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- PDB-4ph3: N-terminal domain of the capsid protein from bovine leukaemia vir... -

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Basic information

Entry
Database: PDB / ID: 4ph3
TitleN-terminal domain of the capsid protein from bovine leukaemia virus (with no beta-hairpin)
ComponentsBLV capsid
KeywordsVIRAL PROTEIN / retroviral capsid NTD with no beta-hairpin / 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 / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / gag protein p24 N-terminal domain / Integrase DNA binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / RNase H / Integrase core domain ...Delta-retroviral matrix protein / Major core protein p19 / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / 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
IODIDE ION / Gag-Pro-Pol polyprotein
Similarity search - Component
Biological speciesBovine leukemia virus
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.44 Å
Model detailsNTD lacking the N-term beta-hairpin
AuthorsTrajtenberg, F. / Obal, G. / Pritsch, O. / Buschiazzo, A.
Funding support France, Uruguay, 4items
OrganizationGrant numberCountry
Centre national de la recherche scientifiqueLaboratoire International Associe LIA 316 France
Mercosur/FOCEMCOF 03/11Uruguay
Mercosur Structural Biology Center CeBEMUruguay
Agencia Nacional de Investigacion e Innovacion (ANII)Uruguay
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_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_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.4May 15, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 15, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,01252
Polymers28,7022
Non-polymers6,31050
Water1,47782
1
A: BLV capsid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,37733
Polymers14,3511
Non-polymers4,02632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BLV capsid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,63519
Polymers14,3511
Non-polymers2,28418
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.613, 66.242, 81.355
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BLV capsid


Mass: 14351.041 Da / Num. of mol.: 2 / Fragment: N-terminal domain NTD (UNP Residues 109-237)
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: L0PI28
#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 49 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.08 Å3/Da / Density % sol: 60.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 100 mM MES pH 5.0, 1.6 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 12, 2011
RadiationMonochromator: multilayer mirrors Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.439→81.355 Å / Num. obs: 13762 / % possible obs: 100 % / Redundancy: 14.2 % / Biso Wilson estimate: 49.51 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 39.7
Reflection shellResolution: 2.439→2.447 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 11.1 / % possible all: 98.4

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Processing

Software
NameVersionClassification
XDSdata scaling
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.14data extraction
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.44→51.37 Å / Cor.coef. Fo:Fc: 0.9025 / Cor.coef. Fo:Fc free: 0.8658 / SU R Cruickshank DPI: 0.285 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.293 / SU Rfree Blow DPI: 0.224 / SU Rfree Cruickshank DPI: 0.223
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 1037 7.57 %RANDOM
Rwork0.2063 ---
obs0.2092 13703 99.99 %-
Displacement parametersBiso max: 155.25 Å2 / Biso mean: 43.3 Å2 / Biso min: 16.6 Å2
Baniso -1Baniso -2Baniso -3
1-12.4979 Å20 Å20 Å2
2--4.6204 Å20 Å2
3----17.1183 Å2
Refine analyzeLuzzati coordinate error obs: 0.318 Å
Refinement stepCycle: final / Resolution: 2.44→51.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1783 0 60 82 1925
Biso mean--66.17 42.76 -
Num. residues----230
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d631SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes64HARMONIC2
X-RAY DIFFRACTIONt_gen_planes260HARMONIC5
X-RAY DIFFRACTIONt_it1856HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion251SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2280SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1856HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2540HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion19.18
LS refinement shellResolution: 2.44→2.63 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2733 197 7.14 %
Rwork0.2179 2562 -
all0.2219 2759 -
obs--99.99 %

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