[English] 日本語
Yorodumi
- PDB-5e6u: Structures of leukocyte integrin aLb2: The aI domain, the headpie... -

+
Open data


ID or keywords:

Loading...

-
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 / memory T cell extravasation / cellular extravasation / positive regulation of neutrophil degranulation / 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 / cell-cell adhesion via plasma-membrane adhesion molecules / complement component C3b binding ...integrin alphaX-beta2 complex / memory T cell extravasation / cellular extravasation / positive regulation of neutrophil degranulation / 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 / cell-cell adhesion via plasma-membrane adhesion molecules / complement component C3b binding / negative regulation of dopamine metabolic process / Toll Like Receptor 4 (TLR4) Cascade / neutrophil migration / leukocyte migration involved in inflammatory response / RUNX3 Regulates Immune Response and Cell Migration / positive regulation of leukocyte adhesion to vascular endothelial cell / integrin complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / heterotypic cell-cell adhesion / regulation of peptidyl-tyrosine phosphorylation / leukocyte cell-cell adhesion / phagocytosis, engulfment / cell adhesion mediated by integrin / receptor clustering / endodermal cell differentiation / amyloid-beta clearance / tertiary granule membrane / cellular response to low-density lipoprotein particle stimulus / ficolin-1-rich granule membrane / plasma membrane raft / positive regulation of protein targeting to membrane / Integrin cell surface interactions / phagocytosis / endothelial cell migration / specific granule membrane / cell adhesion molecule binding / heat shock protein binding / neutrophil chemotaxis / receptor-mediated endocytosis / positive regulation of superoxide anion generation / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / cell-cell adhesion / receptor internalization / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of nitric oxide biosynthetic process / integrin binding / 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 subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / 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 subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrins beta chain EGF (I-EGF) domain profile. / Integrin alpha cytoplasmic region / 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) / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / 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 / 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 / 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
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Sugars , 1 types, 3 molecules

#6: 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.: 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

-
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


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


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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more