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- PDB-5e6r: Structures of leukocyte integrin aLb2: The aI domain, the headpie... -

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Basic information

Entry
Database: PDB / ID: 5e6r
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 / memory T cell extravasation / positive regulation of neutrophil degranulation / cellular extravasation / integrin alphaM-beta2 complex / 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 / : / complement component C3b binding ...integrin alphaX-beta2 complex / memory T cell extravasation / positive regulation of neutrophil degranulation / cellular extravasation / integrin alphaM-beta2 complex / 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 / : / complement component C3b binding / Toll Like Receptor 4 (TLR4) Cascade / leukocyte migration involved in inflammatory response / neutrophil migration / RUNX3 Regulates Immune Response and Cell Migration / positive regulation of leukocyte adhesion to vascular endothelial cell / heterophilic cell-cell adhesion / integrin complex / heterotypic cell-cell adhesion / regulation of peptidyl-tyrosine phosphorylation / leukocyte cell-cell adhesion / phagocytosis, engulfment / cell adhesion mediated by integrin / negative regulation of dopamine metabolic process / receptor clustering / endodermal cell differentiation / amyloid-beta clearance / tertiary granule membrane / plasma membrane raft / cellular response to low-density lipoprotein particle stimulus / ficolin-1-rich granule membrane / positive regulation of protein targeting to membrane / phagocytosis / Integrin cell surface interactions / endothelial cell migration / specific granule membrane / positive regulation of superoxide anion generation / cell adhesion molecule binding / heat shock protein binding / neutrophil chemotaxis / receptor-mediated endocytosis / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / cell-cell adhesion / receptor internalization / integrin binding / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of nitric oxide biosynthetic process / cell-cell signaling / extracellular vesicle / regulation of cell shape / amyloid-beta binding / 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 / metal ion binding / membrane / plasma membrane
Similarity search - Function
Integrin beta-2 subunit / ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / ligand-binding face of the semaphorins, domain 2 / Integrin alpha, N-terminal / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin EGF domain ...Integrin beta-2 subunit / ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / ligand-binding face of the semaphorins, domain 2 / Integrin alpha, N-terminal / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin alpha cytoplasmic region / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / 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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / MOLECULAR REPLACEMENT / Resolution: 2.901 Å
AuthorsSen, M. / Springer, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)NCI CA031798 United States
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 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Jul 20, 2016Group: Data collection
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _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 / _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
Revision 1.7Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.8Oct 30, 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
A: Integrin alpha-L
B: Integrin beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,81011
Polymers144,7412
Non-polymers1,0699
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-27 kcal/mol
Surface area43880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.929, 153.929, 116.454
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 26-615
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 / Mutation: N232R
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, 4 molecules

#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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 , 3 types, 211 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.5, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03321 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 33981 / % possible obs: 99.9 % / Redundancy: 3.11 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 9.47

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4neh

4neh


Resolution: 2.901→46.242 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 24.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 2737 8.05 %Random selection
Rwork0.1928 ---
obs0.1957 33981 97.71 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.901→46.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7946 0 61 206 8213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128267
X-RAY DIFFRACTIONf_angle_d0.78811249
X-RAY DIFFRACTIONf_dihedral_angle_d16.0924946
X-RAY DIFFRACTIONf_chiral_restr0.0481235
X-RAY DIFFRACTIONf_plane_restr0.0041477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9013-2.95130.39341170.37441294X-RAY DIFFRACTION82
2.9513-3.0050.35861230.361430X-RAY DIFFRACTION89
3.005-3.06270.41751380.35851523X-RAY DIFFRACTION94
3.0627-3.12520.34231340.32871515X-RAY DIFFRACTION98
3.1252-3.19320.34571380.30321585X-RAY DIFFRACTION100
3.1932-3.26740.31411390.27961600X-RAY DIFFRACTION100
3.2674-3.34910.30321420.23891592X-RAY DIFFRACTION100
3.3491-3.43970.24691420.22931608X-RAY DIFFRACTION100
3.4397-3.54080.2491410.2151573X-RAY DIFFRACTION100
3.5408-3.65510.25041360.20161599X-RAY DIFFRACTION100
3.6551-3.78570.23331390.19311598X-RAY DIFFRACTION100
3.7857-3.93720.22421400.17971602X-RAY DIFFRACTION100
3.9372-4.11620.18811440.16571574X-RAY DIFFRACTION100
4.1162-4.33310.19721340.16311601X-RAY DIFFRACTION100
4.3331-4.60440.15461380.14631588X-RAY DIFFRACTION99
4.6044-4.95950.17611380.1431591X-RAY DIFFRACTION99
4.9595-5.45790.18981410.15211586X-RAY DIFFRACTION99
5.4579-6.2460.25251370.18021593X-RAY DIFFRACTION98
6.246-7.8630.22611330.18791582X-RAY DIFFRACTION98
7.863-46.24830.20421430.16871610X-RAY DIFFRACTION98
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)
11.45050.3537-0.93710.5388-0.74982.0407-0.10690.32140.04760.01550.1228-0.1371-0.0566-0.207200.61860.0265-0.08730.6868-0.05390.68765.778533.1985-26.6919
20.7989-0.1056-0.90171.0308-0.63820.808-0.01130.39090.0435-0.08310.0690.0632-0.0713-0.3797-0.00020.65010.0503-0.10470.7395-0.01080.743971.944723.1207-24.6704
31.698-0.6620.70260.96750.17153.0148-0.0914-0.0720.0829-0.0346-0.1648-0.22610.0680.4544-0.00010.5362-0.0223-0.09370.65790.02860.658571.2815.6301-4.1662
41.5049-0.7057-0.70131.5275-0.78791.5553-0.0432-0.36060.1270.5792-0.0042-0.2317-0.2995-0.0807-00.75990.0873-0.1380.6663-0.07780.587260.992222.676213.9866
50.15320.01210.2521-0.0150.00180.26120.2521-0.43490.4688-0.2682-1.1009-0.443-1.1458-0.4974-0.00520.9960.24370.04971.409-0.11671.120957.2305-6.136547.7858
61.1298-0.4441.06920.5063-0.84690.4562-0.208-0.47250.0884-0.12780.15330.13710.0073-0.6290.00040.5636-0.1263-0.01780.767-0.10280.703646.3241-12.240515.9542
70.77210.11770.2441.3565-0.66471.4164-0.1139-0.04720.0229-0.13430.21860.24230.1005-0.324900.5877-0.0598-0.05490.726-0.00840.711643.69763.4678-11.3064
80.3676-0.98861.04340.4503-0.70421.10860.0491-0.00150.01280.0610.4054-0.051-0.01720.4543-0.00020.6973-0.20670.03270.8986-0.07350.696751.404-13.802812.2792
90.37410.17050.0210.0754-0.01280.01380.1571-0.4317-0.34210.30920.4160.2644-0.9701-1.24420.00340.71160.1589-0.00091.16830.13140.7743.4999-9.852730.3572
101.0014-0.21160.98370.49460.21821.505-0.01610.04830.5642-1.2363-0.3978-0.4215-1.18080.6765-0.08131.59080.75720.07041.9026-0.15880.87944.0313-3.771861.999
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 281 )
2X-RAY DIFFRACTION2chain 'A' and (resid 282 through 342 )
3X-RAY DIFFRACTION3chain 'A' and (resid 343 through 478 )
4X-RAY DIFFRACTION4chain 'A' and (resid 479 through 590 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 27 )
6X-RAY DIFFRACTION6chain 'B' and (resid 28 through 149 )
7X-RAY DIFFRACTION7chain 'B' and (resid 150 through 328 )
8X-RAY DIFFRACTION8chain 'B' and (resid 329 through 401 )
9X-RAY DIFFRACTION9chain 'B' and (resid 402 through 431 )
10X-RAY DIFFRACTION10chain 'B' and (resid 432 through 459 )

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