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- PDB-4ph2: mature N-terminal domain of capsid protein from bovine leukemia virus -

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Basic information

Entry
Database: PDB / ID: 4ph2
Titlemature N-terminal domain of capsid protein from bovine leukemia virus
ComponentsBLV capsid - N-terminal domain
KeywordsVIRAL PROTEIN / mature retroviral capsid NTD with 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
Gag-Pro-Pol polyprotein
Similarity search - Component
Biological speciesBovine leukemia virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.44 Å
Model detailsNTD lacking the N-term beta-hairpin
AuthorsTrajtenberg, F. / Obal, G. / Pritsch, O. / Buschiazzo, A.
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: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BLV capsid - N-terminal domain
B: BLV capsid - N-terminal domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4786
Polymers30,1022
Non-polymers3764
Water6,377354
1
A: BLV capsid - N-terminal domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3314
Polymers15,0511
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BLV capsid - N-terminal domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1472
Polymers15,0511
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.670, 56.040, 103.070
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 - N-terminal domain


Mass: 15050.766 Da / Num. of mol.: 2 / Fragment: N-terminal domain NTD (UNP Residues 110-237)
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 1.95 Å3/Da / Density % sol: 36.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.2M AmAc, 1M 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: Nov 14, 2012
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: 1.44→51.53 Å / Num. obs: 40094 / % possible obs: 92.2 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 7.9 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.065 / Χ2: 0.97 / Net I/σ(I): 16.31 / Num. measured all: 174086
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.44-1.544.30.9710.2256.8230541778771380.25591.7
1.54-1.80.990.13710.345419813124123550.15594.1
1.8-20.9950.08814.3925100600357030.195
2-30.9980.04424.144455911475101880.05188.8
3-50.9990.03131.9915342391236180.03692.5
5-6.50.9990.02931.6424686085980.03498.4
6.5-80.9990.03330.079502492380.03895.6
8-150.9990.03130.847922522160.03785.7
150.9990.02824.4813655400.03372.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4PH3

4ph3


Resolution: 1.44→27.74 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1858 1255 3.13 %
Rwork0.1633 38828 -
obs0.164 40083 92.22 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.91 Å2 / Biso mean: 13.0242 Å2 / Biso min: 3.11 Å2
Refinement stepCycle: final / Resolution: 1.44→27.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 22 359 2369
Biso mean--35.64 22.34 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062127
X-RAY DIFFRACTIONf_angle_d1.0522912
X-RAY DIFFRACTIONf_chiral_restr0.042320
X-RAY DIFFRACTIONf_plane_restr0.006391
X-RAY DIFFRACTIONf_dihedral_angle_d14.265804
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.44-1.49770.22891240.18794185430991
1.4977-1.56580.1981360.1624296443293
1.5658-1.64840.19421420.15614300444293
1.6484-1.75160.18341400.15944387452795
1.7516-1.88680.17771360.15914395453195
1.8868-2.07660.21011560.17294452460895
2.0766-2.3770.1661130.14763590370376
2.377-2.99420.19431420.16074652479498
2.9942-27.74520.16931660.16724571473793
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)
10.5697-0.05170.08350.4136-0.07740.33010.00460.0134-0.0073-0.01980.0071-0.0059-0.00140.0120.00050.0403-0.00370.00190.039-0.0020.03210.45827.383439.4538
20.69750.15660.03610.4630.06210.3273-0.00410.00960.03270.0113-0.00090.0454-0.0045-0.0107-0.00010.03970.0034-0.00210.03850.00070.03249.797525.529363.2794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 127
2X-RAY DIFFRACTION2chain BB1 - 127

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