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- PDB-2kjx: Solution structure of the extracellular domain of JTB -

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Basic information

Entry
Database: PDB / ID: 2kjx
TitleSolution structure of the extracellular domain of JTB
ComponentsJumping translocation breakpoint protein
KeywordsMEMBRANE PROTEIN / cysteine-rich domain / Membrane / Transmembrane
Function / homology
Function and homology information


microtubule organizing center / plasma membrane => GO:0005886 / mitotic cytokinesis / positive regulation of protein kinase activity / spindle / mitotic cell cycle / midbody / apoptotic process / protein kinase binding / mitochondrion ...microtubule organizing center / plasma membrane => GO:0005886 / mitotic cytokinesis / positive regulation of protein kinase activity / spindle / mitotic cell cycle / midbody / apoptotic process / protein kinase binding / mitochondrion / membrane / cytoplasm
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 - #220 / Jumping translocation breakpoint / Jumping translocation breakpoint protein (JTB) / Signal recognition particle alu RNA binding heterodimer, srp9/1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsRousseau, F. / Lingel, A. / Pan, B. / Fairbrother, W.J. / Bazan, F.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: The structure of the extracellular domain of the jumping translocation breakpoint protein reveals a variation of the midkine fold.
Authors: Rousseau, F. / Pan, B. / Fairbrother, W.J. / Bazan, J.F. / Lingel, A.
History
DepositionJun 10, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 23, 2011Group: Database references
Revision 1.3Apr 18, 2012Group: Database references
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Jumping translocation breakpoint protein


Theoretical massNumber of molelcules
Total (without water)7,2971
Polymers7,2971
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Jumping translocation breakpoint protein / / Protein JTB / Prostate androgen-regulated protein / PAR protein


Mass: 7297.307 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 47-104)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JTB / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: O76095

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1332D 1H-1H NOESY
1423D HNCA
1523D CBCA(CO)NH
1623D HN(CA)CB
1723D HNHA
1823D HNHB
1923D H(CCO)NH
11023D C(CO)NH
11123D (H)CCH-TOCSY
11223D 1H-15N NOESY
11323D 1H-13C NOESY
11423D HBHA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] JTB, 50 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] JTB, 50 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31 mM JTB, 50 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMJTB-1[U-100% 15N]1
50 mMsodium phosphate-21
150 mMsodium chloride-31
0.1 mMsodium azide-41
1 mMJTB-5[U-100% 13C; U-100% 15N]2
50 mMsodium phosphate-62
150 mMsodium chloride-72
0.1 mMsodium azide-82
1 mMJTB-93
50 mMsodium phosphate-103
150 mMsodium chloride-113
0.1 mMsodium azide-123
Sample conditionsIonic strength: 0.2 / pH: 5.6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameDeveloperClassification
TOPSPINBrukercollection
CCPNCCPNdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Distance restraints were derived from 15N- or 13C-resolved 3D NOESY experiments and a 2D homonuclear 1H NOESY experiment. Restraints for the backbone angles phi and psi were derived from ...Details: Distance restraints were derived from 15N- or 13C-resolved 3D NOESY experiments and a 2D homonuclear 1H NOESY experiment. Restraints for the backbone angles phi and psi were derived from 3J(HN,Ha) coupling constants and TALOS. Stereospecific assignments of Leu, Val methyl groups were obtained using a 10% fractionally 13C-labeled sample. For the definition of H-bonds, slowly exchanging amide protons were identified from 1H, 15N correlation experiments after redissolving lyophilized protein in D2O.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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