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- PDB-5e6u: Structures of leukocyte integrin aLb2: The aI domain, the headpie... -

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Basic information

Entry
Database: PDB / ID: 5e6u
TitleStructures of leukocyte integrin aLb2: The aI domain, the headpiece, and the pocket for the internal ligand
Components
  • Integrin alpha-L
  • Integrin beta-2
KeywordsCELL ADHESION / lymphocyte function-associated antigen-1 / LFA-1
Function / homology
Function and homology information


integrin alphaX-beta2 complex / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / memory T cell extravasation / positive regulation of neutrophil degranulation / 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 / complement component C3b binding / neutrophil migration ...integrin alphaX-beta2 complex / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / memory T cell extravasation / positive regulation of neutrophil degranulation / 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 / complement component C3b binding / neutrophil migration / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of dopamine metabolic process / cell-cell adhesion via plasma-membrane adhesion molecules / RUNX3 Regulates Immune Response and Cell Migration / heterotypic cell-cell adhesion / integrin complex / positive regulation of leukocyte adhesion to vascular endothelial cell / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / phagocytosis, engulfment / leukocyte cell-cell adhesion / receptor clustering / amyloid-beta clearance / endodermal cell differentiation / plasma membrane raft / tertiary granule membrane / ficolin-1-rich granule membrane / cellular response to low-density lipoprotein particle stimulus / positive regulation of protein targeting to membrane / Integrin cell surface interactions / specific granule membrane / phagocytosis / regulation of peptidyl-tyrosine phosphorylation / heat shock protein binding / receptor-mediated endocytosis / cell adhesion molecule binding / cell-matrix adhesion / neutrophil chemotaxis / positive regulation of superoxide anion generation / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / receptor internalization / cell-cell adhesion / extracellular vesicle / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell-cell signaling / amyloid-beta binding / regulation of cell shape / Interleukin-4 and Interleukin-13 signaling / receptor complex / cell adhesion / inflammatory response / external side of plasma membrane / focal adhesion / apoptotic process / Neutrophil degranulation / protein kinase binding / cell surface / signal transduction / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
Integrin beta-2 subunit / ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / ligand-binding face of the semaphorins, domain 2 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin beta subunit, tail ...Integrin beta-2 subunit / ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / ligand-binding face of the semaphorins, domain 2 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / 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 / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / 7 Propeller / Methylamine Dehydrogenase; Chain H / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Integrin beta-2 / Integrin alpha-L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsSen, M. / Springer, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Leukocyte integrin alpha L beta 2 headpiece structures: The alpha I domain, the pocket for the internal ligand, and concerted movements of its loops.
Authors: Sen, M. / Springer, T.A.
History
DepositionOct 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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 beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,64912
Polymers144,7412
Non-polymers90810
Water11,782654
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-65 kcal/mol
Surface area43730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.980, 154.980, 115.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Integrin alpha-L / CD11 antigen-like family member A / Leukocyte adhesion glycoprotein LFA-1 alpha chain / LFA-1A / ...CD11 antigen-like family member A / Leukocyte adhesion glycoprotein LFA-1 alpha chain / LFA-1A / Leukocyte function-associated molecule 1 alpha chain


Mass: 87841.086 Da / Num. of mol.: 1 / Fragment: UNP residues 26-770
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAL, CD11A / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: P20701
#2: Protein Integrin beta-2 / Cell surface adhesion glycoproteins LFA-1/CR3/p150 / 95 subunit beta / Complement receptor C3 subunit beta


Mass: 56899.809 Da / Num. of mol.: 1 / Fragment: UNP residues 23-482
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB2, CD18, MFI7 / Cell line (production host): HEK / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P05107

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Sugars , 1 types, 3 molecules

#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 661 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 654 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Mg-formate dehydrate and 15% PEG 3350 / PH range: 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 18, 2012
RadiationCollimation: ?en / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 54239 / % possible obs: 99.5 % / Redundancy: 5.2 % / Net I/σ(I): 6.2

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
RefinementResolution: 2.5→46.443 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 1645 3.03 %Random selection
Rwork0.1789 ---
obs0.1802 54232 99.53 %-
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→46.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7987 0 49 654 8690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078350
X-RAY DIFFRACTIONf_angle_d0.76211374
X-RAY DIFFRACTIONf_dihedral_angle_d15.6775018
X-RAY DIFFRACTIONf_chiral_restr0.0471241
X-RAY DIFFRACTIONf_plane_restr0.0041492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.57370.38631350.3724220X-RAY DIFFRACTION97
2.5737-2.65680.32831380.32184349X-RAY DIFFRACTION99
2.6568-2.75170.34711390.29154393X-RAY DIFFRACTION100
2.7517-2.86190.30831370.2544358X-RAY DIFFRACTION100
2.8619-2.99210.27891410.22274383X-RAY DIFFRACTION100
2.9921-3.14980.29941310.21224378X-RAY DIFFRACTION100
3.1498-3.34710.28271410.19254398X-RAY DIFFRACTION100
3.3471-3.60550.22451390.16264420X-RAY DIFFRACTION100
3.6055-3.96810.19491360.14944382X-RAY DIFFRACTION100
3.9681-4.54190.15361340.11684414X-RAY DIFFRACTION100
4.5419-5.72070.15161380.11464436X-RAY DIFFRACTION100
5.7207-46.45130.1841360.15664456X-RAY DIFFRACTION99
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)
10.28970.3378-0.08510.4257-0.10070.26220.15110.0198-0.0805-0.1417-0.08750.0490.2948-0.5021-00.35060.0176-0.05590.4605-0.07370.3838-4.0374-62.9863-5.5545
20.36720.2744-0.15321.2145-0.3025-0.0170.0899-0.0682-0.03280.0781-0.09790.1555-0.0295-0.2768-0.00010.30360.0075-0.00040.3989-0.03240.3211.436-68.592814.3718
30.94610.3414-0.3110.9825-0.35660.82530.2109-0.33050.04420.3779-0.192-0.0637-0.04470.08220.00010.3606-0.0291-0.03050.3385-0.00070.26697.3757-79.145146.2077
4-0.03270.5122-0.08150.6612-0.86830.82340.05370.0535-0.0861-0.0522-0.1496-0.1813-0.09220.2115-0.0010.30240.03820.00390.32350.02870.382412.7213-78.793831.2489
50.156-0.4394-0.05560.4548-0.2690.44640.02370.0116-0.0666-0.0108-0.1085-0.13810.0945-0.0676-0.00010.3010.0235-0.00860.2887-0.0350.35816.7208-72.999910.1274
60.9445-0.44420.10.8665-0.06221.98710.06670.1869-0.0643-0.2299-0.051-0.04180.04530.0188-0.00010.30740.02990.01170.3122-0.05980.299516.2183-66.4625-8.5092
70.37860.29850.27440.33840.3560.30960.36750.1209-0.6145-0.4924-0.8665-0.27680.133-1.02150.01820.53310.17520.01760.8932-0.0720.53934.7981-47.0438-48.0115
8-0.03640.2539-0.37110.0849-0.17320.25690.20980.309-0.094-0.4271-0.3971-0.0809-0.7282-0.8116-0.00040.61250.2585-0.03830.7081-0.04610.404138.4947-40.0795-42.7837
90.74310.09750.10350.70510.18450.02410.2599-0.12220.2113-0.0359-0.11540.082-0.19130.26410.00010.4282-0.03450.05540.272-0.0670.387830.0249-29.36029.1797
100.00360.0971-0.07030.05110.05460.08580.0173-0.07930.18180.18430.01550.3865-0.619-0.07650.00010.373-0.01220.06540.3581-0.06320.361211.3985-45.315824.5022
110.73440.5501-0.70391.03660.04780.49260.03730.04540.1209-0.00840.03280.0679-0.1378-0.0507-0.00010.28890.01180.00520.2412-0.01840.341520.6257-38.73578.2595
120.292-0.0515-0.8374-0.0680.19760.94640.10.235-0.00920.1171-0.0223-0.09770.4498-0.207-0.00010.4556-0.05760.01990.4457-0.09160.410637.4875-38.119-12.9418
130.18970.4487-0.26590.7753-0.77221.24930.59310.30450.0592-0.0729-0.227-0.1128-0.8723-0.77380.0680.47990.4854-0.03630.7931-0.09780.370630.6601-33.2066-30.7815
140.0052-0.00220.00820.03680.0269-0.0074-0.3945-0.2128-0.25030.1994-0.09690.3763-0.1065-0.2797-0.00020.91310.3776-0.14931.131-0.12910.914727.4074-36.9782-63.3743
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 248 )
4X-RAY DIFFRACTION4chain 'A' and (resid 249 through 326 )
5X-RAY DIFFRACTION5chain 'A' and (resid 327 through 393 )
6X-RAY DIFFRACTION6chain 'A' and (resid 394 through 591 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 27 )
8X-RAY DIFFRACTION8chain 'B' and (resid 28 through 90 )
9X-RAY DIFFRACTION9chain 'B' and (resid 91 through 149 )
10X-RAY DIFFRACTION10chain 'B' and (resid 150 through 181 )
11X-RAY DIFFRACTION11chain 'B' and (resid 182 through 329 )
12X-RAY DIFFRACTION12chain 'B' and (resid 330 through 401 )
13X-RAY DIFFRACTION13chain 'B' and (resid 402 through 431 )
14X-RAY DIFFRACTION14chain 'B' and (resid 432 through 459 )

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