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- PDB-2xv6: Crystal structure of the HIV-1 capsid protein C-terminal domain (... -

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Basic information

Entry
Database: PDB / ID: 2xv6
TitleCrystal structure of the HIV-1 capsid protein C-terminal domain (146- 220) in complex with a camelid VHH.
Components
  • CAMELID VHH 9
  • CAPSID PROTEIN P24
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM 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 / establishment of integrated proviral latency / viral penetration into host nucleus / 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
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. / 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 / Immunoglobulins / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
VICUGNA PACOS (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsIgonet, S. / Vaney, M.C. / Bartonova, V. / Helma, J. / Rothbauer, U. / Leonhardt, H. / Stura, E. / Krausslich, H.-G. / Rey, F.A.
CitationJournal: To be Published
Title: Targeting HIV-1 Virion Formation with Nanobodies -Implications for the Design of Assembly Inhibitors
Authors: Igonet, S. / Vaney, M.C. / Bartonova, V. / Helma, J. / Rothbauer, U. / Leonhardt, H. / Stura, E. / Krausslich, H.-G. / Rey, F.A.
History
DepositionOct 22, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAPSID PROTEIN P24
B: CAMELID VHH 9
C: CAPSID PROTEIN P24
D: CAMELID VHH 9


Theoretical massNumber of molelcules
Total (without water)43,3394
Polymers43,3394
Non-polymers00
Water5,999333
1
C: CAPSID PROTEIN P24
D: CAMELID VHH 9


Theoretical massNumber of molelcules
Total (without water)21,6692
Polymers21,6692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-8.6 kcal/mol
Surface area9240 Å2
MethodPISA
2
A: CAPSID PROTEIN P24
B: CAMELID VHH 9


Theoretical massNumber of molelcules
Total (without water)21,6692
Polymers21,6692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-7.4 kcal/mol
Surface area9650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.451, 60.118, 96.662
Angle α, β, γ (deg.)90.00, 99.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CAPSID PROTEIN P24 / / HIV-1 CAPSID PROTEIN


Mass: 8455.631 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 278-352
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Strain: NL4-3 / Plasmid: PET11C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIL / References: UniProt: P12497
#2: Antibody CAMELID VHH 9


Mass: 13213.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VICUGNA PACOS (alpaca) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE VHH RESIDUES (CHAIN B AND D) ARE NUMBERED ACCORDING TO THE KABAT NUMBERING. 6XHISTIDINE C- ...THE VHH RESIDUES (CHAIN B AND D) ARE NUMBERED ACCORDING TO THE KABAT NUMBERING. 6XHISTIDINE C-TERMINAL EXPRESSION TAG.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 45.973 % / Description: NONE
Crystal growDetails: 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2008 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.69→47.63 Å / Num. obs: 42152 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 23.83 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15
Reflection shellResolution: 1.69→1.78 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.6 / % possible all: 82.8

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Processing

Software
NameVersionClassification
BUSTER2.9.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XT1

2xt1


Resolution: 1.89→37.34 Å / Cor.coef. Fo:Fc: 0.9467 / Cor.coef. Fo:Fc free: 0.9397 / SU R Cruickshank DPI: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.149 / SU Rfree Blow DPI: 0.123 / SU Rfree Cruickshank DPI: 0.119
Details: THE 6XHISTIDINE TAG AT THE C-TERMINUS IS DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1952 1563 5.07 %RANDOM
Rwork0.1748 ---
obs0.1759 30838 98.36 %-
Displacement parametersBiso mean: 27.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.3611 Å20 Å20.0996 Å2
2---0.0401 Å20 Å2
3----0.321 Å2
Refine analyzeLuzzati coordinate error obs: 0.182 Å
Refinement stepCycle: LAST / Resolution: 1.89→37.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2842 0 0 333 3175
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012916HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.013940HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1038SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes77HARMONIC2
X-RAY DIFFRACTIONt_gen_planes424HARMONIC5
X-RAY DIFFRACTIONt_it2916HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion16.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion381SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3600SEMIHARMONIC4
LS refinement shellResolution: 1.89→1.96 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2284 128 4.82 %
Rwork0.1786 2529 -
all0.1811 2657 -
obs--98.36 %

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