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- PDB-2di2: NMR structure of the HIV-2 nucleocapsid protein -

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Basic information

Entry
Database: PDB / ID: 2di2
TitleNMR structure of the HIV-2 nucleocapsid protein
ComponentsNucleocapsid protein p7
KeywordsMETAL BINDING PROTEIN / NUCLEOCAPSID PROTEIN / HIV-2 / RNA RECOGNITION / ZINC FINGER / MUTANT
Function / homology
Function and homology information


viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / membrane
Similarity search - Function
gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger ...gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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.
Similarity search - Domain/homology
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsMatsui, T. / Kodera, Y. / Endoh, H. / Miyauchi, E. / Komatsu, H. / Sato, K. / Tanaka, T. / Kohno, T. / Maeda, T.
CitationJournal: J.Biochem.(Tokyo) / Year: 2007
Title: RNA Recognition Mechanism of the Minimal Active Domain of the Human Immunodeficiency Virus Type-2 Nucleocapsid Protein
Authors: Matsui, T. / Kodera, Y. / Endoh, H. / Miyauchi, E. / Komatsu, H. / Sato, K. / Tanaka, T. / Kohno, T. / Maeda, T.
History
DepositionMar 27, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 11, 2019Group: Advisory / Derived calculations / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_struct_assembly ...pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...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
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleocapsid protein p7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4122
Polymers3,3471
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area100 Å2
ΔGint-39 kcal/mol
Surface area3150 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)13 / 100structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Nucleocapsid protein p7 / HIV-2 NUCLEOCAPSID PROTEIN


Mass: 3346.899 Da / Num. of mol.: 1 / Fragment: Residus 1-29 / Mutation: N11A / Source method: obtained synthetically / Details: This peptide has been chemically synthesized / Source: (synth.) synthetic construct (others) / References: UniProt: P18041
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY

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Sample preparation

DetailsContents: 5mM Protein; 5.5mM ZnCl2; 95% H2O, 5% D2O / Solvent system: 95% H2O/5% D2O
Sample conditionspH: 5.8 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR-NIH2.9.9Schwieters C.D.structure solution
X-PLOR-NIH2.9.9Schwieters C.D.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 13

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