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- PDB-2kg4: Three-dimensional structure of human Gadd45alpha in solution by NMR -

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Basic information

Entry
Database: PDB / ID: 2kg4
TitleThree-dimensional structure of human Gadd45alpha in solution by NMR
ComponentsGrowth arrest and DNA-damage-inducible protein GADD45 alpha
KeywordsCELL CYCLE / gadd45 / growth arrest / DNA damage / flexible regions / monomer
Function / homology
Function and homology information


negative regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of protein serine/threonine kinase activity / FOXO-mediated transcription of cell cycle genes / regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of p38MAPK cascade / centrosome cycle / negative regulation of blood vessel endothelial cell migration / signal transduction in response to DNA damage / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of angiogenesis ...negative regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of protein serine/threonine kinase activity / FOXO-mediated transcription of cell cycle genes / regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of p38MAPK cascade / centrosome cycle / negative regulation of blood vessel endothelial cell migration / signal transduction in response to DNA damage / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of angiogenesis / cellular response to ionizing radiation / positive regulation of JNK cascade / promoter-specific chromatin binding / cellular response to mechanical stimulus / kinase binding / positive regulation of reactive oxygen species metabolic process / regulation of cell cycle / nuclear speck / positive regulation of apoptotic process / protein heterodimerization activity / DNA repair / apoptotic process / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Growth arrest and DNA damage-inducible protein GADD45 / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Growth arrest and DNA damage-inducible protein GADD45 alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsSanchez, R. / Pantoja-Uceda, D. / Prieto, J. / Diercks, T. / Campos-Olivas, R. / Blanco, F.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Solution structure of human growth arrest and DNA damage 45alpha (Gadd45alpha) and its interactions with proliferating cell nuclear antigen (PCNA) and Aurora A kinase
Authors: Sanchez, R. / Pantoja-Uceda, D. / Prieto, J. / Diercks, T. / Marcaida, M.J. / Montoya, G. / Campos-Olivas, R. / Blanco, F.J.
History
DepositionMar 4, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 1, 2012Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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 1.5May 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 and DNA-damage-inducible protein GADD45 alpha


Theoretical massNumber of molelcules
Total (without water)18,3521
Polymers18,3521
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 Growth arrest and DNA-damage-inducible protein GADD45 alpha / gadd45a / DNA-damage-inducible transcript 1 / DDIT-1


Mass: 18351.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GADD45A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (BL21)DE3 / References: UniProt: P24522

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-13C HMQC-aliphatic
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D HN(CO)CA
1823D HNHA
1923D 1H-15N NOESY
11032D 1H-1H NOESY
11142D 1H-15N HSQC
11252D 1H-15N HSQC
11362D 1H-15N HSQC
11472D 1H-15N HSQC
11512D 1H-13C HMQC-aromatic
11614D 1H-15N 1H-13C NOESY
11722D 1H-15N HSQC-TROSY
11882D 1H-15N HSQC-TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.45mM [U-99% 13C; U-99% 15N] gadd45a-1, 20mM sodium phosphate-2, 100mM potassium chloride-3, 2mM DTT-4, 2mM EDTA-5, 0.03% sodium azide-6, 93% H2O/7% D2O93% H2O/7% D2O
20.45mM [U-99% 15N] gadd45a-7, 20mM sodium phosphate-8, 100mM potassium chloride-9, 2mM DTT-10, 2mM EDTA-11, 0.03% sodium azide-12, 93% H2O/7% D2O93% H2O/7% D2O
30.195mM gadd45a-13, 20mM sodium phosphate-14, 100mM potassium chloride-15, 2mM DTT-16, 2mM EDTA-17, 0.03% sodium azide-18, 100% D2O100% D2O
40.45mM [U-15N]-Leu gadd45a-19, 20mM sodium phosphate-20, 100mM potassium chloride-21, 2mM DTT-22, 2mM EDTA-23, 0.03% sodium azide-24, 93% H2O/7% D2O93% H2O/7% D2O
50.45mM [U-15N]-Val gadd45a-25, 20mM sodium phosphate-26, 100mM potassium chloride-27, 2mM DTT-28, 2mM EDTA-29, 0.03% sodium azide-30, 93% H2O/7% D2O93% H2O/7% D2O
60.45mM [U-15N]-Ile gadd45a-31, 20mM sodium phosphate-32, 100mM potassium chloride-33, 2mM DTT-34, 2mM EDTA-35, 0.03% sodium azide-36, 93% H2O/7% D2O93% H2O/7% D2O
70.45mM [U-15N]-Phe/Tyr gadd45a-37, 20mM sodium phosphate-38, 100mM potassium chloride-39, 2mM DTT-40, 2mM EDTA-41, 0.03% sodium azide-42, 93% H2O/7% D2O93% H2O/7% D2O
80.45mM [U-99% 15N] gadd45a-43, 20mM sodium phosphate-44, 100mM potassium chloride-45, 2mM DTT-46, 2mM EDTA-47, 0.03% sodium azide-48, 10 mg/mL Pf1 phage-49, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.45 mMgadd45a-1[U-99% 13C; U-99% 15N]1
20 mMsodium phosphate-21
100 mMpotassium chloride-31
2 mMDTT-41
2 mMEDTA-51
0.03 %sodium azide-61
0.45 mMgadd45a-7[U-99% 15N]2
20 mMsodium phosphate-82
100 mMpotassium chloride-92
2 mMDTT-102
2 mMEDTA-112
0.03 %sodium azide-122
0.195 mMgadd45a-133
20 mMsodium phosphate-143
100 mMpotassium chloride-153
2 mMDTT-163
2 mMEDTA-173
0.03 %sodium azide-183
0.45 mMgadd45a-19[U-15N]-Leu4
20 mMsodium phosphate-204
100 mMpotassium chloride-214
2 mMDTT-224
2 mMEDTA-234
0.03 %sodium azide-244
0.45 mMgadd45a-25[U-15N]-Val5
20 mMsodium phosphate-265
100 mMpotassium chloride-275
2 mMDTT-285
2 mMEDTA-295
0.03 %sodium azide-305
0.45 mMgadd45a-31[U-15N]-Ile6
20 mMsodium phosphate-326
100 mMpotassium chloride-336
2 mMDTT-346
2 mMEDTA-356
0.03 %sodium azide-366
0.45 mMgadd45a-37[U-15N]-Phe/Tyr7
20 mMsodium phosphate-387
100 mMpotassium chloride-397
2 mMDTT-407
2 mMEDTA-417
0.03 %sodium azide-427
0.45 mMgadd45a-43[U-99% 15N]8
20 mMsodium phosphate-448
100 mMpotassium chloride-458
2 mMDTT-468
2 mMEDTA-478
0.03 %sodium azide-488
10 mg/mLPf1 phage-498
Sample conditionsIonic strength: 0.27 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker Avance IIBrukerAVANCE II8002
Bruker Avance IIBrukerAVANCE II9003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.02Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XwinNMR3.5Bruker Biospincollection
NMRDraw2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospindata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: AMBER 9 explicit water using Gibbs-Boltzman method
NMR constraintsNOE constraints total: 1234 / NOE intraresidue total count: 221 / NOE long range total count: 245 / NOE medium range total count: 438 / NOE sequential total count: 330 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 96 / Protein psi angle constraints total count: 99
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.43 Å / Representative conformer: 1 / Torsion angle constraint violation method: CYANA
NMR ensemble rmsDistance rms dev: 0.94 Å

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