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- PDB-2j5h: NMR analysis of mouse CRIPTO CFC domain -

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Basic information

Entry
Database: PDB / ID: 2j5h
TitleNMR analysis of mouse CRIPTO CFC domain
ComponentsTERATOCARCINOMA-DERIVED GROWTH FACTOR
KeywordsHORMONE/GROWTH FACTOR / GROWTH FACTOR / EGF-CFC FAMILY / CRIPTO / TUMOUR PROGRESSION / CYSTEINE-RICH DOMAINS / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


type I activin receptor binding / nodal binding / : / morphogenesis of a branching structure / nodal signaling pathway / anatomical structure development / : / anterior/posterior axis specification, embryo / activin receptor binding / Wnt-protein binding ...type I activin receptor binding / nodal binding / : / morphogenesis of a branching structure / nodal signaling pathway / anatomical structure development / : / anterior/posterior axis specification, embryo / activin receptor binding / Wnt-protein binding / cardiac muscle cell differentiation / cellular response to interleukin-6 / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis / determination of left/right symmetry / anterior/posterior axis specification / anterior/posterior pattern specification / positive regulation of cell-matrix adhesion / cellular response to hepatocyte growth factor stimulus / extrinsic component of plasma membrane / blood vessel development / regulation of signal transduction / vasculogenesis / coreceptor activity / gastrulation / regulation of cell migration / cellular response to epidermal growth factor stimulus / positive regulation of endothelial cell migration / negative regulation of transforming growth factor beta receptor signaling pathway / growth factor activity / cellular response to type II interferon / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / cellular response to tumor necrosis factor / heart development / peptidyl-serine phosphorylation / in utero embryonic development / cell differentiation / positive regulation of cell migration / membrane raft / apical plasma membrane / signaling receptor binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Teratocarcinoma-derived growth factor Cripto / Cryptic/Cripto, CFC domain / Cripto_Frl-1_Cryptic (CFC) / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain
Similarity search - Domain/homology
Teratocarcinoma-derived growth factor
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodSOLUTION NMR
AuthorsCalvanese, L. / Saporito, A. / Marasco, D. / D'Auria, G. / Minchiotti, G. / Pedone, C. / Paolillo, L. / Falcigno, L. / Ruvo, M.
CitationJournal: J. Med. Chem. / Year: 2006
Title: Solution structure of mouse Cripto CFC domain and its inactive variant Trp107Ala.
Authors: Calvanese, L. / Saporito, A. / Marasco, D. / D'Auria, G. / Minchiotti, G. / Pedone, C. / Paolillo, L. / Falcigno, L. / Ruvo, M.
History
DepositionSep 18, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 9, 2018Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TERATOCARCINOMA-DERIVED GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)4,4661
Polymers4,4661
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)10 / 100LEAST RESTRAINT VIOLATION AND ENERGY
RepresentativeModel #1

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Components

#1: Protein/peptide TERATOCARCINOMA-DERIVED GROWTH FACTOR / CRIPTO / EPIDERMAL GROWTH FACTOR-LIKE CRIPTO PROTEIN / CRIPTO GROWTH FACTOR


Mass: 4466.311 Da / Num. of mol.: 1 / Fragment: CRIPTO DOMAIN, RESIDUES 96-134 / Source method: obtained synthetically / Details: THREE DISULFIDE BRIDGES / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: P51865

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TOCSY
121NOESY
131DQFCOSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 2D NMR ON UNLABELLED SAMPLE

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Sample preparation

DetailsContents: 90%WATER/10%D2O
Sample conditionspH: 6.0 / Temperature: 298.0 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
AMBERCASE,PEARLMAN,ET. AL.refinement
NMRVIEW;DYANA;AMBERstructure solution
RefinementSoftware ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JOURNAL CITATION ABOVE
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION AND ENERGY
Conformers calculated total number: 100 / Conformers submitted total number: 10

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