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- PDB-4d9l: Fab structure of anti-HIV-1 gp120 V2 mAb 697 -

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Basic information

Entry
Database: PDB / ID: 4d9l
TitleFab structure of anti-HIV-1 gp120 V2 mAb 697
Components
  • Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
  • Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
KeywordsIMMUNE SYSTEM / Ig / antibody / HIV-1 gp120
Function / homology
Function and homology information


immunoglobulin complex / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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 / Mainly Beta
Similarity search - Domain/homology
IGL@ protein / IGH@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.485 Å
AuthorsPan, R.M. / Kong, X.P.
CitationJournal: Virology / Year: 2012
Title: Functional and immunochemical cross-reactivity of V2-specific monoclonal antibodies from HIV-1-infected individuals.
Authors: Gorny, M.K. / Pan, R. / Williams, C. / Wang, X.H. / Volsky, B. / O'Neal, T. / Spurrier, B. / Sampson, J.M. / Li, L. / Seaman, M.S. / Kong, X.P. / Zolla-Pazner, S.
History
DepositionJan 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 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 / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
H: Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
M: Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
I: Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
N: Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
J: Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
O: Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
K: Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697


Theoretical massNumber of molelcules
Total (without water)185,3508
Polymers185,3508
Non-polymers00
Water10,863603
1
L: Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
H: Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697


Theoretical massNumber of molelcules
Total (without water)46,3382
Polymers46,3382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-23 kcal/mol
Surface area19310 Å2
MethodPISA
2
M: Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
I: Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697


Theoretical massNumber of molelcules
Total (without water)46,3382
Polymers46,3382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-22 kcal/mol
Surface area19610 Å2
MethodPISA
3
N: Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
J: Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697


Theoretical massNumber of molelcules
Total (without water)46,3382
Polymers46,3382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-22 kcal/mol
Surface area19350 Å2
MethodPISA
4
O: Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
K: Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697


Theoretical massNumber of molelcules
Total (without water)46,3382
Polymers46,3382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-20 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.322, 82.460, 93.212
Angle α, β, γ (deg.)82.12, 70.41, 86.27
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697


Mass: 22756.029 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293 / Production host: Homo sapiens (human) / References: UniProt: Q6GMX4
#2: Antibody
Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697


Mass: 23581.523 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293 / Production host: Homo sapiens (human) / References: UniProt: Q6GMX6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 603 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 18% polyethylene glycol 8000 and 0.1 M Tris pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0333 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 11, 2011
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 2.485→47.267 Å / Num. all: 66449 / Num. obs: 65386 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.122 / Net I/σ(I): 12.5
Reflection shellResolution: 2.485→2.54 Å / Redundancy: 2.7 % / Num. unique all: 3182 / Rsym value: 0.608 / % possible all: 95.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G75

2g75


Resolution: 2.485→47.267 Å / SU ML: 0.39 / σ(F): 1.97 / Phase error: 24.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 3309 5.06 %Random
Rwork0.1765 ---
obs0.1796 65360 97.68 %-
all-66912 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.669 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4488 Å20.3637 Å20.3903 Å2
2--0.9391 Å20.749 Å2
3----0.4903 Å2
Refinement stepCycle: LAST / Resolution: 2.485→47.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12951 0 0 603 13554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813289
X-RAY DIFFRACTIONf_angle_d1.25518120
X-RAY DIFFRACTIONf_dihedral_angle_d16.2534696
X-RAY DIFFRACTIONf_chiral_restr0.0822065
X-RAY DIFFRACTIONf_plane_restr0.0062324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.485-2.52050.36161230.28942132X-RAY DIFFRACTION79
2.5205-2.55820.35151230.2782509X-RAY DIFFRACTION96
2.5582-2.59810.35651230.27892637X-RAY DIFFRACTION97
2.5981-2.64070.33431430.24262597X-RAY DIFFRACTION98
2.6407-2.68620.3091400.23062547X-RAY DIFFRACTION98
2.6862-2.73510.31331330.21822650X-RAY DIFFRACTION98
2.7351-2.78770.30021390.22052546X-RAY DIFFRACTION98
2.7877-2.84460.30231510.21092609X-RAY DIFFRACTION98
2.8446-2.90640.24641450.18772585X-RAY DIFFRACTION98
2.9064-2.9740.27651400.17432615X-RAY DIFFRACTION98
2.974-3.04840.2511250.17642608X-RAY DIFFRACTION98
3.0484-3.13080.24571500.18472568X-RAY DIFFRACTION98
3.1308-3.22290.26491310.18492632X-RAY DIFFRACTION99
3.2229-3.32690.25291510.17722582X-RAY DIFFRACTION99
3.3269-3.44580.24081420.17182642X-RAY DIFFRACTION99
3.4458-3.58370.22161370.16772657X-RAY DIFFRACTION99
3.5837-3.74670.21421300.15922564X-RAY DIFFRACTION99
3.7467-3.94420.2021590.15152609X-RAY DIFFRACTION99
3.9442-4.19110.23071220.14832615X-RAY DIFFRACTION99
4.1911-4.51450.19681550.1422629X-RAY DIFFRACTION99
4.5145-4.96840.18911330.13192612X-RAY DIFFRACTION99
4.9684-5.68630.19361410.15292652X-RAY DIFFRACTION99
5.6863-7.16010.23141290.19012631X-RAY DIFFRACTION100
7.1601-47.27570.18851440.17682623X-RAY DIFFRACTION99

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