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- PDB-3f78: Crystal structure of wild type LFA1 I domain complexed with isoflurane -

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Basic information

Entry
Database: PDB / ID: 3f78
TitleCrystal structure of wild type LFA1 I domain complexed with isoflurane
ComponentsIntegrin alpha-L
KeywordsCELL ADHESION / integrin / LFA1 / I domain / inactive conformation / wild type / volatile anesthetic / isoflurane / inhibitor of integrin / 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 / 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
Chem-ICF / Integrin alpha-L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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 1.3Sep 6, 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_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)62,98110
Polymers62,2193
Non-polymers7627
Water11,602644
1
A: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0163
Polymers20,7401
Non-polymers2772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1084
Polymers20,7401
Non-polymers3693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8563
Polymers20,7401
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.679, 85.800, 63.917
Angle α, β, γ (deg.)90.000, 118.180, 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-ICF / 1-CHLORO-2,2,2-TRIFLUOROETHYL DIFLUOROMETHYL ETHER / ISOFLURANE / Isoflurane


Mass: 184.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2ClF5O / Comment: medication*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M sodium acetate pH7.5, 0.2M ammonium acetate, 25% PEG3350, 10mM isoflurane, 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: 1.6→50 Å / Num. obs: 76838 / % possible obs: 97.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.065 / Χ2: 1.04 / Net I/σ(I): 22.222
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.663.30.61670430.69190.4
1.66-1.724.20.53776470.729197.4
1.72-1.84.50.38276410.76197.9
1.8-1.94.60.25177070.895198.3
1.9-2.024.60.16576951.055198.5
2.02-2.174.60.11977631.212198.8
2.17-2.394.60.08677711.176199
2.39-2.744.60.06877901.132199.3
2.74-3.454.60.05978631.409199.6
3.45-504.50.04379181.139199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0044refinement
PDB_EXTRACT3.006data extraction
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LFA

1lfa


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.317 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.181 3872 5 %RANDOM
Rwork0.153 ---
obs0.154 76778 97.67 %-
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: 61.85 Å2 / Biso mean: 22.764 Å2 / Biso min: 10.53 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å20.42 Å2
2---0.75 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4362 0 45 644 5051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224604
X-RAY DIFFRACTIONr_bond_other_d0.0010.023166
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.9756220
X-RAY DIFFRACTIONr_angle_other_deg0.83137794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6735572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48825.333210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20215878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4741510
X-RAY DIFFRACTIONr_chiral_restr0.0730.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025008
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02919
X-RAY DIFFRACTIONr_mcbond_it0.71422742
X-RAY DIFFRACTIONr_mcbond_other0.19321107
X-RAY DIFFRACTIONr_mcangle_it1.30234462
X-RAY DIFFRACTIONr_scbond_it2.1451862
X-RAY DIFFRACTIONr_scangle_it3.17151740
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 233 -
Rwork0.25 4715 -
all-4948 -
obs--86.25 %
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)
11.0971-0.4454-0.3482.08450.89981.5922-0.02980.07660.02360.0643-0.04430.27550.0452-0.24770.074-0.0177-0.0050.00240.030.01210.04929.67324.399-2.575
22.06-1.4694-0.89911.81070.9580.58240.11740.17480.103-0.1774-0.10730.1784-0.184-0.1152-0.01020.01360.0208-0.01170.00470.01710.053732.27932.909-5.094
31.311-0.3830.11431.34230.03550.9667-0.0704-0.12930.16870.20450.04670.0526-0.1431-0.00340.02380.0336-0.0125-0.0030.0137-0.00970.040939.86630.1784.751
41.58080.1211-0.45080.7614-0.31140.9767-0.0145-0.0980.01350.07810.042-0.03630.0160.0166-0.02750.0236-0.0022-0.00810.0219-0.00070.013938.81918.7815.329
51.7489-0.3218-0.54072.52480.83481.9047-0.04680.0148-0.15740.08750.0886-0.09270.1822-0.0014-0.04170.0285-0.0104-0.00620.0280.00710.031838.289.6227.645
61.3429-1.7287-1.70642.22532.19034.42030.09090.1604-0.2293-0.0933-0.22220.3467-0.0592-0.5370.1314-0.0382-0.03-0.0150.0305-0.0140.028824.82814.5411.587
71.4447-0.4616-0.24681.0513-0.02250.8613-0.04830.0686-0.1526-0.0103-0.0087-0.03460.2520.07650.0570.04140.0590.01390.0303-0.0098-0.015130.2783.10435.183
80.7917-0.4318-0.50671.0244-0.24881.3796-0.0164-0.04910.05170.00880.0029-0.1585-0.00350.24350.0135-0.01010.0239-0.0120.0649-0.011-0.010933.43115.22934.338
93.7154-0.4408-1.19362.07370.04593.4642-0.0579-0.06330.24610.0350.1039-0.0541-0.0345-0.0163-0.0460.03920.0238-0.00040.0497-0.0009-0.001126.33515.56627.343
101.6635-0.2041-1.08951.5089-0.36642.60730.00570.1256-0.0134-0.04090.0680.18850.0128-0.3929-0.0738-0.02470.017-0.00920.07810.0114-0.011618.94216.28524.914
1120.32936.2131-8.87264.3707-1.13586.8197-0.35990.0883-0.4319-0.0856-0.10620.26120.7398-0.34130.4660.0702-0.02840.0337-0.0424-0.0036-0.020327.1133.44418.948
121.2976-0.7523-0.07152.02450.12930.65640.08260.07380.1037-0.0831-0.0951-0.0756-0.068-0.04630.01250.00820.0283-0.00760.0260.00950.02914.376-3.0890.021
131.767-0.6464-0.78481.36780.38511.85920.09260.10530.0195-0.1101-0.07650.0165-0.0566-0.0359-0.0162-0.00820.0389-0.02590.01220.00560.0289-1.0711.511-0.616
141.405-0.9128-0.36232.5130.7220.9723-0.00920.0823-0.1090.0373-0.04160.29190.0027-0.19520.0509-0.02320.0077-0.0060.0397-0.00810.0258-5.377-6.9025.469
152.47440.131-0.40843.86360.20882.0122-0.09-0.21390.13850.34010.0733-0.0075-0.0444-0.08680.01660.03140.0376-0.03350.0414-0.0283-0.00811.012-0.59717.604
160.4543-0.57390.22456.6407-0.99341.499-0.0497-0.13450.24730.1802-0.0349-0.3838-0.1290.06470.08470.00020.0075-0.022-0.0006-0.02070.068112.962-3.99111.788
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A128 - 173
2X-RAY DIFFRACTION2A174 - 202
3X-RAY DIFFRACTION3A203 - 229
4X-RAY DIFFRACTION4A230 - 265
5X-RAY DIFFRACTION5A266 - 286
6X-RAY DIFFRACTION6A287 - 307
7X-RAY DIFFRACTION7B128 - 200
8X-RAY DIFFRACTION8B201 - 250
9X-RAY DIFFRACTION9B251 - 264
10X-RAY DIFFRACTION10B265 - 296
11X-RAY DIFFRACTION11B297 - 307
12X-RAY DIFFRACTION12C128 - 189
13X-RAY DIFFRACTION13C190 - 217
14X-RAY DIFFRACTION14C218 - 250
15X-RAY DIFFRACTION15C251 - 289
16X-RAY DIFFRACTION16C290 - 307

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