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- PDB-2lkj: Structures and Interaction Analyses of the Integrin Alpha-M Beta-... -

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Entry
Database: PDB / ID: 2lkj
TitleStructures and Interaction Analyses of the Integrin Alpha-M Beta-2 Cytoplasmic Tails
ComponentsIntegrin alpha-M
KeywordsCELL ADHESION / MYRISTOYLATED / MAC-1 ALPHA / CYTOPLASMIC / SERINE PHOSPHORYLATED / DPC MICELLES
Function / homology
Function and homology information


ectodermal cell differentiation / positive regulation of prostaglandin-E synthase activity / response to curcumin / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / response to Gram-positive bacterium / positive regulation of microglial cell mediated cytotoxicity / complement component C3b binding / vertebrate eye-specific patterning / complement-mediated synapse pruning ...ectodermal cell differentiation / positive regulation of prostaglandin-E synthase activity / response to curcumin / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / response to Gram-positive bacterium / positive regulation of microglial cell mediated cytotoxicity / complement component C3b binding / vertebrate eye-specific patterning / complement-mediated synapse pruning / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of dopamine metabolic process / cell-cell adhesion via plasma-membrane adhesion molecules / complement receptor mediated signaling pathway / heterotypic cell-cell adhesion / integrin complex / cargo receptor activity / cell adhesion mediated by integrin / phagocytosis, engulfment / amyloid-beta clearance / plasma membrane raft / tertiary granule membrane / positive regulation of protein targeting to membrane / Integrin cell surface interactions / specific granule membrane / response to mechanical stimulus / forebrain development / heat shock protein binding / cell-matrix adhesion / receptor-mediated endocytosis / positive regulation of superoxide anion generation / response to ischemia / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / cell-cell adhesion / integrin binding / response to estradiol / amyloid-beta binding / Interleukin-4 and Interleukin-13 signaling / cell adhesion / external side of plasma membrane / innate immune response / Neutrophil degranulation / cell surface / extracellular space / extracellular exosome / metal ion binding / 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 Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site ...: / Integrin alpha-X-like, Ig-like domain 3 / 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 alpha, N-terminal / Integrin domain superfamily / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
Model detailslowest energy, model 1
AuthorsChua, G.L. / Tang, X.Y. / Amalraj, M. / Tan, S.M. / Bhattacharjya, S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structures and interaction analyses of the integrin alphaMbeta2 cytoplasmic tails
Authors: Chua, G.L. / Tang, X.Y. / Amalraj, M. / Tan, S.M. / Bhattacharjya, S.
History
DepositionOct 12, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrin alpha-M


Theoretical massNumber of molelcules
Total (without water)2,7831
Polymers2,7831
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Integrin alpha-M


Mass: 2783.078 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP residues 1129-1152 / Source method: obtained synthetically / Details: Peptide purchased from GL Biochem / Source: (synth.) Homo sapiens (human) / References: UniProt: P11215
Sequence detailsTHIS PEPTIDE IS CHEMICALLY SYNTHESIZED WITH A N-TERMINAL MYRISTATE GROUP AND SERINE 14 ...THIS PEPTIDE IS CHEMICALLY SYNTHESIZED WITH A N-TERMINAL MYRISTATE GROUP AND SERINE 14 PHOSPHORYLATED. THE CORRECT SEQUENCE IS (MYR)KLGFFKRQYKDMM(SEP)EGGPPGAEPQ, BUT N-TERMINAL MYR AND A PART OF PHOSPHATE GROUP IN SEP ARE MISSING.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-1H TOCSY
1222D 1H-1H NOESY
1312D 1H-1H NOESY
1412D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [1H] MYR-P-ALPHA-M-1, 200 mM [U-99% 2H] Dodecylphosphocholine-2, 10 mM sodium phosphate-3, 10 % [U-99% 2H] D2O-4, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM [1H] MYR-P-ALPHA-M-5, 200 mM [U-99% 2H] Dodecylphosphocholine-6, 10 mM sodium phosphate-7, 100 % [U-99% 2H] D2O-8, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMMYR-P-ALPHA-M-1[1H]1
200 mMDodecylphosphocholine-2[U-99% 2H]1
10 mMsodium phosphate-31
10 %D2O-4[U-99% 2H]1
0.7 mMMYR-P-ALPHA-M-5[1H]2
200 mMDodecylphosphocholine-6[U-99% 2H]2
10 mMsodium phosphate-72
100 %D2O-8[U-99% 2H]2
Sample conditionsIonic strength: 0 / pH: 5.6 / Pressure: ambient / Temperature: 308 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 software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TOPSPIN1.3Bruker Biospinprocessing
TOPSPIN1.3Bruker Biospincollection
SPARKY3.11Goddardchemical shift assignment
SPARKY3.11Goddarddata analysis
SPARKY3.11Goddardpeak picking
CYANArefinement
NMR constraintsNOE constraints total: 171 / NOE intraresidue total count: 36 / NOE long range total count: 8 / NOE medium range total count: 69 / NOE sequential total count: 58 / Protein chi angle constraints total count: 43 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 20 / Protein psi angle constraints total count: 23
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 7.11 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 8.89 ° / Maximum upper distance constraint violation: 0.46 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.1 Å

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