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- PDB-1wje: SOLUTION STRUCTURE OF H12C MUTANT OF THE N-TERMINAL ZN BINDING DO... -

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Database: PDB / ID: 1wje
TitleSOLUTION STRUCTURE OF H12C MUTANT OF THE N-TERMINAL ZN BINDING DOMAIN OF HIV-1 INTEGRASE COMPLEXED TO CADMIUM, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsHIV-1 INTEGRASE
KeywordsZN-BINDING PROTEIN / AIDS / POLYPROTEIN / HYDROLASE / ASPARTYL PROTEASE
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
Integrase, N-terminal zinc-binding 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 / 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. / Arc Repressor Mutant, subunit A / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / simulated annealing
AuthorsCai, M. / Gronenborn, A.M. / Clore, G.M.
CitationJournal: Protein Sci. / Year: 1998
Title: Solution structure of the His12 --> Cys mutant of the N-terminal zinc binding domain of HIV-1 integrase complexed to cadmium.
Authors: Cai, M. / Huang, Y. / Caffrey, M. / Zheng, R. / Craigie, R. / Clore, G.M. / Gronenborn, A.M.
History
DepositionJun 11, 1998Processing site: BNL
Revision 1.0Dec 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: HIV-1 INTEGRASE
B: HIV-1 INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6974
Polymers10,4722
Non-polymers2252
Water00
1
A: HIV-1 INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3482
Polymers5,2361
Non-polymers1121
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 40REGULARIZED MEAN STRUCTURE
Representative

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Components

#1: Protein/peptide HIV-1 INTEGRASE


Mass: 5235.964 Da / Num. of mol.: 2 / Mutation: H12C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Cell line: BL21 / Gene: POTENTIAL / Plasmid: PET-15B / Species (production host): Escherichia coli / Gene (production host): T7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P04587
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 4.5 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX600BrukerDMX6005001
Bruker DMX500BrukerDMX5006002

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Processing

Software
NameClassification
CNSrefinement
CNSphasing
NMR software
NameVersionDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON,WARRENrefinement
CNS MODIFIEDMODIFIEDstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136, USING THE PROGRAM XPLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE COUPLING ...Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136, USING THE PROGRAM XPLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J. MAGN RESON. SERIES B 104, 99-103), CARBON CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92-96) RESTRAINTS AND A CONFORMATIONAL DATABASE POTENTIAL (KUSZEWSKI ET AL. (1996) PROTEIN SCI 5, 1067-1080 AND (1997) J. MAGN. RESON. 125, 171-177). THE 3D STRUCTURE OF THE N-TERMINAL DOMAIN OF THE H12C MUTANT OF HIV-1 INTEGRASE COMPLEXED TO CADMIUM WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON 757 EXPERIMENTAL RESTRAINTS (PER MONOMER): (A) INTRASUBUNIT: 203 SEQUENTIAL (|I-J|=1), 161 MEDIUM RANGE (1 < |I-J| >=5) AND 82 LONG RANGE (|I-J| >5) INTERRESIDUE, AND 5 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; 16 DISTANCE RESTRAINTS FOR 8 HYDROGEN BONDS; 117 TORSION ANGLE (45 PHI, 35 PSI, 26 CHI1, 10 CHI2 AND 1 CHI3) RESTRAINTS; 47 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; 99 (50 CALPHA AND 49 CBETA) 13C SHIFT RESTRAINTS. (B) 20 INTERSUBUNIT INTERPROTON DISTANCE RESTRAINTS. (C) 7 AMBIGUOUS INTERPROTON DISTANCE RESTRAINTS THAT CAN ARISE FROM INTRA AND/OR INTERSUBUNIT INTERACTIONS. THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136, USING THE PROGRAM XPLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J. MAGN RESON. SERIES B 104, 99-103), CARBON CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92-96) RESTRAINTS AND A CONFORMATIONAL DATABASE POTENTIAL (KUSZEWSKI ET AL. (1996) PROTEIN SCI 5, 1067-1080 AND (1997) J. MAGN. RESON. 125, 171-177). THE 3D STRUCTURE OF THE N-TERMINAL DOMAIN OF THE H12C MUTANT OF HIV-1 INTEGRASE COMPLEXED TO CADMIUM WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON 757 EXPERIMENTAL RESTRAINTS (PER MONOMER): (A) INTRASUBUNIT: 203 SEQUENTIAL (|I-J|=1), 161 MEDIUM RANGE (1 < |I-J| >=5) AND 82 LONG RANGE (|I-J| >5) INTERRESIDUE, AND 5 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; 16 DISTANCE RESTRAINTS FOR 8 HYDROGEN BONDS; 117 TORSION ANGLE (45 PHI, 35 PSI, 26 CHI1, 10 CHI2 AND 1 CHI3) RESTRAINTS; 47 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; 99 (50 CALPHA AND 49 CBETA) 13C SHIFT RESTRAINTS. (B) 20 INTERSUBUNIT INTERPROTON DISTANCE RESTRAINTS. (C) 7 AMBIGUOUS INTERPROTON DISTANCE RESTRAINTS THAT CAN ARISE FROM INTRA AND/OR INTERSUBUNIT INTERACTIONS.
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers calculated total number: 40 / Conformers submitted total number: 1

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