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- PDB-2lx7: Solution NMR structure of SH3 domain of growth arrest-specific pr... -

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Basic information

Entry
Database: PDB / ID: 2lx7
TitleSolution NMR structure of SH3 domain of growth arrest-specific protein 7 (GAS7) (fragment 1-60) from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR8574A
ComponentsGrowth arrest-specific protein 7
KeywordsPROTEIN BINDING / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / Target HR8574A / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


actin filament polymerization / neuron projection morphogenesis / actin filament / actin filament binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Unstructured linker region between on GAS7 protein / GAS7, F-BAR domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Variant SH3 domain / WW domain ...Unstructured linker region between on GAS7 protein / GAS7, F-BAR domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Variant SH3 domain / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Growth arrest-specific protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsYang, Y. / Ramelot, T.A. / Dan, L. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of SH3 domain of growth arrest-specific protein 7 (GAS7) (fragment 1-60) from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR8574A
Authors: Yang, Y. / Ramelot, T.A. / Dan, L. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionAug 15, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2May 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: Growth arrest-specific protein 7


Theoretical massNumber of molelcules
Total (without water)6,7191
Polymers6,7191
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Growth arrest-specific protein 7 / GAS-7


Mass: 6718.573 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GAS7, KIAA0394 / Plasmid: HR8574A-1-60-AV6HT.2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: O60861

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D 1H-15N NOESY
1713D 1H-13C NOESY aliphatic
1813D 1H-13C NOESY aromatic
1934D CC-NOESY
11013D HNCA
11113D HN(CO)CA
11213D H(CCO)NH
11313D C(CO)NH
11413D HBHA(CO)NH
11513D (H)CCH-TOCSY
11613D (H)CCH-COSY
11713D HNHA
11833D (H)CCH-TOCSY
11912D 1H-13C HSQC-arom
12012D 1H-15N HSQC-Histidine
12122D 1H-13C HSQC - NC5

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Sample preparation

Details
Solution-IDContentsSolvent system
10.26 mM [U-100% 13C; U-100% 15N] SH3 domain of GAS7, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.45 mM [U-10% 13C; U-100% 15N] SH3 domain of GAS7, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
30.26 mM [U-100% 13C; U-100% 15N] SH3 domain of GAS7, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.26 mMSH3 domain of GAS7-1[U-100% 13C; U-100% 15N]1
0.02 %NaN3-21
10 mMDTT-31
5 mMCaCL2-41
100 mMNaCL-51
1 mMProteinase Inhibitors-61
20 mMMES pH 6.5-71
10 %D2O-81
50 uMDSS-91
0.45 mMSH3 domain of GAS7-10[U-10% 13C; U-100% 15N]2
0.02 %NaN3-112
10 mMDTT-122
5 mMCaCL2-132
100 mMNaCL-142
1 mMProteinase Inhibitors-152
20 mMMES pH 6.5-162
10 %D2O-172
50 uMDSS-182
0.26 mMSH3 domain of GAS7-19[U-100% 13C; U-100% 15N]3
0.02 %NaN3-203
10 mMDTT-213
5 mMCaCL2-223
100 mMNaCL-233
1 mMProteinase Inhibitors-243
20 mMMES pH 6.5-253
50 uMDSS-263
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8501
Varian INOVAVarianINOVA6002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinemen,structure solution,geometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement,geometry optimization,structure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis,refinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis,chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
VnmrJVariancollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PSVSBhattacharya, Montelionestructure validation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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