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- PDB-2iwj: SOLUTION STRUCTURE OF THE ZN COMPLEX OF HIV-2 NCP(23-49) PEPTIDE,... -

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Entry
Database: PDB / ID: 2iwj
TitleSOLUTION STRUCTURE OF THE ZN COMPLEX OF HIV-2 NCP(23-49) PEPTIDE, ENCOMPASSING PROTEIN CCHC-LINKER, DISTAL CCHC ZN-BINDING MOTIF AND C- TERMINAL TAIL.
ComponentsGAG-POL POLYPROTEIN
KeywordsTRANSFERASE / DNA-DIRECTED DNA POLYMERASE / RETROVIRUS ZINC FINGER-LIKE DOMAINS / RNA-DIRECTED DNA POLYMERASE / POLYPROTEIN / RNA-BINDING / LIPOPROTEIN / VIRION PROTEIN / DNA INTEGRATION / ASPARTYL PROTEASE / CAPSID MATURATION / DNA RECOMBINATION / NUCLEOTIDYLTRANSFERASE / MULTIFUNCTIONAL ENZYME / ZINC / AIDS / MEMBRANE / PROTEASE / NUCLEASE / MYRISTATE / HYDROLASE / MAGNESIUM / LENTIVIRUS / ZINC-FINGER / VIRAL NUCLEOPROTEIN / NUCLEOCAPSID PROTEIN / CORE PROTEIN / ENDONUCLEASE / METAL-BINDING
Function / homology
Function and homology information


HIV-2 retropepsin / host cell / RNA stem-loop binding / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-2 retropepsin / host cell / RNA stem-loop binding / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / symbiont-mediated suppression of host gene expression / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / 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 / zinc ion binding / membrane
Similarity search - Function
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 ...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. / 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
Similarity search - Domain/homology
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS TYPE 2
MethodSOLUTION NMR / SIMULATED ANNEALING-ENERGY MINIMIZATION
AuthorsAmodeo, P. / Castiglione Morelli, M.A. / Ostuni, A. / Cristinziano, P. / Bavoso, A.
CitationJournal: To be Published
Title: Structural Features of the C-Terminal Zinc Finger Domain of the HIV-2 Nc Protein (Residues 23-49).
Authors: Amodeo, P. / Castiglione Morelli, M.A. / Ostuni, A. / Cristinziano, P. / Bavoso, A.
History
DepositionJun 30, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GAG-POL POLYPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,0862
Polymers3,0211
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 150STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, FAVORABLE ENERGY, THE LEAST RESTRAINT VIOLATIONS
RepresentativeModel #1

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Components

#1: Protein/peptide GAG-POL POLYPROTEIN / NUCLEOCAPSID PROTEIN / PR160GAG-POL


Mass: 3020.586 Da / Num. of mol.: 1 / Fragment: RESIDUES 405-431 OF NCP / Source method: obtained synthetically
Details: FRAGMENT 23-49 OF NCP CORRESPONDS TO 405-431 OF THE WHOLE HIV-2 GAG PROTEIN CONTAINS ONE ZN ION IN A CCHC ZN-BINDING DOMAINS
Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 / References: UniProt: P18042
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Sequence detailsCORRESPONDS TO RESIDUES 405-431 OF THE ENTRY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY DQF-COSY TOCSY

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Sample preparation

DetailsContents: 80% WATER/20% D2O
Sample conditionsIonic strength: 130 mM / pH: 7.0 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
AmberPEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON, SEIBEL,SINGH,WEINER,KOLLMANrefinement
Amberstructure solution
RefinementMethod: SIMULATED ANNEALING-ENERGY MINIMIZATION / Software ordinal: 1
Details: SIMULATED ANNEALING FOLLOWED BY ENERGY MINIMIZATION, BOTH PERFORMED WITH A GBSA IMPLICIT SOLVENT APPROACH
NMR ensembleConformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, FAVORABLE ENERGY, THE LEAST RESTRAINT VIOLATIONS
Conformers calculated total number: 150 / Conformers submitted total number: 30

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