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- PDB-2jp2: Solution structure and resonance assignment of the N-terminal EVH... -

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Basic information

Entry
Database: PDB / ID: 2jp2
TitleSolution structure and resonance assignment of the N-terminal EVH1 domain from the human Spred2 protein (Sprouty-related protein with EVH1 domain isoform 2)
ComponentsSprouty-related, EVH1 domain-containing protein 2
KeywordsSIGNALING PROTEIN / EVH1 domain / solution structure / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of protein deacetylation / negative regulation of lens fiber cell differentiation / stem cell factor receptor binding / FGFRL1 modulation of FGFR1 signaling / positive regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of epithelial to mesenchymal transition / protein serine/threonine kinase inhibitor activity / transport vesicle membrane / negative regulation of MAPK cascade / negative regulation of peptidyl-threonine phosphorylation ...regulation of protein deacetylation / negative regulation of lens fiber cell differentiation / stem cell factor receptor binding / FGFRL1 modulation of FGFR1 signaling / positive regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of epithelial to mesenchymal transition / protein serine/threonine kinase inhibitor activity / transport vesicle membrane / negative regulation of MAPK cascade / negative regulation of peptidyl-threonine phosphorylation / RAS signaling downstream of NF1 loss-of-function variants / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / Regulation of RAS by GAPs / protein kinase binding / plasma membrane / cytosol
Similarity search - Function
c-Kit-binding domain / SPRE, EVH1 domain / KBD domain profile. / Sprouty / Sprouty protein (Spry) / Sprouty (SPR) domain profile. / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 ...c-Kit-binding domain / SPRE, EVH1 domain / KBD domain profile. / Sprouty / Sprouty protein (Spry) / Sprouty (SPR) domain profile. / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Sprouty-related, EVH1 domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsSolution structure determination and 1H, 13C, 15N resonance assignments of the human Spred2 EVH1 ...Solution structure determination and 1H, 13C, 15N resonance assignments of the human Spred2 EVH1 domain (residues GS-(1-124))
AuthorsFossi, M. / Zimmermann, J. / Jarchau, T. / Lemak, A. / Walter, U. / Wiegelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Oschkinat, H. ...Fossi, M. / Zimmermann, J. / Jarchau, T. / Lemak, A. / Walter, U. / Wiegelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Oschkinat, H. / Ball, L.J. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biomol.NMR / Year: 2004
Title: 1H, 13C and 15N resonance assignment of the human Spred2 EVH1 domain
Authors: Zimmermann, J. / Jarchau, T. / Walter, U. / Oschkinat, H. / Ball, L.J.
History
DepositionApr 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.6May 8, 2024Group: Database references / Category: 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: Sprouty-related, EVH1 domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)14,2171
Polymers14,2171
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 Sprouty-related, EVH1 domain-containing protein 2 / Spred-2


Mass: 14217.053 Da / Num. of mol.: 1 / Fragment: EVH1/WH1 domain, sequence database residues 1-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPRED2 / Production host: Escherichia coli (E. coli) / Strain (production host): B / Variant (production host): BL21 (DE3) / References: UniProt: Q7Z698

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure determination and 1H, 13C, 15N resonance assignments of the human Spred2 EVH1 domain (residues GS-(1-124))
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D CBCA(CO)NH
1323D CBCANH
1423D H(CCO)NH
1523D C(CO)NH
1623D HNCO
1733D (H)CCH-TOCSY
1813D HNHA
1913D HNHB
11042D 1H-1H TOCSY
11142D DQF-COSY
11242D 1H-1H NOESY
11313D 1H-15N NOESY
11423D 1H-13C NOESY
11533D 1H-13C NOESY
11612D 3JHNHa series
11712D 15N T1 series
11812D 15N T2 series

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] Spred2 EVH1, 20 mM sodium phosphate, 50 mM sodium chloride, 0.1 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] Spred2 EVH1, 20 mM sodium phosphate, 50 mM sodium chloride, 0.1 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 13C; U-100% 15N] Spred2 EVH1, 20 mM sodium phosphate, 50 mM sodium chloride, 0.1 % sodium azide, 100% D2O100% D2O
41 mM [U-100% 15N] Spred2 EVH1, 20 mM sodium phosphate, 50 mM sodium chloride, 0.1 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSpred2 EVH1[U-100% 15N]1
20 mMsodium phosphate1
50 mMsodium chloride1
0.1 %sodium azide1
1 mMSpred2 EVH1[U-100% 13C; U-100% 15N]2
20 mMsodium phosphate2
50 mMsodium chloride2
0.1 %sodium azide2
1 mMSpred2 EVH1[U-100% 13C; U-100% 15N]3
20 mMsodium phosphate3
50 mMsodium chloride3
0.1 %sodium azide3
1 mMSpred2 EVH1[U-100% 15N]4
20 mMsodium phosphate4
50 mMsodium chloride4
0.1 %sodium azide4
Sample conditionsIonic strength: 0.05 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
XWIN-NMR2.6Bruker Biospincollection
ANSIG3.3Kraulisdata analysis
ANSIG3.3Kraulischemical shift assignment
ANSIG3.3Kraulispeak picking
ANSIG3.3Kraulisintegration
Azara2.1Boucherdata analysis
Azara2.1Boucherpeak picking
PSVS1.3Hang, Montelione, et al.refinement
PSVS1.3Hang, Montelione, et al.structure validation
X-PLOR NIH2.14Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.14Schwieters, Kuszewski, Tjandra and Clorerefinement
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: Manual structure refinement, Refinement in explicit water
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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