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- PDB-1l3y: INTEGRIN EGF-LIKE MODULE 3 FROM THE BETA-2 SUBUNIT -

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Basic information

Entry
Database: PDB / ID: 1l3y
TitleINTEGRIN EGF-LIKE MODULE 3 FROM THE BETA-2 SUBUNIT
ComponentsIntegrin beta-2:CYSTEINE-RICH MODULE 3
KeywordsCELL ADHESION / integrin / beta-2 subunit / cysteine-rich module / EGF-like module
Function / homology
Function and homology information


integrin alphaX-beta2 complex / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / complement component C3b binding / neutrophil migration / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of dopamine metabolic process ...integrin alphaX-beta2 complex / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation / integrin alphaL-beta2 complex / 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 / heterotypic cell-cell adhesion / integrin complex / positive regulation of leukocyte adhesion to vascular endothelial cell / leukocyte cell-cell adhesion / phagocytosis, engulfment / 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 / 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 / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
Integrin beta-2 subunit / 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-2 subunit / 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 domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / Laminin / Laminin / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBeglova, N. / Blacklow, S.C. / Takagi, J. / Springer, T.A.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Cysteine-rich module structure reveals a fulcrum for integrin rearrangement upon activation.
Authors: Beglova, N. / Blacklow, S.C. / Takagi, J. / Springer, T.A.
History
DepositionMar 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrin beta-2:CYSTEINE-RICH MODULE 3


Theoretical massNumber of molelcules
Total (without water)4,3331
Polymers4,3331
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with acceptable covalent geometry,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Integrin beta-2:CYSTEINE-RICH MODULE 3 / Cell surface adhesion glycoproteins LFA-1/CR3/p150 / 95 / CD18 / beta-subunit / Complement receptor ...Cell surface adhesion glycoproteins LFA-1/CR3/p150 / 95 / CD18 / beta-subunit / Complement receptor C3 beta-subunit


Mass: 4332.906 Da / Num. of mol.: 1 / Fragment: RESIDUES 535-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P05107

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 15N-separated TOCSY
131HMQC-J
1421H-NOESY
1521H-TOCSY
162DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM I-EGF3 U-15N, 5 mM NaPO490% H2O/10% D2O
21 mM I-EGF3, 5 mM NaPO4100% D2O
Sample conditionsIonic strength: 5mM NaPO4 / pH: 6.2 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Gifa4.3Delsuc, M.A.processing
XEASY1.3.13Wuthrich, K.data analysis
CNS1Brunger, Astructure solution
CNS1Brunger, Arefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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