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- PDB-3f74: Crystal structure of wild type LFA1 I domain -

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Basic information

Entry
Database: PDB / ID: 3f74
TitleCrystal structure of wild type LFA1 I domain
ComponentsIntegrin alpha-L
KeywordsCELL ADHESION / integrin / LFA1 / I domain / inactive conformation / wild type / Glycoprotein / Magnesium / Membrane / Receptor / Transmembrane
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 / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cell adhesion mediated by integrin / 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 / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cell adhesion mediated by integrin / 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 / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / 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 / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / 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 alpha, N-terminal / Integrin domain superfamily / 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 / Resolution: 1.7 Å
AuthorsZhang, H. / Wang, J.-H.
CitationJournal: Faseb J. / Year: 2009
Title: Crystal structure of isoflurane bound to integrin LFA-1 supports a unified mechanism of volatile anesthetic action in the immune and central nervous systems.
Authors: Zhang, H. / Astrof, N.S. / Liu, J.H. / Wang, J.H. / Shimaoka, M.
History
DepositionNov 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-L
B: Integrin alpha-L
C: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4286
Polymers62,2193
Non-polymers2083
Water12,755708
1
A: Integrin alpha-L


Theoretical massNumber of molelcules
Total (without water)20,7401
Polymers20,7401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9243
Polymers20,7401
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7642
Polymers20,7401
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.806, 85.603, 63.554
Angle α, β, γ (deg.)90.000, 117.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: 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: 20739.766 Da / Num. of mol.: 3 / Fragment: UNP residues 153-332, VWFA domain, I domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD11A, integrin LFA1, ITGAL / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20701
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: o.1M sodium acetate, pH7.5, 0.2M ammonium acetate, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 64731 / % possible obs: 99.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.07 / Χ2: 1.049 / Net I/σ(I): 18.895
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.763.70.57364630.892199.8
1.76-1.833.90.42764280.9241100
1.83-1.913.90.29564480.8991100
1.91-2.023.90.19564440.9441100
2.02-2.143.90.14564640.9921100
2.14-2.313.90.10364721.0391100
2.31-2.543.90.08364411.0531100
2.54-2.913.90.07465091.2951100
2.91-3.663.90.05164931.354199.9
3.66-503.90.03465691.083199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0044refinement
PDB_EXTRACT3.006data extraction
HKL-3000data collection
PHASERphasing
RefinementResolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 3.934 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.178 3280 5.1 %RANDOM
Rwork0.146 ---
obs0.147 64661 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 53.43 Å2 / Biso mean: 14.753 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å20.33 Å2
2---0.8 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4362 0 13 708 5083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224538
X-RAY DIFFRACTIONr_bond_other_d0.0010.023113
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9636126
X-RAY DIFFRACTIONr_angle_other_deg0.83737655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7515561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78325.238210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74915859
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2961511
X-RAY DIFFRACTIONr_chiral_restr0.0730.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024967
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02917
X-RAY DIFFRACTIONr_mcbond_it0.77622724
X-RAY DIFFRACTIONr_mcbond_other0.20921101
X-RAY DIFFRACTIONr_mcangle_it1.40934426
X-RAY DIFFRACTIONr_scbond_it2.23151814
X-RAY DIFFRACTIONr_scangle_it3.38151688
LS refinement shellResolution: 1.7→1.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 220 -
Rwork0.227 4440 -
all-4660 -
obs--97.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2023-0.7681-0.39262.02520.56782.02180.00540.0447-0.054-0.0452-0.01990.25720.0081-0.28250.01450.0271-0.0179-0.00990.06760.00860.091312.069-6.688-30.45
21.557-0.9698-0.38721.46560.06050.82010.02540.05870.1124-0.00320.00170.094-0.1365-0.0564-0.0270.0646-0.00520.00770.04790.00650.099719.1970.542-28.811
32.2233-0.2794-0.67440.7283-0.19391.1524-0.0024-0.1005-0.02150.03920.0251-0.0237-0.0233-0.016-0.02270.0725-0.0070.01020.06190.00280.064521.463-11.451-22.492
43.1156-0.2403-0.66321.94960.94891.8182-0.06580.0263-0.19970.03780.1602-0.08680.11550.0335-0.09440.069-0.00970.00440.05190.00120.081721.525-21.024-20.492
52.5774-2.6527-2.99972.73673.23448.14340.05370.1446-0.4203-0.0692-0.16860.42070.0772-0.66660.11480.0461-0.04-0.02060.08030.01430.09717.981-16.097-26.136
62.0082-0.6252-0.73921.32690.03171.3654-0.1150.1099-0.2195-0.04980.00610.10380.27860.03940.1090.09190.03060.00970.067-0.01260.057910.893-25.8475.335
70.8934-0.6881-0.10291.2919-0.29791.1458-0.032-0.0491-0.0194-0.00020.0051-0.11350.14110.26320.0270.05030.0568-0.00580.0975-0.0070.035818.75-23.229.287
80.761-0.5026-0.58711.14760.42971.7416-0.00610.03640.0499-0.0321-0.0225-0.0512-0.0355-0.00310.02860.07140.02050.00410.08960.0040.0519.904-13.8761.448
91.82390.2211-0.26221.71940.07381.7072-0.00110.07540.0275-0.0793-0.02350.13840.0762-0.22610.02450.03790.0143-0.00740.0899-0.00950.03762.694-15.146-3.343
1020.78953.8362-6.43893.3441-1.86095.3378-0.1253-0.1384-0.8-0.0445-0.09870.08940.348-0.28850.22410.1065-0.00680.00620.0512-0.00320.056410.169-27.237-9.096
111.2071-0.3855-0.11332.48490.32170.91940.05660.03960.09470.0064-0.0745-0.1555-0.1127-0.0180.01790.06440.0224-0.00920.06960.01020.0695-8.787-33.34-26.058
120.7109-0.3088-0.6251.76850.18811.56630.0790.075-0.0018-0.1332-0.08670.1172-0.0483-0.03170.00780.04970.0434-0.02390.0727-0.00670.0739-17.054-31.404-30.193
131.0127-0.31-0.41772.33070.13041.40060.02680.0788-0.08080.0527-0.0210.3305-0.0014-0.2333-0.00590.01820.0105-0.00970.0780.00290.0768-21.223-37.464-22.377
141.90470.1822-0.59392.9650.2471.67440.0099-0.10960.09510.2842-0.0123-0.0195-0.16540.02940.00230.12030.0088-0.02350.0493-0.00730.0334-11.678-30.247-11.911
153.25662.2112-2.9258.9856-5.39245.93930.0823-0.13280.16010.6135-0.0575-0.1548-0.5407-0.1849-0.02470.09460.033-0.01390.0534-0.0050.0398-4.146-41.432-15.781
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A128 - 168
2X-RAY DIFFRACTION2A169 - 228
3X-RAY DIFFRACTION3A229 - 265
4X-RAY DIFFRACTION4A266 - 286
5X-RAY DIFFRACTION5A287 - 307
6X-RAY DIFFRACTION6B128 - 176
7X-RAY DIFFRACTION7B177 - 229
8X-RAY DIFFRACTION8B230 - 266
9X-RAY DIFFRACTION9B267 - 296
10X-RAY DIFFRACTION10B297 - 307
11X-RAY DIFFRACTION11C128 - 168
12X-RAY DIFFRACTION12C169 - 217
13X-RAY DIFFRACTION13C218 - 250
14X-RAY DIFFRACTION14C251 - 298
15X-RAY DIFFRACTION15C299 - 307

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