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- PDB-1mqa: Crystal structure of high affinity alphaL I domain in the absence... -

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Basic information

Entry
Database: PDB / ID: 1mqa
TitleCrystal structure of high affinity alphaL I domain in the absence of ligand or metal
ComponentsIntegrin alpha-L
KeywordsIMMUNE SYSTEM / Designed disulfide bridge / Rossmann fold
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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShimaoka, T. / Xiao, T. / Liu, J.-H. / Yang, Y. / Dong, Y. / Jun, C.-D. / Zhang, R. / Takagi, J. / Wang, J.-H. / Springer, T.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: Structures of the aL I domain and its complex with ICAM-1 reveal a shape-shifting pathway for integrin regulation
Authors: Shimaoka, M. / Xiao, T. / Liu, J.-H. / Yang, Y. / Dong, Y. / Jun, C.-D. / McCormack, A. / Zhang, R. / Joachimiak, A. / Takagi, J. / Wang, J.-H. / Springer, T.A.
History
DepositionSep 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-L


Theoretical massNumber of molelcules
Total (without water)20,4961
Polymers20,4961
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.864, 121.324, 54.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingmonoclinic
Space group name H-MC2221

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Components

#1: Protein Integrin alpha-L / Leukocyte adhesion glycoprotein LFA-1 alpha chain / Leukocyte function associated molecule 1 / ...Leukocyte adhesion glycoprotein LFA-1 alpha chain / Leukocyte function associated molecule 1 / alpha chain / CD11a


Mass: 20495.502 Da / Num. of mol.: 1 / Fragment: Integrin alphaL I domain / Mutation: K287C, K294C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LFA-1 (AlphaLbeta2) / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20701
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.55 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.2 M ammonium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-20 mg/mlprotein1drop
21.2 Mammonium phosphate1reservoir
30.1 MTris-Cl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 29, 2001 / Details: mirrors
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 7700 / Num. obs: 7271 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 44.4 Å2 / Rmerge(I) obs: 0.184 / Rsym value: 0.184 / Net I/σ(I): 8.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2 / Num. unique all: 462 / Rsym value: 0.413 / % possible all: 60.4
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. measured all: 41352
Reflection shell
*PLUS
% possible obs: 60.4 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MQ9

1mq9


Resolution: 2.5→40.36 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood refinement target
RfactorNum. reflection% reflectionSelection details
Rfree0.283 727 10.9 %RANDOM
Rwork0.249 ---
all0.28 7344 --
obs0.249 6678 90.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.5453 Å2 / ksol: 0.345475 e/Å3
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1-20.75 Å20 Å20 Å2
2---7.73 Å20 Å2
3----13.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.5→40.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1388 0 0 31 1419
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d1.07
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 97 11.7 %
Rwork0.4 732 -
obs-500 69.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.07

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