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- PDB-1q1j: Crystal Structure Analysis of anti-HIV-1 Fab 447-52D in complex w... -

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Basic information

Entry
Database: PDB / ID: 1q1j
TitleCrystal Structure Analysis of anti-HIV-1 Fab 447-52D in complex with V3 peptide
Components
  • Fab 447-52D, heavy chain
  • Fab 447-52D, light chain
  • gp120 V3 peptide
KeywordsIMMUNE SYSTEM / Fab-peptide complex / HIV-1 / gp120 / V3 loop
Function / homology
Function and homology information


Dectin-2 family / 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 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...Dectin-2 family / 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 / 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 / identical protein binding / 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
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsStanfield, R.L. / Gorny, M.K. / Williams, C. / Zolla-Pazner, S. / Wilson, I.A.
CitationJournal: Structure / Year: 2004
Title: Structural rationale for the broad neutralization of HIV-1 by human monoclonal antibody 447-52D.
Authors: Stanfield, R.L. / Gorny, M.K. / Williams, C. / Zolla-Pazner, S. / Wilson, I.A.
History
DepositionJul 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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
Revision 1.4Nov 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
L: Fab 447-52D, light chain
H: Fab 447-52D, heavy chain
P: gp120 V3 peptide
M: Fab 447-52D, light chain
I: Fab 447-52D, heavy chain
Q: gp120 V3 peptide


Theoretical massNumber of molelcules
Total (without water)98,5506
Polymers98,5506
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.673, 74.903, 100.047
Angle α, β, γ (deg.)90.00, 100.57, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Antibody Fab 447-52D, light chain


Mass: 22684.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: isolated from peripheral blood cells / Source: (natural) Homo sapiens (human) / Organ: blood
#2: Antibody Fab 447-52D, heavy chain


Mass: 24763.775 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: isolated from peripheral blood cells / Source: (natural) Homo sapiens (human) / Organ: blood
#3: Protein/peptide gp120 V3 peptide


Mass: 1827.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs in HIV-1 gp120 / References: UniProt: P05877*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.23M ammonium sulfate, 0.1M sodium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlFab1drop
210 mg/mlpeptide1drop
31.23 Mammonium sulfate1reservoir
40.1 Msodium cacodylate1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.984 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.5→29.8 Å / Num. all: 35179 / Num. obs: 35179 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 49.9 Å2 / Rsym value: 0.077 / Net I/σ(I): 13.7
Reflection shellResolution: 2.5→2.54 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.531 / % possible all: 0.952
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 67571 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 95.2 % / Num. unique obs: 1816 / Num. measured obs: 3553 / Rmerge(I) obs: 0.531

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 8FAB

8fab


Resolution: 2.5→29.8 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1776 5 %RANDOM
Rwork0.25 ---
all0.2501 35173 --
obs0.2501 35173 90.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.3505 Å2 / ksol: 0.337844 e/Å3
Displacement parametersBiso mean: 48.1 Å2
Baniso -1Baniso -2Baniso -3
1--7.03 Å20 Å20.84 Å2
2--9.56 Å20 Å2
3----2.53 Å2
Refine analyze
ObsFree
Luzzati d res low5 Å-
Luzzati sigma a0.47 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6822 0 0 53 6875
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 2.5→2.59 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.51 -5.1 %
Rwork0.392 5775 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.249
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91
LS refinement shell
*PLUS
Rfactor Rfree: 0.51

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