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- PDB-1qmc: C-terminal DNA-binding domain of HIV-1 integrase, NMR, 42 structures -

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Basic information

Entry
Database: PDB / ID: 1qmc
TitleC-terminal DNA-binding domain of HIV-1 integrase, NMR, 42 structures
ComponentsHIV-1 INTEGRASE
KeywordsTRANSFERASE / INTEGRASE / DNA-BINDING PROTEIN / SRC HOMOLOGY 3 (SH3)-LIKE FOLD / AIDS / POLYPROTEIN
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / RNA-directed DNA polymerase activity / 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 / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Integrase, C-terminal domain superfamily, retroviral / 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, C-terminal domain superfamily, retroviral / 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. / SH3 type barrels. / 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 / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Roll / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS TYPE 1 BH10
MethodSOLUTION NMR / simulated annealing
AuthorsEijkelenboom, A.P.A.M. / Sprangers, R. / Hard, K. / Puras Lutzke, R.A. / Plasterk, R.H.A. / Boelens, R. / Kaptein, R.
Citation
Journal: Proteins: Struct.,Funct., Genet. / Year: 1999
Title: Refined Solution Structure of the C-Terminal DNA-Binding Domain of Human Immunovirus-1 Integrase.
Authors: Eijkelenboom, A.P.A.M. / Sprangers, R. / Hard, K. / Puras Lutzke, R.A. / Plasterk, R.H.A. / Boelens, R. / Kaptein, R.
#1: Journal: Nat.Struct.Biol. / Year: 1995
Title: The DNA-Binding Domain of HIV-1 Integrase Has an SH3-Like Fold
Authors: Eijkelenboom, A.P.A.M. / Puras Lutzke, R.A. / Boelens, R. / Plasterk, R.H.A. / Kaptein, R. / Hard, K.
History
DepositionSep 27, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Remark 700 SHEET THE FIVE-STRANDED SHEET STRUCTURE OF THIS MOLECULE CONTAINS TWO BIFURCATED SHEETS IN THIS ... SHEET THE FIVE-STRANDED SHEET STRUCTURE OF THIS MOLECULE CONTAINS TWO BIFURCATED SHEETS IN THIS STRUCTURE. EACH IS REPRESENTED BY SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS AB AND AC (CHAIN A) REPRESENT THE BIFURCATED CONTRIBUTIONS TO THE MAIN 5-STRANDED SHEET STRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 INTEGRASE
B: HIV-1 INTEGRASE


Theoretical massNumber of molelcules
Total (without water)12,3042
Polymers12,3042
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-7 kcal/mol
Surface area7810 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)42 / 50LOW OVERALL ENERGY
RepresentativeModel #1

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Components

#1: Protein HIV-1 INTEGRASE


Mass: 6152.228 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 BH10
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03366

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: MODEL 1 IS CLOSEST TO THE AVERAGE FOR RESIDUES 220-270. RESIDUE 219 IS DISORDERED.

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Sample preparation

Sample conditionspH: 4.7 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS7501
Bruker AMXBrukerAMX6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLOR3.851structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOW OVERALL ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 42

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