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- PDB-4ic9: Crystal structure of the full-length matrix subunit (p15) of the ... -

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Basic information

Entry
Database: PDB / ID: 4ic9
TitleCrystal structure of the full-length matrix subunit (p15) of the Feline Immunodeficiency Virus (FIV) Gag polyprotein
ComponentsMatrix protein p15
KeywordsVIRAL PROTEIN / FIV / p15 / Retroviral matrix protein
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
Immunodeficiency lentiviruses, gag gene matrix protein p17 / : / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / DNA polymerase; domain 1 / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle ...Immunodeficiency lentiviruses, gag gene matrix protein p17 / : / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / DNA polymerase; domain 1 / 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: 2 Å
AuthorsSerriere, J. / Robert, X. / Perez, M. / Gouet, P. / Guillon, C.
CitationJournal: Retrovirology / Year: 2013
Title: Biophysical characterization and crystal structure of the Feline Immunodeficiency Virus p15 matrix protein.
Authors: Serriere, J. / Robert, X. / Perez, M. / Gouet, P. / Guillon, C.
History
DepositionDec 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix protein p15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6075
Polymers16,3591
Non-polymers2484
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.010, 71.200, 28.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Matrix protein p15


Mass: 16358.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline immunodeficiency virus / Strain: Petaluma / Gene: FIV Gag, gag / Plasmid: pRSET-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P16087
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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

Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M sodium acetate, 25% (w/v) polyethylene glycol 3,000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2012
RadiationMonochromator: Kirkpatrick-Baez pair of bi-morph mirrors + channel-cut cryo-cooled silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 7647 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 %
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 4.78 / Num. unique all: 544 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MrBUMPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ECW, SIV matrix protein

1ecw


Resolution: 2→19.31 Å / SU ML: 0.21 / σ(F): 2.01 / Phase error: 24.85 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 383 5.01 %RANDOM
Rwork0.1905 ---
obs0.1937 7646 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→19.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms984 0 16 28 1028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071009
X-RAY DIFFRACTIONf_angle_d1.0051343
X-RAY DIFFRACTIONf_dihedral_angle_d14.124389
X-RAY DIFFRACTIONf_chiral_restr0.067144
X-RAY DIFFRACTIONf_plane_restr0.005176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.28890.24061240.16952357X-RAY DIFFRACTION100
2.2889-2.88220.26641260.21112386X-RAY DIFFRACTION100
2.8822-19.3110.25381330.18742520X-RAY DIFFRACTION100

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