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- PDB-3ds5: HIV-1 capsid C-terminal domain mutant (N183A) -

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Basic information

Entry
Database: PDB / ID: 3ds5
TitleHIV-1 capsid C-terminal domain mutant (N183A)
ComponentsHIV-1 CAPSID PROTEIN
KeywordsVIRAL PROTEIN / HIV / CAPSID / MUTANT / ASSEMBLY / POLYPROTEIN / MAINLY ALPHA
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 / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...viral budding via host ESCRT complex / 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 / host cell cytoplasm / 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 / RNA binding / zinc ion binding / membrane / cytoplasm
Similarity search - Function
Retrovirus capsid C-terminal domain / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain ...Retrovirus capsid C-terminal domain / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / 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
Gag-Pol polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsIgonet, S. / Vaney, M.C. / Rey, F.A.
Citation
Journal: J.Biol.Chem. / Year: 2008
Title: Residues in the HIV-1 Capsid Assembly Inhibitor Binding Site Are Essential for Maintaining the Assembly-competent Quaternary Structure of the Capsid Protein.
Authors: Bartonova, V. / Igonet, S. / Sticht, J. / Glass, B. / Habermann, A. / Vaney, M.C. / Sehr, P. / Lewis, J. / Rey, F.A. / Krausslich, H.G.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2005
Title: The HIV-1 capsid protein C-terminal domain in complex with a virus assembly inhibitor
Authors: Ternois, F. / Sticht, J. / Duquerroy, S. / Krausslich, H.-G. / Rey, F.A.
History
DepositionJul 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 CAPSID PROTEIN
B: HIV-1 CAPSID PROTEIN
C: HIV-1 CAPSID PROTEIN
D: HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)37,9524
Polymers37,9524
Non-polymers00
Water39622
1
C: HIV-1 CAPSID PROTEIN
D: HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,9762
Polymers18,9762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-12 kcal/mol
Surface area7910 Å2
MethodPISA
2
A: HIV-1 CAPSID PROTEIN
B: HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,9762
Polymers18,9762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-12 kcal/mol
Surface area7990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.359, 51.321, 51.358
Angle α, β, γ (deg.)109.20, 109.63, 109.55
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A
13C
23A
33D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 2 / Auth seq-ID: 149 - 221 / Label seq-ID: 4 - 76

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11BB
21AA
12CC
22AA
13C - DC - D
23AA

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
HIV-1 CAPSID PROTEIN


Mass: 9487.895 Da / Num. of mol.: 4 / Fragment: C-terminal domain, UNP residues 278-363 / Mutation: N183A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL4-3 / Gene: gag / Plasmid: pET11c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus-RIL / References: UniProt: Q72497, UniProt: P12497*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 4.6
Details: 30% PEG 4000, 100mM ammonium acetate, 10mM MgCl2, pH 4.6, EVAPORATION, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.044 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 25, 2007 / Details: Dynamically bendable mirror
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.044 Å / Relative weight: 1
ReflectionResolution: 2.4→42 Å / Num. obs: 13571 / % possible obs: 86.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 61.8 Å2 / Rmerge(I) obs: 0.025 / Rsym value: 0.025 / Net I/σ(I): 36.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 5 / Num. unique all: 692 / Rsym value: 0.139 / % possible all: 43.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
RemDAqdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A80

1a80


Resolution: 2.4→41.96 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.104 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.451 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26977 677 5 %RANDOM
Rwork0.22015 ---
obs0.22269 12892 85.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.251 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20.78 Å20.77 Å2
2---0.81 Å2-1.57 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.4→41.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2292 0 0 22 2314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222328
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.9813144
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3395288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75525104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.61815432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8911516
X-RAY DIFFRACTIONr_chiral_restr0.0920.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021728
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.21070
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21630
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8091.51497
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42722348
X-RAY DIFFRACTIONr_scbond_it2.3013940
X-RAY DIFFRACTIONr_scangle_it3.7614.5796
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11B292tight positional0.020.05
21C292tight positional0.020.05
33D292tight positional0.040.05
11B281medium positional0.340.5
21C281medium positional0.110.5
33D281medium positional0.240.5
11B292tight thermal0.080.5
21C292tight thermal0.070.5
33D292tight thermal0.080.5
11B281medium thermal0.452
21C281medium thermal0.422
33D281medium thermal0.462
LS refinement shellResolution: 2.398→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 18 -
Rwork0.294 471 -
obs-471 41.55 %

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