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- PDB-2exf: Solution structure of the HIV-1 nucleocapsid (NCp7(12-55)) comple... -

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Basic information

Entry
Database: PDB / ID: 2exf
TitleSolution structure of the HIV-1 nucleocapsid (NCp7(12-55)) complexed with the DNA (-) Primer Binding Site
Components
  • 5'-D(*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*C)-3'
  • Nucleocapsid protein* (NC*)Capsid
KeywordsViral Protein/DNA / protein-DNA complex / stem-loop / bulge / zinc-finger / Viral Protein-DNA COMPLEX
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / 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 / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / 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 / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / 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 ...Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / 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 / Few Secondary Structures / Irregular / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Gag-Pol polyprotein / Gag-Pol polyprotein
Similarity search - Component
MethodSOLUTION NMR / restrained molecular dynamics restrained simulated annealing energy minimization
AuthorsBourbigot, S. / Bouaziz, S. / Morellet, N.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: How the HIV-1 nucleocapsid protein binds and destabilises the (-)primer binding site during reverse transcription.
Authors: Bourbigot, S. / Ramalanjaona, N. / Boudier, C. / Salgado, G.F. / Roques, B.P. / Mely, Y. / Bouaziz, S. / Morellet, N.
History
DepositionNov 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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 / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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_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

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*C)-3'
A: Nucleocapsid protein* (NC*)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4174
Polymers9,2872
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain 5'-D(*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*C)-3'


Mass: 4263.751 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: the sequence is naturally found in human immunodeficiency virus type 1 (HIV-1)
#2: Protein/peptide Nucleocapsid protein* (NC*) / Capsid


Mass: 5022.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized by solid phase / References: UniProt: P03368, UniProt: P03366*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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
1112D TOCSY
1212D NOESY
1322D TOCSY
1422D NOESY
2512D TOCSY
2612D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM NCp7(12-55), 1mM DP(-)PBS, 90% H2O, 10% D2O90% H2O/10% D2O
21mM NCp7(12-55), 1mM DP(-)PBS, 90% H2O, 10% D2O, 30mM NaCl, 0.2mM MgCl290% H2O, 10% D2O, 30mM NaCl, 0.2mM MgCl2
32mM NCp7(12-55), 1mM DP(-)PBS, 90% H2O, 10% D2O90% H2O/10% D2O
42mM NCp7(12-55), 1mM DP(-)PBS, 90% H2O, 10% D2O, 30mM NaCl, 0.2mM MgCl290% H2O, 10% D2O, 30mM NaCl, 0.2mM MgCl2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11mM protein, 1mM oligonucleotide 6.5 ambient 283 K
21mM protein, 1mM oligonucleotide, 30mM NaCl, 0.2mM MgCl2 6.5 ambient 283 K
31mM protein, 1mM oligonucleotide 6.5 ambient 293 K
41mM protein, 1mM oligonucleotide, 30mM NaCl, 0.2mM MgCl2 6.5 ambient 293 K
51mM protein, 1mM oligonucleotide 6.5 ambient 303 K
61mM protein, 1mM oligonucleotide, 30mM NaCl, 0.2mM MgCl2 6.5 ambient 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3Brukercollection
XwinNMR3Brukerprocessing
Discover2.98Accelrysrefinement
RefinementMethod: restrained molecular dynamics restrained simulated annealing energy minimization
Software ordinal: 1
Details: structures are based on 705 restraints (NOE derived distance constraints)
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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