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- PDB-2k8o: Solution structure of integrin Alpha L -

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Basic information

Entry
Database: PDB / ID: 2k8o
TitleSolution structure of integrin Alpha L
ComponentsIntegrin alpha-L
KeywordsCELL ADHESION / Integrin / Alpha L / Beta 2 / Beta 3 / Alternative splicing / Calcium / Glycoprotein / Magnesium / Membrane / Polymorphism / 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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2120 / Integrin alpha cytoplasmic region / 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. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2120 / Integrin alpha cytoplasmic region / 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 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsBhunia, A. / Bhattacharjya, S. / Tan, S.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: NMR Solution Conformations and Interactions of Integrin {alpha}L{beta}2 Cytoplasmic Tails
Authors: Bhunia, A. / Tang, X.-Y. / Mohanram, H. / Tan, S.-M. / Bhattacharjya, S.
History
DepositionSep 17, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 24, 2018Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Source and taxonomy
Category: entity_src_gen / pdbx_nmr_sample_details ...entity_src_gen / pdbx_nmr_sample_details / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_nmr_sample_details.contents
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrin alpha-L


Theoretical massNumber of molelcules
Total (without water)6,2601
Polymers6,2601
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4090 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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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: 6259.923 Da / Num. of mol.: 1 / Fragment: Cytoplasmic / Mutation: M14I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20701

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCA
1513D HN(CO)CA
1613D 1H-15N TOCSY
1713D 1H-15N NOESY

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Sample preparation

DetailsContents: 0.5 mM [U-15N;U-13C] aL, % NaCl, % TCEP, % Phosphate buffer, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingSolution-ID
0.5 mMaL[U-15N;U-13C]1
%NaCl1
%TCEP1
%Phosphate buffer1
Sample conditionspH: 6.2 / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR softwareName: DYANA / Version: 1.5 / Developer: Guntert, Braun and Wuthrich / Classification: refinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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