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- PDB-1e0e: N-terminal zinc-binding HHCC domain of HIV-2 integrase -

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Basic information

Entry
Database: PDB / ID: 1e0e
TitleN-terminal zinc-binding HHCC domain of HIV-2 integrase
ComponentsHUMAN IMMUNODEFICIENCY VIRUS TYPE 2 INTEGRASE
KeywordsINTEGRASE / AIDS / POLYPROTEIN / DIMER / ZINC-BINDING PROTEIN / HELIX-TURN-HELIX MOTIF
Function / homology
Function and homology information


HIV-2 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-2 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 / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Integrase, N-terminal zinc-binding domain / 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, N-terminal zinc-binding domain / 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. / Arc Repressor Mutant, subunit A / 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 TYPE 2
MethodSOLUTION NMR / simulated annealing
AuthorsEijkelenboom, A.P.A.M. / Van Den ent, F.M.I. / Plasterk, R.H.A. / Kaptein, R. / Boelens, R.
Citation
Journal: J.Biomol.NMR / Year: 2000
Title: Refined Solution Structure of the Dimeric N-Terminal Hhcc Domain of HIV-2 Integrase
Authors: Eijkelenboom, A.P.A.M. / Van Den Ent, F.M.I. / Wechselberger, R. / Plasterk, R.H.A. / Kaptein, R. / Boelens, R.
#1: Journal: Curr.Biol. / Year: 1997
Title: Solution Structure of the N-Terminal Hhcc Domain of HIV-2 Integrase: A Three-Helix Bundle Stabilized by Zinc
Authors: Eijkelenboom, A.P.A.M. / Van Den Ent, F.M.I. / Vos, A. / Doreleijers, J.F. / Hard, K. / Tullius, T.D. / Plasterk, R.H.A. / Kaptein, R. / Boelens, R.
History
DepositionMar 25, 2000Deposition site: PDBE / Processing site: PDBE
SupersessionApr 11, 2000ID: 1AUB
Revision 1.0Mar 19, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jun 14, 2017Group: Advisory / Atomic model / Structure summary
Category: atom_site / pdbx_nmr_representative ...atom_site / pdbx_nmr_representative / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.type_symbol / _pdbx_nmr_representative.conformer_id / _pdbx_nmr_representative.selection_criteria
Revision 2.1Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 2.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _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

Downloads & links

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Assembly

Deposited unit
A: HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 INTEGRASE
B: HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6634
Polymers12,5322
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)32 / 50LOW OVERALL ENERGY
RepresentativeModel #1closest to the average

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Components

#1: Protein HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 INTEGRASE


Mass: 6266.040 Da / Num. of mol.: 2 / Fragment: N-TERMINAL HHCC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 (ISOLATE ROD)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04584
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Sequence detailsTER LYS: RESIDUES 47-55 ARE DISORDERED IN CHAIN A AND B, AND NOT INCLUDED IN THE STRUCTURE CALCULATIONS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: DETAILS CAN BE FOUND IN THE JRNL CITATION

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Sample preparation

DetailsContents: D2O AND 5% D2O/95% H2O
Sample conditionspH: 6.5 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Bruker AMXBrukerAMX6002
Varian UNITYPLUSVarianUNITYPLUS7503

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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
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: LOW OVERALL ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 32

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