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- PDB-3ujj: Crystal structure of anti-HIV-1 V3 Fab 4025 in complex with Con A... -

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Basic information

Entry
Database: PDB / ID: 3ujj
TitleCrystal structure of anti-HIV-1 V3 Fab 4025 in complex with Con A peptide
Components
  • Fab region of the heavy chain of anti-HIV-1 V3 monoclonal antibody 4025
  • Gp120
  • Light chain of anti-HIV-1 V3 monoclonal antibody 4025
KeywordsIMMUNE SYSTEM / Ig domains / antibody Fab / antigen binding / The third variable region of HIV-1 gp120
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...membrane fusion involved in viral entry into host cell / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Envelope glycoprotein gp160 / Gp120
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKong, X.P. / Sampson, J.
CitationJournal: Plos One / Year: 2011
Title: Human Anti-V3 HIV-1 Monoclonal Antibodies Encoded by the VH5-51/VL Lambda Genes Define a Conserved Antigenic Structure.
Authors: Gorny, M.K. / Sampson, J. / Li, H. / Jiang, X. / Totrov, M. / Wang, X.H. / Williams, C. / O'Neal, T. / Volsky, B. / Li, L. / Cardozo, T. / Nyambi, P. / Zolla-Pazner, S. / Kong, X.P.
History
DepositionNov 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 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
L: Light chain of anti-HIV-1 V3 monoclonal antibody 4025
H: Fab region of the heavy chain of anti-HIV-1 V3 monoclonal antibody 4025
P: Gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,62837
Polymers49,6963
Non-polymers2,93234
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11760 Å2
ΔGint-144 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.143, 136.143, 73.411
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe Fab is the biological assembly and there is only one Fab in the asymmetric subunit.

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Components

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide Gp120


Mass: 2452.747 Da / Num. of mol.: 1 / Fragment: unp residues 30-52 / Source method: obtained synthetically
Details: Synthesized based on HIV-1 strain of consensus clade A
Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YXJ8, UniProt: Q9Q714*PLUS

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Antibody , 2 types, 2 molecules LH

#1: Antibody Light chain of anti-HIV-1 V3 monoclonal antibody 4025


Mass: 22903.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody Fab region of the heavy chain of anti-HIV-1 V3 monoclonal antibody 4025


Mass: 24340.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Non-polymers , 4 types, 523 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.95 Å3/Da / Density % sol: 68.86 %
Crystal growTemperature: 296 K / Method: evaporation / pH: 3.8
Details: 1.6 M ammonium sulfate, 80 mM sodium acetate, 30% glycerol, pH 3.8, EVAPORATION, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97883 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 12, 2009
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97883 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 52860 / Num. obs: 52523 / % possible obs: 91.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rsym value: 0.081 / Net I/σ(I): 17.3
Reflection shellResolution: 2→2.07 Å / % possible all: 67.4

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2B0S

2b0s


Resolution: 2→39.301 Å / SU ML: 0.61 / σ(F): 1.35 / Phase error: 19.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 2665 5.08 %random
Rwork0.1766 ---
obs0.1784 52488 98.41 %-
all-55153 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.199 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2404 Å20 Å20 Å2
2---0.2404 Å2-0 Å2
3---0.4843 Å2
Refinement stepCycle: LAST / Resolution: 2→39.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 182 489 4119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073689
X-RAY DIFFRACTIONf_angle_d1.1494979
X-RAY DIFFRACTIONf_dihedral_angle_d12.6221293
X-RAY DIFFRACTIONf_chiral_restr0.078536
X-RAY DIFFRACTIONf_plane_restr0.006619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9973-2.03360.31421260.28172248X-RAY DIFFRACTION85
2.0336-2.07270.28681220.24952371X-RAY DIFFRACTION90
2.0727-2.1150.2851430.23262539X-RAY DIFFRACTION96
2.115-2.1610.2551490.21572620X-RAY DIFFRACTION99
2.161-2.21130.25861500.21122593X-RAY DIFFRACTION99
2.2113-2.26660.26551680.20592614X-RAY DIFFRACTION100
2.2666-2.32780.22281290.20462656X-RAY DIFFRACTION100
2.3278-2.39630.22481460.19342643X-RAY DIFFRACTION100
2.3963-2.47370.24331330.18722661X-RAY DIFFRACTION100
2.4737-2.56210.22221260.1752659X-RAY DIFFRACTION100
2.5621-2.66460.21571560.18132647X-RAY DIFFRACTION100
2.6646-2.78590.21641470.17662647X-RAY DIFFRACTION100
2.7859-2.93270.23981300.17342671X-RAY DIFFRACTION100
2.9327-3.11640.19581310.16922671X-RAY DIFFRACTION100
3.1164-3.35690.2021480.16032675X-RAY DIFFRACTION100
3.3569-3.69440.17981310.15642697X-RAY DIFFRACTION100
3.6944-4.22850.19691480.14112676X-RAY DIFFRACTION100
4.2285-5.32540.16511430.14632723X-RAY DIFFRACTION100
5.3254-39.30870.21631390.20042812X-RAY DIFFRACTION100

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