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- PDB-4e91: Crystal Structure of the N-Terminal Domain of HIV-1 Capsid in Com... -

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Basic information

Entry
Database: PDB / ID: 4.0E+91
TitleCrystal Structure of the N-Terminal Domain of HIV-1 Capsid in Complex With Inhibitor BD3
ComponentsGag proteinHIV-1 protease
KeywordsSTRUCTURAL PROTEIN/INHIBITOR / Structural protein Capsid / STRUCTURAL PROTEIN / STRUCTURAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


viral budding via host ESCRT complex / : / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase ...viral budding via host ESCRT complex / : / : / 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 / host cell cytoplasm / 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 / identical protein binding / cytoplasm
Similarity search - Function
Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain ...Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / 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. / 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
Chem-0OE / Chem-0OF / IODIDE ION / Gag-Pol polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLemke, C.T.
Citation
Journal: J.Virol. / Year: 2012
Title: Distinct Effects of Two HIV-1 Capsid Assembly Inhibitor Families That Bind the Same Site within the N-Terminal Domain of the Viral CA Protein.
Authors: Lemke, C.T. / Titolo, S. / von Schwedler, U. / Goudreau, N. / Mercier, J.F. / Wardrop, E. / Faucher, A.M. / Coulombe, R. / Banik, S.S. / Fader, L. / Gagnon, A. / Kawai, S.H. / Rancourt, J. / ...Authors: Lemke, C.T. / Titolo, S. / von Schwedler, U. / Goudreau, N. / Mercier, J.F. / Wardrop, E. / Faucher, A.M. / Coulombe, R. / Banik, S.S. / Fader, L. / Gagnon, A. / Kawai, S.H. / Rancourt, J. / Tremblay, M. / Yoakim, C. / Simoneau, B. / Archambault, J. / Sundquist, W.I. / Mason, S.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: A novel inhibitor-binding site on the HIV-1 capsid N-terminal domain leads to improved crystallization via compound-mediated dimerization.
Authors: Lemke, C.T. / Titolo, S. / Goudreau, N. / Faucher, A.M. / Mason, S.W. / Bonneau, P.
History
DepositionMar 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references
Revision 1.2Jun 12, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Gag protein
B: Gag protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4809
Polymers32,4092
Non-polymers2,0717
Water4,954275
1
A: Gag protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7537
Polymers16,2051
Non-polymers1,5486
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Gag protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7282
Polymers16,2051
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.783, 65.783, 143.323
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Gag protein / HIV-1 protease


Mass: 16204.573 Da / Num. of mol.: 2 / Fragment: N-terminal domain, UNP residues 133-278
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: Q79791, UniProt: P12497*PLUS
#2: Chemical ChemComp-0OE / 4-{2-[5-(3-chlorophenyl)-1H-pyrazol-4-yl]-1-[3-(1H-imidazol-1-yl)propyl]-1H-benzimidazol-5-yl}benzoic acid


Mass: 522.985 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H23ClN6O2
#3: Chemical ChemComp-0OF / (3S)-1-ethyl-3-[3-hydroxy-5-(pyridin-3-yl)phenyl]-5-phenyl-7-(trifluoromethyl)-1H-1,5-benzodiazepine-2,4(3H,5H)-dione


Mass: 517.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H22F3N3O3
#4: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.7M Na/K tartrate, 0.1M bis-tris pH7.0, 0.2M NaI, 16% glyerol, VAPOR DIFFUSION, HANGING DROP, temperature 284K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: Osmic HiRes2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→57 Å / Num. all: 40348 / Num. obs: 39464 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 14.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.37 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIX(phenix.refine: 1.7_650)model building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→36.606 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 22.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2432 1979 5.01 %Random
Rwork0.2196 ---
obs0.2208 39464 97.74 %-
all-40348 --
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.77 Å2 / ksol: 0.373 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2311 Å2-0 Å20 Å2
2--0.2311 Å2-0 Å2
3----0.4623 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 118 275 2494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062278
X-RAY DIFFRACTIONf_angle_d1.023106
X-RAY DIFFRACTIONf_dihedral_angle_d18.892862
X-RAY DIFFRACTIONf_chiral_restr0.062329
X-RAY DIFFRACTIONf_plane_restr0.006395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74240.32741280.31922444X-RAY DIFFRACTION90
1.7424-1.78950.3441370.26772518X-RAY DIFFRACTION94
1.7895-1.84210.27471450.23752578X-RAY DIFFRACTION96
1.8421-1.90160.27791440.21542613X-RAY DIFFRACTION97
1.9016-1.96960.22811360.20232634X-RAY DIFFRACTION98
1.9696-2.04840.23061350.20072689X-RAY DIFFRACTION98
2.0484-2.14160.24631260.21012670X-RAY DIFFRACTION99
2.1416-2.25450.23261330.20882711X-RAY DIFFRACTION99
2.2545-2.39580.21531560.21142679X-RAY DIFFRACTION99
2.3958-2.58070.22881280.21362728X-RAY DIFFRACTION99
2.5807-2.84030.23711660.21642723X-RAY DIFFRACTION100
2.8403-3.25110.251650.22762747X-RAY DIFFRACTION100
3.2511-4.09520.21231470.2082803X-RAY DIFFRACTION100
4.0952-36.61490.27141330.2292948X-RAY DIFFRACTION100

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