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- PDB-3vrl: Crystal structure of BMJ4 p24 capsid protein in complex with A10F9 Fab -

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Basic information

Entry
Database: PDB / ID: 3vrl
TitleCrystal structure of BMJ4 p24 capsid protein in complex with A10F9 Fab
Components
  • A10F9 Fab heavy chain
  • A10F9 Fab light chain
  • Gag protein
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / HIV-1 capside p24 / capsid protein / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


immunoglobulin complex / viral budding via host ESCRT complex / immunoglobulin mediated immune response / antigen binding / viral nucleocapsid / host cell cytoplasm / blood microparticle / immune response / host cell nucleus / structural molecule activity ...immunoglobulin complex / viral budding via host ESCRT complex / immunoglobulin mediated immune response / antigen binding / viral nucleocapsid / host cell cytoplasm / blood microparticle / immune response / host cell nucleus / structural molecule activity / RNA binding / extracellular space / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Retroviral nucleocapsid Gag protein p24, N-terminal / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) ...Retroviral nucleocapsid Gag protein p24, N-terminal / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Immunoglobulin V-set 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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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
Mc5 VHCH1 / Igk protein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGu, Y. / Cao, F. / Li, S. / Yuan, Y.A. / Xia, N.
CitationJournal: To be Published
Title: Structure of the HIV-1 capsid protein p24 in complex with the broad-spectrum antibody A10F9
Authors: Gu, Y. / Cao, F. / Li, S. / Yuan, Y.A. / Xia, N.
History
DepositionApr 12, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: A10F9 Fab heavy chain
L: A10F9 Fab light chain
C: Gag protein
E: A10F9 Fab heavy chain
F: A10F9 Fab light chain
D: Gag protein


Theoretical massNumber of molelcules
Total (without water)146,5216
Polymers146,5216
Non-polymers00
Water00
1
H: A10F9 Fab heavy chain
L: A10F9 Fab light chain
C: Gag protein


Theoretical massNumber of molelcules
Total (without water)73,2603
Polymers73,2603
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-32 kcal/mol
Surface area23610 Å2
MethodPISA
2
E: A10F9 Fab heavy chain
F: A10F9 Fab light chain
D: Gag protein


Theoretical massNumber of molelcules
Total (without water)73,2603
Polymers73,2603
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-32 kcal/mol
Surface area23540 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12570 Å2
ΔGint-73 kcal/mol
Surface area45610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.109, 124.058, 150.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody A10F9 Fab heavy chain


Mass: 24009.850 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A0N7J2*PLUS
#2: Antibody A10F9 Fab light chain


Mass: 23626.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: I6L978*PLUS
#3: Protein Gag protein / p24 capsid protein


Mass: 25624.422 Da / Num. of mol.: 2 / Fragment: UNP residues 130-360
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: Q9DGV7

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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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, NaBr, NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 25000 / Num. obs: 24996 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14 % / Rmerge(I) obs: 0.127
Reflection shellResolution: 3.2→3.26 Å / Rmerge(I) obs: 0.448 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E6J (for FAB chains)

1e6j


Resolution: 3.2→37.02 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.863 / SU B: 51.06 / SU ML: 0.388 / Cross valid method: THROUGHOUT / ESU R Free: 0.532 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29189 1335 5.1 %RANDOM
Rwork0.21092 ---
all0.22 25000 --
obs0.21484 24996 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.991 Å2
Baniso -1Baniso -2Baniso -3
1-7.05 Å20 Å20 Å2
2---1.12 Å20 Å2
3----5.93 Å2
Refinement stepCycle: LAST / Resolution: 3.2→37.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7806 0 0 0 7806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227988
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.94910860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.67751012
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28224.472322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.717151310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7251534
X-RAY DIFFRACTIONr_chiral_restr0.1120.21218
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026002
X-RAY DIFFRACTIONr_nbd_refined0.2640.23774
X-RAY DIFFRACTIONr_nbtor_refined0.3180.25354
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2307
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.21
X-RAY DIFFRACTIONr_mcbond_it0.5461.55154
X-RAY DIFFRACTIONr_mcangle_it0.98428206
X-RAY DIFFRACTIONr_scbond_it1.24333258
X-RAY DIFFRACTIONr_scangle_it2.1224.52654
LS refinement shellResolution: 3.197→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 101 -
Rwork0.276 1695 -
obs--94.48 %
Refinement TLS params.Method: refined / Origin x: 25.7373 Å / Origin y: -8.6688 Å / Origin z: -7.6906 Å
111213212223313233
T-0.2179 Å20.0164 Å20.016 Å2--0.2037 Å20.0038 Å2---0.1324 Å2
L0.2189 °20.0322 °2-0.0598 °2-0.1475 °20.125 °2--2.1656 °2
S-0.0393 Å °-0.0404 Å °-0.0169 Å °0.0519 Å °0.0145 Å °0.0224 Å °0.1835 Å °0.1986 Å °0.0248 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 219
2X-RAY DIFFRACTION1L1 - 214
3X-RAY DIFFRACTION1C149 - 221
4X-RAY DIFFRACTION1E1 - 219
5X-RAY DIFFRACTION1F1 - 214
6X-RAY DIFFRACTION1D149 - 221

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