920.99920.05490.00320.3044-0.0178-0.0065-0.0357-0.26610.0534-0.04850.11260.0009-0.00770.09720.01880.118824.594622.392521.8459
103.86381.24571.35911.54160.62882.09190.02580.10130.25380.0014-0.00370.0103-0.23820.1704-0.02210.1030.00950.02530.0670.02190.084623.353621.0726.2753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 108
2X-RAY DIFFRACTION2A109 - 291
3X-RAY DIFFRACTION3B22 - 96
4X-RAY DIFFRACTION4B97 - 291
5X-RAY DIFFRACTION5C22 - 96
6X-RAY DIFFRACTION6C97 - 291
7X-RAY DIFFRACTION7D22 - 106
8X-RAY DIFFRACTION8D107 - 291
9X-RAY DIFFRACTION9E22 - 227
10X-RAY DIFFRACTION10E228 - 291

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