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- PDB-1u6a: Crystal Structure of the Broadly Neutralizing Anti-HIV Fab F105 -

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Basic information

Entry
Database: PDB / ID: 1u6a
TitleCrystal Structure of the Broadly Neutralizing Anti-HIV Fab F105
Components
  • F105 HEAVY CHAIN
  • F105 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / FAB / F105 / GP120 / HIV
Function / homology
Function and homology information


immunoglobulin complex / extracellular region / 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
Ig-like domain-containing protein / IGK@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsWilkinson, R.A. / Piscitelli, C. / Teintze, M. / Lawrence, C.M.
CitationJournal: J.Virol. / Year: 2005
Title: Structure of the Fab fragment of F105, a broadly reactive anti-human immunodeficiency virus (HIV) antibody that recognizes the CD4 binding site of HIV type 1 gp120.
Authors: Wilkinson, R.A. / Piscitelli, C. / Teintze, M. / Cavacini, L.A. / Posner, M.R. / Lawrence, C.M.
History
DepositionJul 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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

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Assembly

Deposited unit
L: F105 LIGHT CHAIN
H: F105 HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)47,2532
Polymers47,2532
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-24 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.403, 120.403, 72.977
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody F105 LIGHT CHAIN


Mass: 23495.043 Da / Num. of mol.: 1 / Fragment: ANTIGEN-BINDING FRAGMENT, FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Expression: EPSTEIN-BARR VIRUS IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER
References: UniProt: Q6PIL8*PLUS
#2: Antibody F105 HEAVY CHAIN


Mass: 23757.689 Da / Num. of mol.: 1 / Fragment: ANTIGEN-BINDING FRAGMENT, FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Expression: EPSTEIN-BARR VIRUS IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER
References: UniProt: Q6N089
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.86 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, ISOPROPANOL, NACL, NA-CITRATE, PEPTIDE 44 (RLTPEPDD-NH2), pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 25, 2003 / Details: OSMIC BLUE
RadiationMonochromator: NI MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.81→20 Å / Num. all: 13404 / Num. obs: 13338 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Redundancy: 12.5 % / Biso Wilson estimate: 32.3 Å2 / Rsym value: 0.092 / Net I/σ(I): 16.4
Reflection shellResolution: 2.81→2.9 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 1292 / Rsym value: 0.324 / % possible all: 98.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2fgw

2fgw


Resolution: 2.81→15 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1990470.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 662 5 %RANDOM
Rwork0.21 ---
all0.248 13413 --
obs0.246 13338 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.4035 Å2 / ksol: 0.312196 e/Å3
Displacement parametersBiso mean: 26.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20 Å2
2---1.36 Å20 Å2
3---2.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.81→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3299 0 0 85 3384
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it2.712
X-RAY DIFFRACTIONc_scangle_it3.562.5
LS refinement shellResolution: 2.81→2.94 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 93 5.8 %
Rwork0.299 1834 -
obs-1566 95.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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