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- PDB-4ica: Crystal structure of a C-terminal truncated form of the matrix su... -

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Basic information

Entry
Database: PDB / ID: 4ica
TitleCrystal structure of a C-terminal truncated form of the matrix subunit (p15) of Feline Immunodeficiency Virus (FIV)
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 / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / DNA polymerase; domain 1 / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily ...Immunodeficiency lentiviruses, gag gene matrix protein p17 / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / DNA polymerase; domain 1 / 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
Chem-7PE / Gag polyprotein
Similarity search - Component
Biological speciesFeline immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix protein p15
B: Matrix protein p15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1874
Polymers29,5662
Non-polymers6212
Water41423
1
A: Matrix protein p15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0932
Polymers14,7831
Non-polymers3101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Matrix protein p15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0932
Polymers14,7831
Non-polymers3101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.480, 71.300, 57.060
Angle α, β, γ (deg.)90.00, 99.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Matrix protein p15


Mass: 14782.980 Da / Num. of mol.: 2
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-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT / Polyethylene glycol


Mass: 310.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 1.93 Å3/Da / Density % sol: 36.33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris-HCl, 25% (W/v) polyethylene glycol 6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2012
RadiationMonochromator: cylindrical grazing incidence mirror + channel-cut cryo-cooled silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 6139 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 %
Reflection shellResolution: 2.7→2.77 Å / Mean I/σ(I) obs: 4.8 / Num. unique all: 448 / % possible all: 97.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MrBUMPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: full-length FIV p15

Resolution: 2.7→19.676 Å / SU ML: 0.4 / σ(F): 2 / Phase error: 29.14 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2787 306 4.99 %RANDOM
Rwork0.2117 ---
obs0.2151 6138 98.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→19.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1806 0 42 23 1871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021868
X-RAY DIFFRACTIONf_angle_d0.4172488
X-RAY DIFFRACTIONf_dihedral_angle_d12.759730
X-RAY DIFFRACTIONf_chiral_restr0.028270
X-RAY DIFFRACTIONf_plane_restr0.002320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-3.39860.30021510.23482893X-RAY DIFFRACTION98
3.3986-19.67630.26941550.20032939X-RAY DIFFRACTION98

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