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- PDB-1b92: MOBILITY OF AN HIV-1 INTEGRASE ACTIVE SITE LOOP IS CORRELATED WIT... -

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Basic information

Entry
Database: PDB / ID: 1b92
TitleMOBILITY OF AN HIV-1 INTEGRASE ACTIVE SITE LOOP IS CORRELATED WITH CATALYTIC ACTIVITY
ComponentsPROTEIN (INTEGRASE)
KeywordsTRANSFERASE / DNA INTEGRATION
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Ribonuclease H-like superfamily/Ribonuclease H / 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 ...Ribonuclease H-like superfamily/Ribonuclease H / 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsGreenwald, J. / Le, V. / Butler, S.L. / Bushman, F.D. / Choe, S.
CitationJournal: Biochemistry / Year: 1999
Title: The mobility of an HIV-1 integrase active site loop is correlated with catalytic activity.
Authors: Greenwald, J. / Le, V. / Butler, S.L. / Bushman, F.D. / Choe, S.
History
DepositionFeb 19, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 19, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Aug 9, 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: PROTEIN (INTEGRASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2974
Polymers17,9271
Non-polymers3703
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (INTEGRASE)
hetero molecules

A: PROTEIN (INTEGRASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5938
Polymers35,8532
Non-polymers7406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4480 Å2
ΔGint-34 kcal/mol
Surface area12940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.260, 72.260, 65.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

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Components

#1: Protein PROTEIN (INTEGRASE) / E.C.2.7.7.49


Mass: 17926.506 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN / Mutation: F185K, G149A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus / Genus: Lentivirus / Strain: 1 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P12497, RNA-directed DNA polymerase
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE CAC RESIDUE IS A MODIFIED CACODYLATE WHERE THE SULFUR OF A CYS RESIDUE HAS REPLACED THE OH OF ...THE CAC RESIDUE IS A MODIFIED CACODYLATE WHERE THE SULFUR OF A CYS RESIDUE HAS REPLACED THE OH OF CACODYLIC ACID.
Sequence detailsPDB SEQUENCE IS SINGLE DOMAIN OF POL_HV1N5 ENTRY. THERE ARE ALSO TWO POINT MUTATIONS OF F185K, G149A

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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: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 %PEG80001reservoir
2100 mMcacodylic acid1reservoir
3200 mMammonium sulfate1reservoir
45 mMdithiothreitol1reservoir
55 mM1reservoirMnCl2
65 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: May 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→24 Å / Num. obs: 13085 / % possible obs: 98.5 % / Redundancy: 4.6 % / Biso Wilson estimate: 29.5 Å2 / Rsym value: 0.032 / Net I/σ(I): 11.9
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.039

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B9D

1b9d


Resolution: 2.02→20 Å / SU B: 4.29 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.289 654 5 %RANDOM
Rwork0.225 ---
obs-12346 98.5 %-
Displacement parametersBiso mean: 39.2 Å2
Refinement stepCycle: LAST / Resolution: 2.02→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 13 100 1205
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0280.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.030.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 39.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0370.04
X-RAY DIFFRACTIONp_planar_d0.05

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