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- PDB-2l6e: NMR Structure of the monomeric mutant C-terminal domain of HIV-1 ... -

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Basic information

Entry
Database: PDB / ID: 2l6e
TitleNMR Structure of the monomeric mutant C-terminal domain of HIV-1 Capsid in complex with stapled peptide Inhibitor
Components
  • Capsid protein p24
  • NYAD-13 stapled peptide inhibitor
KeywordsVIRAL PROTEIN/INHIBITOR / Protein-stapled peptide complex / VIRAL PROTEIN - PEPTIDE INHIBITOR complex / VIRAL PROTEIN-INHIBITOR 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 penetration into host nucleus ...: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral penetration into host nucleus / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Retrovirus capsid C-terminal domain / 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 ...Retrovirus capsid C-terminal domain / 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
[(5S)-5-[[(2S)-6-azaniumyl-2-[[(2S)-6-azaniumyl-2-[2-[[(2S)-2-[[(2S)-2-[[(2S,5S,8S,11S,20S)-20-[[(2S)-2-[[(2S,3R)-2-[[(2S,3S)-2-azanyl-3-methyl-pentanoyl]amino]-3-oxidanyl-butanoyl]amino]-3-phenyl-propanoyl]amino]-2-(2-hydroxy-2-oxoethyl)-11,20-dimethyl-5,8-bis(2-methylpropyl)-3,6,9,21-tetrakis(oxidanylidene)-1,4,7,10-tetrazacyclohenicos-11-yl]carbonylamino]-3-(4-hydroxyphenyl)propanoyl]amino]-3-(4-hydroxyphenyl)propanoyl]amino]ethanoylamino]hexanoyl]amino]hexanoyl]amino]-6-oxidanyl-6-oxidanylidene-hexyl]azanium / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsBhattacharya, S. / Zhang, H. / Debnath, A.K. / Cowburn, D.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Solution structure of a hydrocarbon stapled peptide inhibitor in complex with monomeric C-terminal domain of HIV-1 capsid.
Authors: Bhattacharya, S. / Zhang, H. / Debnath, A.K. / Cowburn, D.
History
DepositionNov 18, 2010Deposition site: BMRB / Processing site: RCSB
SupersessionDec 29, 2010ID: 2K1C
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein p24
B: NYAD-13 stapled peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)13,2342
Polymers13,2342
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Capsid protein p24 /


Mass: 11488.063 Da / Num. of mol.: 1 / Fragment: unp residues 280-363 / Mutation: W80A, M81A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35963
#2: Protein/peptide NYAD-13 stapled peptide inhibitor


Type: Peptide-like / Class: Inhibitor / Mass: 1746.160 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: [(5S)-5-[[(2S)-6-azaniumyl-2-[[(2S)-6-azaniumyl-2-[2-[[(2S)-2-[[(2S)-2-[[(2S,5S,8S,11S,20S)-20-[[(2S)-2-[[(2S,3R)-2-[[(2S,3S)-2-azanyl-3-methyl-pentanoyl]amino]-3-oxidanyl-butanoyl]amino]- ...References: [(5S)-5-[[(2S)-6-azaniumyl-2-[[(2S)-6-azaniumyl-2-[2-[[(2S)-2-[[(2S)-2-[[(2S,5S,8S,11S,20S)-20-[[(2S)-2-[[(2S,3R)-2-[[(2S,3S)-2-azanyl-3-methyl-pentanoyl]amino]-3-oxidanyl-butanoyl]amino]-3-phenyl-propanoyl]amino]-2-(2-hydroxy-2-oxoethyl)-11,20-dimethyl-5,8-bis(2-methylpropyl)-3,6,9,21-tetrakis(oxidanylidene)-1,4,7,10-tetrazacyclohenicos-11-yl]carbonylamino]-3-(4-hydroxyphenyl)propanoyl]amino]-3-(4-hydroxyphenyl)propanoyl]amino]ethanoylamino]hexanoyl]amino]hexanoyl]amino]-6-oxidanyl-6-oxidanylidene-hexyl]azanium
Sequence detailsTHE SIDE CHAINS OF MK8 RESIDUE OF CHAIN B AND NUMBERS 4 AND 8 ARE LINKED BY A DOUBLE BOND AT THE CE ATOMS.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D HN(CO)CA
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D 1H-15N NOESY
1923D 1H-13C NOESY
11012D f1,f2 filtered 1H-1H NOESY
11112D f2 filtered 1H-1H NOESY
11213D H(CCO)NH
11313D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1600 uM [U-100% 13C; U-100% 15N] Capsid protein p24, 900 uM NYAD-13 Peptide Inhibitor, 2 mM DTT, 100 mM ammonium acetate, 90% H2O/10% D2O90% H2O/10% D2O
2600 uM [U-100% 13C; U-100% 15N] Capsid protein p24, 900 uM NYAD-13 Peptide Inhibitor, 2 mM DTT, 100 mM ammonium acetate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMCapsid protein p24-1[U-100% 13C; U-100% 15N]1
900 uMNYAD-13 Peptide Inhibitor-21
2 mMDTT-31
100 mMammonium acetate-41
600 uMCapsid protein p24-5[U-100% 13C; U-100% 15N]2
900 uMNYAD-13 Peptide Inhibitor-62
2 mMDTT-72
100 mMammonium acetate-82
Sample conditionsIonic strength: 100 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
CARA1.5Keller, Wuthrichchemical shift assignment
CARA1.5Keller, Wuthrichpeak picking
TopSpin1.3Bruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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