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- PDB-4ph0: capsid protein from bovine leukemia virus -

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Basic information

Entry
Database: PDB / ID: 4ph0
Titlecapsid protein from bovine leukemia virus
ComponentsBLV capsid
KeywordsVIRAL PROTEIN / retroviral capsid / all alpha
Function / homology
Function and homology information


DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / structural molecule activity ...DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / structural molecule activity / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Delta-retroviral matrix protein / Major core protein p19 / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Integrase DNA binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. ...Delta-retroviral matrix protein / Major core protein p19 / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Integrase DNA binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Gag-Pro-Pol polyprotein
Similarity search - Component
Biological speciesBovine leukemia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7497 Å
Model detailsmature form
AuthorsTrajtenberg, F. / Obal, G. / Pritsch, O. / Buschiazzo, A.
Funding support France, Uruguay, 3items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS)Laboratoire International Associe LIA 316 France
Mercosur Structural Biology Center (CeBEM)Uruguay
Mercosur/FOCEMCOF 03/11Uruguay
CitationJournal: Science / Year: 2015
Title: STRUCTURAL VIROLOGY. Conformational plasticity of a native retroviral capsid revealed by x-ray crystallography.
Authors: Obal, G. / Trajtenberg, F. / Carrion, F. / Tome, L. / Larrieux, N. / Zhang, X. / Pritsch, O. / Buschiazzo, A.
History
DepositionMay 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords
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_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BLV capsid
B: BLV capsid
C: BLV capsid
D: BLV capsid
E: BLV capsid
F: BLV capsid


Theoretical massNumber of molelcules
Total (without water)141,6226
Polymers141,6226
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-53 kcal/mol
Surface area60670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.280, 94.280, 257.250
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
BLV capsid


Mass: 23603.625 Da / Num. of mol.: 6 / Fragment: UNP Residues 110-324
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine leukemia virus / Gene: gag-pro-pol / Production host: Escherichia coli (E. coli) / References: UniProt: A7KWZ1

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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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20mM Tris.HCl, 130mM NaCl, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.42
ReflectionResolution: 2.7497→47.14 Å / Num. obs: 33567 / % possible obs: 99.9 % / Redundancy: 10.5 % / Rmerge F obs: 1 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.07 / Χ2: 1.056 / Net I/σ(I): 22.42 / Num. measured all: 351378
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.7497-2.920.8091.0152.0555559540053741.06899.5
2.92-3.120.9230.5873.7253367508450840.617100
3.12-3.360.9790.2897.6550864474847480.303100
3.36-3.680.9940.14415.2345129431743170.152100
3.68-4.120.9970.08925.6741841398839880.093100
4.12-4.750.9980.05741.0836384347134710.06100
4.75-5.80.9990.0547.1131149295729560.052100
5.8-8.140.9990.03757.9823973231023090.039100
8.1410.02677.4913112133713200.02898.7

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Processing

Software
NameVersionClassification
XDSdata scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7497→47.14 Å / FOM work R set: 0.567 / Cross valid method: THROUGHOUT / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2213 1676 5 %
Rwork0.1797 31817 -
obs0.1871 33497 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 220.44 Å2 / Biso mean: 101.97 Å2 / Biso min: 45.83 Å2
Refinement stepCycle: final / Resolution: 2.7497→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9078 0 0 0 9078
Num. residues----1178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099260
X-RAY DIFFRACTIONf_angle_d1.36212633
X-RAY DIFFRACTIONf_chiral_restr0.0571427
X-RAY DIFFRACTIONf_plane_restr0.0061672
X-RAY DIFFRACTIONf_dihedral_angle_d12.4293396
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 95 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7497-2.83060.32221380.321426122750
2.8306-2.9220.2981410.299426682809
2.922-3.02640.3021390.286826452784
3.0264-3.14750.29231410.259726682809
3.1475-3.29070.26081380.254526302768
3.2907-3.46420.27391410.239726672808
3.4642-3.68110.26451370.222426152752
3.6811-3.96520.25771400.200326692809
3.9652-4.3640.25351390.1926462785
4.364-4.99480.18121400.159526672807
4.9948-6.29040.221410.164726672808
6.2904-46.37450.17921410.125126632804
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)
12.1890.39940.25762.45420.24231.8122-0.4185-0.5796-0.42860.42380.4403-0.43190.2248-0.5687-0.10430.82270.07810.0771.05140.2921.052846.578164.1621-12.8365
22.61320.8952-0.21783.02080.42252.288-0.16040.11640.7021-0.11740.41-0.4340.2222-0.2192-0.24330.67530.01720.0110.64310.10670.82677.806860.3815-27.6679
33.78890.79161.4392.0667-1.08782.3103-0.0399-0.4553-0.27410.11730.23370.1647-0.1999-0.41-0.22780.77010.00340.07760.7775-0.04110.300621.4878102.3027-14.294
41.9301-0.4784-0.52631.7521-1.02171.7135-0.1885-0.0558-0.747-0.1432-0.24-0.6846-0.0883-0.04790.1960.801-0.03980.02550.67060.06061.18543.620180.2687-31.2086
52.6664-0.1482-1.75223.9196-1.98082.82770.1307-0.13660.55860.52380.05210.1377-0.55380.5015-0.1120.781-0.01410.01770.8003-0.09220.286944.5341116.2986-10.2066
61.7518-1.00790.06711.9933-0.62623.2467-0.33050.53610.0726-0.13030.36080.689-0.3920.3312-0.14950.7574-0.0973-0.00130.80440.18530.690917.475122.1041-30.9071
72.8791-0.3436-2.60833.4440.27882.32830.2365-0.51960.65940.54180.2217-0.4826-0.01690.5925-0.39070.78010.1257-0.04930.9013-0.17061.101468.4153104.4341-9.8269
81.50750.3431-0.6321.08710.32071.2188-0.20180.20060.29-0.50850.13590.49170.17770.31820.08470.9860.0005-0.01720.75120.23741.22958.7517131.3227-26.9631
91.99360.2740.9671.98481.84763.03630.2753-0.142-0.53590.4649-0.3920.55220.9594-0.33780.13221.2033-0.01890.03530.83330.04671.15323.459675.6699-16.8451
101.58850.1544-0.3663.17190.52532.8478-0.2110.21450.4019-1.008-0.9325-1.5619-0.02030.19720.96761.03680.17350.23250.75370.26631.835835.690347.5926-29.2309
113.9275-0.49130.04691.90652.62823.7665-0.0547-0.3921-0.37180.54250.3601-1.10980.0150.121-0.25890.95440.0309-0.09140.55910.03261.538270.518978.3814-10.9479
127.90951.9413-1.71766.5427-0.31054.38390.54750.3010.7905-0.3047-0.61280.6396-0.05650.35040.18280.62240.0356-0.0090.64450.04450.604287.8639101.3756-26.7303
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 1:122)A1 - 122
2X-RAY DIFFRACTION2(chain A and resseq 137:204)A137 - 204
3X-RAY DIFFRACTION3(chain C and resseq 1:122)C1 - 122
4X-RAY DIFFRACTION4(chain C and resseq 137:204)C137 - 204
5X-RAY DIFFRACTION5(chain D and resseq 1:122)D1 - 122
6X-RAY DIFFRACTION6(chain D and resseq 137:204)D137 - 204
7X-RAY DIFFRACTION7(chain E and resseq 1:122)E1 - 122
8X-RAY DIFFRACTION8(chain E and resseq 137:204)E137 - 204
9X-RAY DIFFRACTION9(chain B and resseq 1:122)B1 - 122
10X-RAY DIFFRACTION10(chain B and resseq 137:204)B137 - 204
11X-RAY DIFFRACTION11(chain F and resseq 1:122)F1 - 122
12X-RAY DIFFRACTION12(chain F and resseq 137:204)F137 - 204

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