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- PDB-1hiw: TRIMERIC HIV-1 MATRIX PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1hiw
TitleTRIMERIC HIV-1 MATRIX PROTEIN
ComponentsHIV-1 MATRIX PROTEIN
KeywordsMATRIX PROTEIN / HIV-1 / P17 / HIV-1 MA
Function / homology
Function and homology information


viral budding via host ESCRT complex / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / ISG15 antiviral mechanism / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase ...viral budding via host ESCRT complex / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / ISG15 antiviral mechanism / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / viral penetration into host nucleus / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Immunodeficiency lentiviruses, gag gene matrix protein p17 / Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...Immunodeficiency lentiviruses, gag gene matrix protein p17 / Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / 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 / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / DNA polymerase; domain 1 / 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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 polyprotein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.3 Å
AuthorsHill, C.P. / Worthylake, D. / Bancroft, D.P. / Christensen, A.M. / Sundquist, W.I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Crystal structures of the trimeric human immunodeficiency virus type 1 matrix protein: implications for membrane association and assembly.
Authors: Hill, C.P. / Worthylake, D. / Bancroft, D.P. / Christensen, A.M. / Sundquist, W.I.
History
DepositionFeb 28, 1996Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

Downloads & links

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Assembly

Deposited unit
A: HIV-1 MATRIX PROTEIN
B: HIV-1 MATRIX PROTEIN
C: HIV-1 MATRIX PROTEIN
Q: HIV-1 MATRIX PROTEIN
R: HIV-1 MATRIX PROTEIN
S: HIV-1 MATRIX PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,79214
Polymers90,0246
Non-polymers7698
Water1,26170
1
A: HIV-1 MATRIX PROTEIN
B: HIV-1 MATRIX PROTEIN
C: HIV-1 MATRIX PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3006
Polymers45,0123
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Q: HIV-1 MATRIX PROTEIN
R: HIV-1 MATRIX PROTEIN
S: HIV-1 MATRIX PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4928
Polymers45,0123
Non-polymers4805
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.423, 91.163, 73.997
Angle α, β, γ (deg.)90.00, 102.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HIV-1 MATRIX PROTEIN / HIV-1 MA / P17 / MATRIX PROTEIN


Mass: 15003.958 Da / Num. of mol.: 6
Fragment: CORE PROTEIN P17, RESIDUES 1 - 131 OF GAG POLYPROTEIN WITH N-TERMINAL HIS AND MET
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN HAS AN N-TERMINAL HISTIDINE AND THE INITIATOR METHIONINE. THE PROTEIN IS NOT MYRISTOYLATED.
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: NL4-3 / Description: T7 PROMOTER / Plasmid: WISP93-93 / Production host: Escherichia coli (E. coli) / References: UniProt: P12493, UniProt: P12497*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
111 mg/mlprotein1drop
210 mMTris-HCl1drop
31 mMEGTA1drop
45 mM2-mercaptoethanol1drop
630 %(w/w)PEG20001reservoir
70.1 Mammonium sulfate1reservoir
80.1 M1reservoirNa(CH3CO2)
5reservoir solution1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 36171 / % possible obs: 98.4 % / Observed criterion σ(I): -2 / Redundancy: 3 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 7.7
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.195 / % possible all: 81.6
Reflection
*PLUS
Num. measured all: 104117

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.332 1770 5 %
Rwork0.259 --
obs0.259 35264 97.4 %
Displacement parametersBiso mean: 27.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5244 0 40 70 5354
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.67
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.4 Å
RfactorNum. reflection% reflection
Rfree0.393 199 5 %
Rwork0.355 3508 -
obs--82.3 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHSCDX.PRO
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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