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- PDB-9ecm: Structure of the human integrin alphaX transmembrane domain -

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Basic information

Entry
Database: PDB / ID: 9ecm
TitleStructure of the human integrin alphaX transmembrane domain
ComponentsIntegrin alpha-X
KeywordsCELL ADHESION / Integrin / receptor
Function / homology
Function and homology information


integrin alphaX-beta2 complex / positive regulation of endothelial tube morphogenesis / positive regulation of myelination / integrin complex / heterotypic cell-cell adhesion / cell adhesion mediated by integrin / tertiary granule membrane / ficolin-1-rich granule membrane / ECM proteoglycans / Integrin cell surface interactions ...integrin alphaX-beta2 complex / positive regulation of endothelial tube morphogenesis / positive regulation of myelination / integrin complex / heterotypic cell-cell adhesion / cell adhesion mediated by integrin / tertiary granule membrane / ficolin-1-rich granule membrane / ECM proteoglycans / Integrin cell surface interactions / secretory granule membrane / animal organ morphogenesis / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cell-cell adhesion / receptor tyrosine kinase binding / integrin binding / positive regulation of angiogenesis / signaling receptor activity / Interleukin-4 and Interleukin-13 signaling / defense response to virus / cell adhesion / positive regulation of cell migration / external side of plasma membrane / positive regulation of cell population proliferation / Neutrophil degranulation / positive regulation of gene expression / cell surface / metal ion binding / membrane / plasma membrane
Similarity search - Function
: / Integrin alpha-X-like, Ig-like domain 3 / Integrin alpha cytoplasmic region / 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-X-like, Ig-like domain 3 / Integrin alpha cytoplasmic region / 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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
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
Revision 1.1Oct 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Integrin alpha-X


Theoretical massNumber of molelcules
Total (without water)4,6411
Polymers4,6411
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 / 26target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Integrin alpha-X / CD11 antigen-like family member C / Leu M5 / Leukocyte adhesion glycoprotein p150 / 95 alpha chain ...CD11 antigen-like family member C / Leu M5 / Leukocyte adhesion glycoprotein p150 / 95 alpha chain / Leukocyte adhesion receptor p150 / 95


Mass: 4640.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAX, CD11C
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P20702
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-dihexanoly-sn-glycero-3-phosphocholine, 105 mM 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 25 mM HEPES, 95% H2O/5% D2O
Label: 2H/13C/15N_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-dihexanoly-sn-glycero-3-phosphocholinenone1
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: target function / Conformers calculated total number: 26 / Conformers submitted total number: 21

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