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- PDB-5na2: Crystal structure of the full-length Feline Immunodeficiency Viru... -

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Basic information

Entry
Database: PDB / ID: 5na2
TitleCrystal structure of the full-length Feline Immunodeficiency Virus capsid protein unveils original features
ComponentsCapsid protein (p24)
KeywordsVIRAL PROTEIN / FIV / Capsid / p24 / CA / Feline Immunodeficiency Virus
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / structural constituent of virion / nucleic acid binding / zinc ion binding
Similarity search - Function
Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily ...Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / 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 speciesFeline immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsFolio, C. / Sierra, N. / Dujardin, M. / Alvarez, G. / Guillon, C.
CitationJournal: Viruses / Year: 2017
Title: Crystal Structure of the Full-Length Feline Immunodeficiency Virus Capsid Protein Shows an N-Terminal beta-Hairpin in the Absence of N-Terminal Proline.
Authors: Folio, C. / Sierra, N. / Dujardin, M. / Alvarez, G. / Guillon, C.
History
DepositionFeb 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.page_first ..._citation.journal_id_ISSN / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _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: Capsid protein (p24)
B: Capsid protein (p24)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8258
Polymers47,2722
Non-polymers5536
Water12,214678
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-24 kcal/mol
Surface area22010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.190, 74.580, 77.000
Angle α, β, γ (deg.)90.00, 128.68, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-701-

HOH

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Components

#1: Protein Capsid protein (p24) /


Mass: 23636.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline immunodeficiency virus (isolate Petaluma)
Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P16087
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 678 / 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: 2.85 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium sulfate, 20% PEG 4000, 10% glycerol, 10% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.99187 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 1.9→59.719 Å / Num. obs: 39411 / % possible obs: 91.2 % / Redundancy: 2.38 % / Rsym value: 0.0354 / Net I/σ(I): 16.42
Reflection shellResolution: 1.9→2.01 Å / Mean I/σ(I) obs: 3.33 / Rrim(I) all: 0.0325 / Rsym value: 0.0258 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XGU (N-terminal domain) and 5DCK (C-terminal domain)

2xgu

5dck


Resolution: 1.67→38.499 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 2904 5 %
Rwork0.197 --
obs0.1992 58094 92.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→38.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3274 0 36 699 4009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073391
X-RAY DIFFRACTIONf_angle_d0.8884584
X-RAY DIFFRACTIONf_dihedral_angle_d14.2072121
X-RAY DIFFRACTIONf_chiral_restr0.044508
X-RAY DIFFRACTIONf_plane_restr0.006598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.69740.33471440.3372736X-RAY DIFFRACTION97
1.6974-1.72670.34271420.31832690X-RAY DIFFRACTION96
1.7267-1.75810.29311420.30812700X-RAY DIFFRACTION95
1.7581-1.79190.41711420.34142704X-RAY DIFFRACTION96
1.7919-1.82840.3711370.33072604X-RAY DIFFRACTION93
1.8284-1.86820.34891330.29882551X-RAY DIFFRACTION90
1.8682-1.91170.27631420.24512707X-RAY DIFFRACTION96
1.9117-1.95950.28281410.23142684X-RAY DIFFRACTION95
1.9595-2.01240.26061420.21442681X-RAY DIFFRACTION95
2.0124-2.07170.26631400.20542676X-RAY DIFFRACTION95
2.0717-2.13850.23031400.18892661X-RAY DIFFRACTION94
2.1385-2.21490.2451360.18572583X-RAY DIFFRACTION91
2.2149-2.30360.27041370.19812587X-RAY DIFFRACTION92
2.3036-2.40840.2381390.18882653X-RAY DIFFRACTION93
2.4084-2.53540.22141370.18432599X-RAY DIFFRACTION93
2.5354-2.69420.22811390.19372646X-RAY DIFFRACTION93
2.6942-2.90220.25741350.19292563X-RAY DIFFRACTION90
2.9022-3.19410.22031370.18142591X-RAY DIFFRACTION91
3.1941-3.6560.22121340.17812551X-RAY DIFFRACTION90
3.656-4.60490.20891310.15732491X-RAY DIFFRACTION87
4.6049-38.50940.22261340.2022532X-RAY DIFFRACTION87

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