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

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Basic information

Entry
Database: PDB / ID: 2xxm
TitleCrystal structure of the HIV-1 capsid protein C-terminal domain in complex with a camelid VHH and the CAI peptide.
Components
  • CAMELID VHH 9
  • CAPSID PROTEIN P24
  • INHIBITOR OF CAPSID ASSEMBLY
KeywordsIMMUNE SYSTEM/PEPTIDE / IMMUNE SYSTEM-PEPTIDE COMPLEX / CAPSID INHIBITOR / PROTEIN BINDING / PROTEIN INTERFACE / VIRUS ASSEMBLY
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / telomerase activity / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / viral translational frameshifting / 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 / 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain 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. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS
VICUGNA PACOS (alpaca)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
DepositionNov 10, 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAPSID PROTEIN P24
B: CAMELID VHH 9
T: INHIBITOR OF CAPSID ASSEMBLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1956
Polymers23,0183
Non-polymers1773
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-20 kcal/mol
Surface area9570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.720, 39.510, 35.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-2009-

HOH

21B-2057-

HOH

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Components

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


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


Mass: 13213.812 Da / Num. of mol.: 1
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: Protein/peptide INHIBITOR OF CAPSID ASSEMBLY


Mass: 1348.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.4 % / Description: NONE
Crystal growDetails: 30% PEG4000, 200MM AMMONIUM ACETATE, 100MM SODIUM ACETATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2009 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. obs: 22400 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 19.96 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.1
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 77.8

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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 2XV6

2xv6


Resolution: 1.65→37.89 Å / Cor.coef. Fo:Fc: 0.9453 / Cor.coef. Fo:Fc free: 0.9427 / SU R Cruickshank DPI: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.116 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.1
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 1145 5.15 %RANDOM
Rwork0.1923 ---
obs0.1935 22242 95.52 %-
Displacement parametersBiso mean: 22.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.2493 Å20 Å20 Å2
2---0.5178 Å20 Å2
3---0.767 Å2
Refine analyzeLuzzati coordinate error obs: 0.193 Å
Refinement stepCycle: LAST / Resolution: 1.65→37.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 12 180 1688
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0071546HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.882087HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d540SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes42HARMONIC2
X-RAY DIFFRACTIONt_gen_planes224HARMONIC5
X-RAY DIFFRACTIONt_it1546HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.33
X-RAY DIFFRACTIONt_other_torsion15.8
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion201SEMIHARMONIC5
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_contact1951SEMIHARMONIC4
LS refinement shellResolution: 1.65→1.73 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2115 119 5.09 %
Rwork0.225 2217 -
all0.2244 2336 -
obs--95.52 %

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