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- PDB-2m8n: HIV-1 capsid monomer structure -

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Basic information

Entry
Database: PDB / ID: 2m8n
TitleHIV-1 capsid monomer structure
ComponentsCapsid protein p24
KeywordsVIRAL PROTEIN / capsid / HIV / monomer
Function / homology
Function and homology information


HIV-1 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-1 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 / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus type 1
MethodSOLUTION NMR / SOLUTION SCATTERING / simulated annealing
Model detailslowest energy, model1
AuthorsDeshmukh, L. / Schwieters, C.D. / Grishaev, A. / Clore, G. / Ghirlando, R.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Structure and Dynamics of Full-Length HIV-1 Capsid Protein in Solution.
Authors: Deshmukh, L. / Schwieters, C.D. / Grishaev, A. / Ghirlando, R. / Baber, J.L. / Clore, G.M.
History
DepositionMay 24, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Apr 27, 2016Group: Database references / Structure summary
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl / pdbx_nmr_software / pdbx_soln_scatter / Item: _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)25,6301
Polymers25,6301
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)100 / 480structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Capsid protein p24 / IN


Mass: 25630.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Gene: gag-pol / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P12497

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Experimental details

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Experiment

Experiment
MethodDetails
SOLUTION NMRHIV capsid monomer structure. This is equilibrium with a dimer (deposited separately) at NMR conditions.
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aliphatic
1412D 1H-13C HSQC aromatic
1513D HNCO
1613D HN(CA)CB
1713D HNCA
1813D HN(CO)CA
1913D 1H-15N NOESY
11012D TROSY-Artsy
11112D 1H-15N R1
11212D 1H-15N R1
11312D 1H-15N R1r
11412D 1H-15N R1r
11512D 1H-15N HetNOE
11612D 1H-15N HetNOE

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N; U-2H] entity, 1 mM EDTA, 50 mM sodium chloride, 1 mM DTT, 20 mM sodium phosphate, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity-1[U-13C; U-15N; U-2H]1
1 mMEDTA-21
50 mMsodium chloride-31
1 mMDTT-41
20 mMsodium phosphate-51
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 308 K

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Data collection

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE5002
Soln scatterType: x-ray / Conc. range: 3.25 - 6.5 / Detector type: PILATUS 2M / Sample pH: 6.5 / Source beamline: 12-ID-B / Source class: synchrotron / Source type: APS / Temperature: 298 K

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.32Schwieters, Kuszewski, Tjandra and Clorerefinement
TopSpin1.3Bruker Biospincollection
CCPN-Analysis2.2.2(CCPN-Analysis)-Vranken, Boucher, Stevens..Laue.data analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: This is an ensemble refinement. The MODEL entries appear in groups of 5, representing 20 ensembles. Ensemble 1: MODEL 1, weight: 0.255 MODEL 2, weight: 0.230 MODEL 3, weight: 0.204 MODEL 4, ...Details: This is an ensemble refinement. The MODEL entries appear in groups of 5, representing 20 ensembles. Ensemble 1: MODEL 1, weight: 0.255 MODEL 2, weight: 0.230 MODEL 3, weight: 0.204 MODEL 4, weight: 0.176 MODEL 5, weight: 0.135 Ensemble 2: MODEL 6, weight: 0.120 MODEL 7, weight: 0.142 MODEL 8, weight: 0.173 MODEL 9, weight: 0.221 MODEL 10, weight: 0.344 Ensemble 3: MODEL 11, weight: 0.194 MODEL 12, weight: 0.197 MODEL 13, weight: 0.199 MODEL 14, weight: 0.202 MODEL 15, weight: 0.208 Ensemble 4: MODEL 16, weight: 0.104 MODEL 17, weight: 0.128 MODEL 18, weight: 0.164 MODEL 19, weight: 0.221 MODEL 20, weight: 0.383 Ensemble 5: MODEL 21, weight: 0.126 MODEL 22, weight: 0.147 MODEL 23, weight: 0.176 MODEL 24, weight: 0.220 MODEL 25, weight: 0.331 Ensemble 6: MODEL 26, weight: 0.133 MODEL 27, weight: 0.153 MODEL 28, weight: 0.179 MODEL 29, weight: 0.219 MODEL 30, weight: 0.316 Ensemble 7: MODEL 31, weight: 0.167 MODEL 32, weight: 0.178 MODEL 33, weight: 0.192 MODEL 34, weight: 0.212 MODEL 35, weight: 0.252 Ensemble 8: MODEL 36, weight: 0.073 MODEL 37, weight: 0.100 MODEL 38, weight: 0.141 MODEL 39, weight: 0.216 MODEL 40, weight: 0.470 Ensemble 9: MODEL 41, weight: 0.056 MODEL 42, weight: 0.082 MODEL 43, weight: 0.125 MODEL 44, weight: 0.209 MODEL 45, weight: 0.528 Ensemble 10: MODEL 46, weight: 0.067 MODEL 47, weight: 0.093 MODEL 48, weight: 0.135 MODEL 49, weight: 0.214 MODEL 50, weight: 0.491 Ensemble 11: MODEL 51, weight: 0.222 MODEL 52, weight: 0.213 MODEL 53, weight: 0.203 MODEL 54, weight: 0.191 MODEL 55, weight: 0.171 Ensemble 12: MODEL 56, weight: 0.153 MODEL 57, weight: 0.168 MODEL 58, weight: 0.188 MODEL 59, weight: 0.215 MODEL 60, weight: 0.275 Ensemble 13: MODEL 61, weight: 0.236 MODEL 62, weight: 0.221 MODEL 63, weight: 0.204 MODEL 64, weight: 0.185 MODEL 65, weight: 0.155 Ensemble 14: MODEL 66, weight: 0.249 MODEL 67, weight: 0.227 MODEL 68, weight: 0.204 MODEL 69, weight: 0.178 MODEL 70, weight: 0.141 Ensemble 15: MODEL 71, weight: 0.517 MODEL 72, weight: 0.279 MODEL 73, weight: 0.136 MODEL 74, weight: 0.056 MODEL 75, weight: 0.013 Ensemble 16: MODEL 76, weight: 0.224 MODEL 77, weight: 0.214 MODEL 78, weight: 0.203 MODEL 79, weight: 0.190 MODEL 80, weight: 0.169 Ensemble 17: MODEL 81, weight: 0.323 MODEL 82, weight: 0.257 MODEL 83, weight: 0.198 MODEL 84, weight: 0.142 MODEL 85, weight: 0.080 Ensemble 18: MODEL 86, weight: 0.134 MODEL 87, weight: 0.154 MODEL 88, weight: 0.180 MODEL 89, weight: 0.219 MODEL 90, weight: 0.313 Ensemble 19: MODEL 91, weight: 0.184 MODEL 92, weight: 0.190 MODEL 93, weight: 0.197 MODEL 94, weight: 0.206 MODEL 95, weight: 0.224 Ensemble 20: MODEL 96, weight: 0.175 MODEL 97, weight: 0.184 MODEL 98, weight: 0.195 MODEL 99, weight: 0.209 MODEL 100, weight: 0.238
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 480 / Conformers submitted total number: 100

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