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- PDB-2v4x: Crystal Structure of Jaagsiekte Sheep Retrovirus Capsid N-termina... -

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Basic information

Entry
Database: PDB / ID: 2v4x
TitleCrystal Structure of Jaagsiekte Sheep Retrovirus Capsid N-terminal domain
ComponentsCAPSID PROTEIN P27
KeywordsVIRAL PROTEIN / CAPSID / VIRION / RETROVIRUS / ZINC-FINGER / METAL-BINDING / CAPSID PROTEIN / STRUCTURAL PROTEIN / VIRAL NUCLEOPROTEIN / VIRAL MATRIX PROTEIN
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / structural constituent of virion / nucleic acid binding / viral translational frameshifting / zinc ion binding
Similarity search - Function
Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / : / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain ...Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / : / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesJAAGSIEKTE SHEEP RETROVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsMortuza, G.B. / Goldstone, D.C. / Pashley, C. / Haire, L.F. / Palmarini, M. / Taylor, W.R. / Stoye, J.P. / Taylor, I.A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure of the Capsid Amino-Terminal Domain from the Betaretrovirus, Jaagsiekte Sheep Retrovirus.
Authors: Mortuza, G.B. / Goldstone, D.C. / Pashley, C. / Haire, L.F. / Palmarini, M. / Taylor, W.R. / Stoye, J.P. / Taylor, I.A.
History
DepositionSep 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAPSID PROTEIN P27


Theoretical massNumber of molelcules
Total (without water)16,1201
Polymers16,1201
Non-polymers00
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)29.595, 57.826, 40.927
Angle α, β, γ (deg.)90.00, 109.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CAPSID PROTEIN P27 / JSRV CAPSID


Mass: 16119.737 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 257-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) JAAGSIEKTE SHEEP RETROVIRUS / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31622
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 41 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 0.97695
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97695 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 20920 / % possible obs: 98.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.9
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.9 / % possible all: 90.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.5→14.79 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.639 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1067 5.1 %RANDOM
Rwork0.15 ---
obs0.152 19678 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.96 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20 Å20.98 Å2
2---0.64 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.5→14.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1043 0 0 201 1244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221120
X-RAY DIFFRACTIONr_bond_other_d0.0050.02785
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.9471527
X-RAY DIFFRACTIONr_angle_other_deg0.87131906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6265140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.54224.42661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15615188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.31159
X-RAY DIFFRACTIONr_chiral_restr0.0690.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021270
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02236
X-RAY DIFFRACTIONr_nbd_refined0.2280.2239
X-RAY DIFFRACTIONr_nbd_other0.1820.2784
X-RAY DIFFRACTIONr_nbtor_refined0.1930.2552
X-RAY DIFFRACTIONr_nbtor_other0.0850.2543
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2123
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.791.5718
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.99321084
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0153505
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8374.5438
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 72 -
Rwork0.214 1340 -
obs--92.05 %
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)
16.8685-0.0354-3.13091.83220.92395.3909-0.1106-0.1691-0.3830.1330.1643-0.21780.0850.23-0.05370.00570.00610.00320.0012-0.00950.094639.7321.413-0.881
20.7399-0.3662-1.25012.00921.1112.3545-0.08-0.0648-0.05250.27080.0305-0.01980.13420.06240.04950.02420.0094-0.00880.01390.00660.008525.69931.16410.223
32.25360.8783-2.05111.2944-1.012.59070.05740.05470.113-0.1240.01560.0588-0.0805-0.09-0.0730.0338-0.0072-0.00720.0358-0.01270.02323.59335.555-5.787
41.1387-0.1417-0.511.60460.36861.6727-0.0124-0.0019-0.0217-0.18280.0002-0.044-0.0084-0.03390.01220.0277-0.00460.00750.0130.00430.020428.34131.955-5.774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 14
2X-RAY DIFFRACTION2A15 - 53
3X-RAY DIFFRACTION3A54 - 91
4X-RAY DIFFRACTION4A92 - 131

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