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- PDB-1a8o: HIV CAPSID C-TERMINAL DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1a8o
TitleHIV CAPSID C-TERMINAL DOMAIN
ComponentsHIV CAPSID
KeywordsVIRAL PROTEIN / CAPSID / CORE PROTEIN / HIV / C-TERMINAL DOMAIN
Function / homology
Function and homology information


HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / 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 / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / 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 ...Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / 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. / 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
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MULTI-WAVELENGTH ANOMALOUS DISPERSION / Resolution: 1.7 Å
AuthorsGamble, T.R. / Yoo, S. / Vajdos, F.F. / Von Schwedler, U.K. / Worthylake, D.K. / Wang, H. / Mccutcheon, J.P. / Sundquist, W.I. / Hill, C.P.
CitationJournal: Science / Year: 1997
Title: Structure of the carboxyl-terminal dimerization domain of the HIV-1 capsid protein.
Authors: Gamble, T.R. / Yoo, S. / Vajdos, F.F. / von Schwedler, U.K. / Worthylake, D.K. / Wang, H. / McCutcheon, J.P. / Sundquist, W.I. / Hill, C.P.
History
DepositionMar 27, 1998Processing site: BNL
SupersessionOct 14, 1998ID: 1AM3
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV CAPSID


Theoretical massNumber of molelcules
Total (without water)8,1761
Polymers8,1761
Non-polymers00
Water1,58588
1
A: HIV CAPSID

A: HIV CAPSID


Theoretical massNumber of molelcules
Total (without water)16,3512
Polymers16,3512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)41.980, 41.980, 88.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein HIV CAPSID


Mass: 8175.718 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 151 - 231
Mutation: SELENOMETHIONINE SUBSTITUTIONS, L151MSE, M185MSE, M214MSE, M215MSE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Cell line: BL21 / Plasmid: WISP97-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P12497
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.21 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: CRYSTALS OF CA(151-231) WERE GROWN AT 4C IN 4 MICROLITER SITTING DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN SOLUTION (2.1 MM CA(151-231) IN 10MM TRIS (PH 8.0) AND 2 MM 2-MERCAPTOETHANOL) AND ...Details: CRYSTALS OF CA(151-231) WERE GROWN AT 4C IN 4 MICROLITER SITTING DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN SOLUTION (2.1 MM CA(151-231) IN 10MM TRIS (PH 8.0) AND 2 MM 2-MERCAPTOETHANOL) AND RESERVOIR SOLUTION (2.0 M AMMONIUM SULFATE), vapor diffusion - sitting drop, temperature 277K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.1 mMprotein1drop
210 mMTris1drop
32 mM2-mercaptoethanol1drop
420 %PEG80001reservoir
50.1 Msodium cacodylate1reservoir
60.2 Mcalcium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.24
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 9307 / % possible obs: 99.6 % / Observed criterion σ(I): -2 / Biso Wilson estimate: 21.1 Å2 / Rsym value: 0.036 / Net I/σ(I): 15
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 5 / Rsym value: 0.232 / % possible all: 98.6
Reflection
*PLUS
Redundancy: 4.7 % / Rmerge(I) obs: 0.048

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843model building
X-PLOR3.843refinement
X-PLOR3.843phasing
RefinementMethod to determine structure: MULTI-WAVELENGTH ANOMALOUS DISPERSION
Resolution: 1.7→25 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): -2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.253 969 10.5 %RANDOM
Rwork0.215 ---
obs0.215 9254 99.5 %-
Displacement parametersBiso mean: 22.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å20 Å20 Å2
2--1.85 Å20 Å2
3----3.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms556 0 0 88 644
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.01
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.311.5
X-RAY DIFFRACTIONx_mcangle_it2.122
X-RAY DIFFRACTIONx_scbond_it2.412
X-RAY DIFFRACTIONx_scangle_it3.922.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 153 10.4 %
Rwork0.276 1320 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TIP3P.PARAMETERTIP3P.TOPOLOGY
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.01

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