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- PDB-9ecl: Structure of the human integrin beta2 transmembrane domain -

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Basic information

Entry
Database: PDB / ID: 9ecl
TitleStructure of the human integrin beta2 transmembrane domain
ComponentsIntegrin beta-2
KeywordsCELL ADHESION / Integrin / receptor
Function / homology
Function and homology information


integrin alphaX-beta2 complex / positive regulation of neutrophil degranulation / cellular extravasation / integrin alphaM-beta2 complex / integrin alphaL-beta2 complex / ICAM-3 receptor activity / : / complement component C3b binding / Toll Like Receptor 4 (TLR4) Cascade / leukocyte migration involved in inflammatory response ...integrin alphaX-beta2 complex / positive regulation of neutrophil degranulation / cellular extravasation / integrin alphaM-beta2 complex / integrin alphaL-beta2 complex / ICAM-3 receptor activity / : / complement component C3b binding / Toll Like Receptor 4 (TLR4) Cascade / leukocyte migration involved in inflammatory response / neutrophil migration / positive regulation of leukocyte adhesion to vascular endothelial cell / 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 / 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 / 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 / extracellular exosome / metal ion binding / membrane / plasma membrane
Similarity search - Function
Integrin beta-2 subunit / 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 / Integrins beta chain EGF (I-EGF) domain profile. ...Integrin beta-2 subunit / 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 / 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) / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsUlmer, T.S. / Vu, H.N. / Situ, A.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG072442 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Functional unfolding of the integrin alpha X transmembrane helix
Authors: Vu, H.N. / Lee, M. / Situ, A.J. / An, W. / Ley, K. / Kim, C. / Ulmer, T.S.
History
DepositionNov 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrin beta-2


Theoretical massNumber of molelcules
Total (without water)4,4291
Polymers4,4291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 21all calculated structures submitted
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Integrin beta-2 / Cell surface adhesion glycoproteins LFA-1/CR3/p150 / 95 subunit beta / Complement receptor C3 subunit beta


Mass: 4429.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB2, CD18, MFI7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P05107
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic13D HN(CA)CB
131isotropic13D HNCO
141isotropic13D HN(CA)CO
151isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: bicelle
Contents: 1.2 mM [U-100% 13C; U-100% 15N; U-80% 2H] alphaX peptide, 350 mM 1,2-dihexanoyl-sn-glycero-3-phosphoholine, 105 mM 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 25 mM HEPES, 95% H2O/5% D2O
Label: 2H13C15N_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMalphaX peptide[U-100% 13C; U-100% 15N; U-80% 2H]1
350 mM1,2-dihexanoyl-sn-glycero-3-phosphoholinenone1
105 mM1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholinenone1
25 mMHEPESnone1
Sample conditionsIonic strength: 0.025 M / Label: condition 1 / pH: 7.4 pH* / Pressure: 1 atm / Temperature: 313.2 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 21 / Conformers submitted total number: 21

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