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- PDB-3eob: Crystal structure the Fab fragment of Efalizumab in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3eob
TitleCrystal structure the Fab fragment of Efalizumab in complex with LFA-1 I domain, Form II
Components
  • Efalizumab Fab fragment, heavy chain
  • Efalizumab Fab fragment, light chain
  • Integrin alpha-L
KeywordsIMMUNE SYSTEM/CELL ADHESION / Efalizumab / Fab / antibody / LFA-1 / CD11a / I domain / Alternative splicing / Calcium / Cell adhesion / Glycoprotein / Integrin / Magnesium / Membrane / Polymorphism / Receptor / Transmembrane / IMMUNE SYSTEM-CELL ADHESION COMPLEX
Function / homology
Function and homology information


memory T cell extravasation / integrin alphaL-beta2 complex / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / ICAM-3 receptor activity / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / receptor clustering ...memory T cell extravasation / integrin alphaL-beta2 complex / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / ICAM-3 receptor activity / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / receptor clustering / Integrin cell surface interactions / specific granule membrane / phagocytosis / cell adhesion molecule binding / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell adhesion / inflammatory response / external side of plasma membrane / Neutrophil degranulation / cell surface / signal transduction / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. ...Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsLi, S. / Ding, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Efalizumab binding to the LFA-1 alphaL I domain blocks ICAM-1 binding via steric hindrance.
Authors: Li, S. / Wang, H. / Peng, B. / Zhang, M. / Zhang, D. / Hou, S. / Guo, Y. / Ding, J.
History
DepositionSep 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Efalizumab Fab fragment, light chain
H: Efalizumab Fab fragment, heavy chain
I: Integrin alpha-L
A: Efalizumab Fab fragment, light chain
B: Efalizumab Fab fragment, heavy chain
J: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,8648
Polymers135,7336
Non-polymers1312
Water0
1
L: Efalizumab Fab fragment, light chain
H: Efalizumab Fab fragment, heavy chain
I: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9324
Polymers67,8663
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Efalizumab Fab fragment, light chain
B: Efalizumab Fab fragment, heavy chain
J: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9324
Polymers67,8663
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.096, 111.096, 470.726
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Antibody Efalizumab Fab fragment, light chain


Mass: 23436.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGG1
#2: Antibody Efalizumab Fab fragment, heavy chain


Mass: 23751.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGG1
#3: Protein Integrin alpha-L / Leukocyte adhesion glycoprotein LFA-1 alpha chain / LFA-1A / Leukocyte function-associated molecule ...Leukocyte adhesion glycoprotein LFA-1 alpha chain / LFA-1A / Leukocyte function-associated molecule 1 alpha chain / CD11 antigen-like family member A


Mass: 20678.686 Da / Num. of mol.: 2 / Fragment: I domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LFA-1 I domain / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20701
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 3.09 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1M sodium cacodylate, 0.2M zinc acetate, 11% w/v PEG 8000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 27, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. all: 21109 / Num. obs: 20645 / % possible obs: 97.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.203 / Rsym value: 0.203 / Net I/σ(I): 7.5
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 2 / Num. unique all: 2014 / Rsym value: 0.622 / % possible all: 98.9

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→50 Å / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.333 1026 -RANDOM
Rwork0.267 ---
all0.269 21109 --
obs0.269 20553 97.7 %-
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: LAST / Resolution: 3.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9452 0 2 0 9454
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_refined_d0.011
X-RAY DIFFRACTIONc_angle_refined_deg1.7
LS refinement shellResolution: 3.6→3.83 Å
RfactorNum. reflection% reflection
Rfree0.324 170 -
Rwork0.29 --
obs-3182 98.4 %

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