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

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Basic information

Entry
Database: PDB / ID: 3eoa
TitleCrystal structure the Fab fragment of Efalizumab in complex with LFA-1 I domain, Form I
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 / 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 / ICAM-3 receptor activity / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / receptor clustering ...memory T cell extravasation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / receptor clustering / Integrin cell surface interactions / phagocytosis / specific granule membrane / 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 / metal ion binding / membrane / 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 chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / 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 chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / 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: 2.8 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
Revision 1.2Nov 1, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Oct 16, 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: Efalizumab Fab fragment, light chain
A: Efalizumab Fab fragment, light chain
H: Efalizumab Fab fragment, heavy chain
B: Efalizumab Fab fragment, heavy chain
I: Integrin alpha-L
J: Integrin alpha-L


Theoretical massNumber of molelcules
Total (without water)135,7336
Polymers135,7336
Non-polymers00
Water6,413356
1
L: Efalizumab Fab fragment, light chain
H: Efalizumab Fab fragment, heavy chain
I: Integrin alpha-L


Theoretical massNumber of molelcules
Total (without water)67,8663
Polymers67,8663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Efalizumab Fab fragment, light chain
B: Efalizumab Fab fragment, heavy chain
J: Integrin alpha-L


Theoretical massNumber of molelcules
Total (without water)67,8663
Polymers67,8663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.719, 81.696, 281.882
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: ITGAL, CD11A / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20701
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.1M sodium citric, 0.2M sodium potassium tartrate, 1.6M ammonium sulfate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 24, 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: 2.8→50 Å / Num. all: 37885 / Num. obs: 37165 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.5 % / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 21.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3139 / Rsym value: 0.343 / % possible all: 84.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A0Q, 1ZOP

1a0q

1zop


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.873 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26438 1850 5 %RANDOM
Rwork0.22475 ---
obs0.22672 35307 98.05 %-
all-36009 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.434 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--1.61 Å20 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9448 0 0 356 9804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229660
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.95413092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46351208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05724.627402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.127151638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8711532
X-RAY DIFFRACTIONr_chiral_restr0.0850.21470
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027210
X-RAY DIFFRACTIONr_nbd_refined0.1960.24143
X-RAY DIFFRACTIONr_nbtor_refined0.3050.26372
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2440
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.212
X-RAY DIFFRACTIONr_mcbond_it0.8551.56040
X-RAY DIFFRACTIONr_mcangle_it1.53929774
X-RAY DIFFRACTIONr_scbond_it1.30233620
X-RAY DIFFRACTIONr_scangle_it2.0164.53318
X-RAY DIFFRACTIONr_rigid_bond_restr1.27539660
X-RAY DIFFRACTIONr_sphericity_free0.783356
X-RAY DIFFRACTIONr_sphericity_bonded0.40639442
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 113 -
Rwork0.319 2149 -
obs--83.38 %

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