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- PDB-1e6j: Crystal structure of HIV-1 capsid protein (p24) in complex with F... -

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Basic information

Entry
Database: PDB / ID: 1e6j
TitleCrystal structure of HIV-1 capsid protein (p24) in complex with Fab13B5
Components
  • (IMMUNOGLOBULIN) x 2
  • CAPSID PROTEIN P24
KeywordsVIRAL PROTEIN / HIV CAPSID PROTEIN (P24) / P24 / FAB / HIV-1 / VIRUS ASSEMBLY / CAPSID / CA / ANTIGEN / ANTIBODY / PROTEIN-PROTEIN INTERACTIONS
Function / homology
Function and homology information


host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / viral budding via host ESCRT complex ...host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / viral budding via host ESCRT complex / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / immunoglobulin complex, circulating / immunoglobulin receptor binding / Membrane binding and targetting of GAG proteins / viral process / complement activation, classical pathway / antigen binding / Assembly Of The HIV Virion / Budding and maturation of HIV virion / host multivesicular body / viral capsid / antibacterial humoral response / viral nucleocapsid / blood microparticle / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / extracellular exosome / membrane / metal ion binding
Similarity search - Function
Retroviral nucleocapsid Gag protein p24, N-terminal / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Immunoglobulin V-Type / Immunoglobulin V-set domain ...Retroviral nucleocapsid Gag protein p24, N-terminal / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Immunoglobulin V-set domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Gag protein / Gag polyprotein / Igh protein
Similarity search - Component
Biological speciesHIV-1 M\:B_HXB2R (virus)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBerthet-Colominas, C. / Monaco, S. / Novelli, A. / Sibai, G. / Mallet, F. / Cusack, S.
Citation
Journal: Structure / Year: 2000
Title: Mutual Conformational Adaptations in Antigen and Antibody Upon Complex Formation between an Fab and HIV-1 Capsid Protein P24
Authors: Monaco-Malbet, S. / Berthet-Colominas, C. / Novelli, A. / Battai, N. / Piga, N. / Cheynet, V. / Mallet, F. / Cusack, S.
#1: Journal: Embo J. / Year: 1999
Title: Head-to-Tail Dimers and Interdomain Flexibility Revealed by the Crystal Structure of HIV-1 Capsid Protein (P24) Complexed with a Monoclonal Antibody Fab
Authors: Berthet-Colominas, C. / Monaco, S. / Novelli, A. / Sibai, G. / Mallet, F. / Cusack, S.
#2: Journal: Protein Expr.Purif. / Year: 1993
Title: Overexpression of HIV-1 Proteins in E. Coli by a Modified Expression Vector and Their One-Step Purification
Authors: Cheynet, V. / Verrier, B. / Mallet, F.
History
DepositionAug 18, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2000Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
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

Downloads & links

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Assembly

Deposited unit
H: IMMUNOGLOBULIN
L: IMMUNOGLOBULIN
P: CAPSID PROTEIN P24


Theoretical massNumber of molelcules
Total (without water)70,0283
Polymers70,0283
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-41.4 kcal/mol
Surface area39220 Å2
MethodPQS
Unit cell
Length a, b, c (Å)193.080, 45.600, 132.470
Angle α, β, γ (deg.)90.00, 132.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody IMMUNOGLOBULIN


Mass: 23552.301 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN 1-219 / Source method: isolated from a natural source / Details: OBTAINED BY PAPAIN CLEAVAGE (FAB) / Source: (natural) MUS MUSCULUS (house mouse) / References: UniProt: Q99LC4*PLUS
#2: Antibody IMMUNOGLOBULIN


Mass: 23053.477 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN 1-210 / Source method: isolated from a natural source / Details: OBTAINED BY PAPAIN CLEAVAGE (FAB) / Source: (natural) MUS MUSCULUS (house mouse)
#3: Protein CAPSID PROTEIN P24 / CA


Mass: 23421.795 Da / Num. of mol.: 1 / Fragment: GAG POLYPROTEIN RESIDUES 143-352
Source method: isolated from a genetically manipulated source
Details: HIS6 TAG AT N-TERM, PRO1 AND ILE2 DELETED, C-TERMINUS MODIFIED
Source: (gene. exp.) HIV-1 M\:B_HXB2R (virus) / Description: SEE REFERENCE 2 / Variant: CLONE 12 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04591, UniProt: H9A150*PLUS

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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: 3.07 Å3/Da / Density % sol: 58.6 %
Description: PATTERSON CORRELATION ALGORITHM OF XPLOR USED IN CONJUNCTION WITH AMORE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PROTEIN AT 7MG/ML IN 7% PEG8000, 0.1M TRIS-HCL PH=7.5, 5MM DTT, 0.5MM K2PTCL4 AT 4C USING THE HANGING DROP SYSTEM, pH 7.50
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.945
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.945 Å / Relative weight: 1
ReflectionResolution: 3→27.7 Å / Num. obs: 14742 / % possible obs: 84.7 % / Redundancy: 2.4 % / Rsym value: 0.094
Reflection shellHighest resolution: 3 Å / Redundancy: 1.6 % / Rsym value: 0.276 / % possible all: 33.1
Reflection
*PLUS
Rmerge(I) obs: 0.094
Reflection shell
*PLUS
% possible obs: 33.1 % / Rmerge(I) obs: 0.276

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Processing

Software
NameVersionClassification
X-PLOR3.8refinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FAB13B5, 1AFV, 1AM3

1afv

1am3
PDB Unreleased entry


Resolution: 3→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: PARTIALLY DISORDERED REGIONS: L152 - L155 AND H134 - H140 MISSING RESIDUES IN P24: HIS TAG, 12 FIRSTS AA, P146, P86 TO P95
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1528 11.6 %RANDOM
Rwork0.21 ---
obs0.21 14740 84.7 %-
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4914 0 0 0 4914
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.201
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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