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- PDB-5zaz: Solution structure of integrin b2 monomer tranmembrane domain in ... -

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Basic information

Entry
Database: PDB / ID: 5zaz
TitleSolution structure of integrin b2 monomer tranmembrane domain in bicelle
ComponentsIntegrin beta-2
KeywordsCELL ADHESION / integrin b2 / protein-lipid interaction / phospholipids / Ca2+
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 / cell adhesion mediated by integrin / leukocyte cell-cell adhesion / phagocytosis, engulfment / amyloid-beta clearance / endodermal cell differentiation / receptor clustering / 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 / cell adhesion molecule binding / heat shock protein binding / receptor-mediated endocytosis / neutrophil chemotaxis / cell-matrix adhesion / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / extracellular vesicle / 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 / Cytochrome c1, transmembrane anchor, C-terminal / 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-2 subunit / Cytochrome c1, transmembrane anchor, C-terminal / 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 / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / 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 / torsion angle dynamics
AuthorsLi, H. / Guo, J. / Xu, C.
Funding support China, 12items
OrganizationGrant numberCountry
NSFC31470734 China
NSFC31670751 China
MOST2014CB541903 China
CAS Key Research Program of Frontier SciencesQYZDB-SSW-SMC048 China
CAS Facility-based Open Research Program China
NSFC Innovative Research Group31621003 China
NSFC Key Program31530022 China
Ten Thousand Talent Program National Program for Support of Top-notch Young Professionals of China China
STSMC Key Program16JC1404800 China
NSFC National Science Fund for Distinguished Young Scholars31425009 China
STSMC Outstanding Academic Leader Program15XD1504200 China
CAS Strategic Priority Research ProgramXDB08020100 China
CitationJournal: PLoS Biol. / Year: 2018
Title: Intramembrane ionic protein-lipid interaction regulates integrin structure and function.
Authors: Guo, J. / Zhang, Y. / Li, H. / Chu, H. / Wang, Q. / Jiang, S. / Li, Y. / Shen, H. / Li, G. / Chen, J. / Xu, C.
History
DepositionFeb 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)5,6481
Polymers5,6481
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5620 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

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


Mass: 5647.616 Da / Num. of mol.: 1 / Mutation: C695S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB2, CD18, MFI7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05107

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D 1H-15N NOESY
121isotropic23D 1H-13C NOESY aliphatic
131isotropic23D 1H-13C NOESY aromatic
141isotropic13D HNCA
151isotropic13D HN(CA)CB
161isotropic13D CBCA(CO)NH
171isotropic13D HNCO
181isotropic12D 1H-15N HSQC
191isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: bicelle
Contents: 0.6 mM [U-13C; U-15N] integrin b2, 20 mM Bis-Tris, 240 mM DHPC, 48 mM POPC, 24 mM POPG, 90% H2O/10% D2O
Label: 13C15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMintegrin b2[U-13C; U-15N]1
20 mMBis-Trisnatural abundance1
240 mMDHPCnatural abundance1
48 mMPOPCnatural abundance1
24 mMPOPGnatural abundance1
1 %Protease inhibitor cocktailnatural abundance1
0.2 %NaN3natural abundance1
Sample conditionsIonic strength: 20 mM / Label: conditions_1 / pH: 6.7 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III9002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert P.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
KUJIRAKobayashi N.chemical shift assignment
KUJIRAKobayashi N.peak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
NMRViewJohnson, One Moon Scientificdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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