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- PDB-2kw6: Solution NMR Structure of Cyclin-dependent kinase 2-associated pr... -

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Basic information

Entry
Database: PDB / ID: 2kw6
TitleSolution NMR Structure of Cyclin-dependent kinase 2-associated protein 1 (CDK2-associated protein 1; oral cancer suppressor Deleted in oral cancer 1, DOC-1) from H.sapiens, Northeast Structural Genomics Consortium Target Target HR3057H
ComponentsCyclin-dependent kinase 2-associated protein 1
KeywordsCELL CYCLE / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-2 / Protein Structure Initiative / CANCER SUPPRESSOR
Function / homology
Function and homology information


NuRD complex / DNA polymerase binding / DNA-templated DNA replication / positive regulation of protein phosphorylation / chromatin / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #1300 / Cyclin-dependent kinase 2-associated protein 1/2 / Cyclin-dependent kinase 2-associated protein / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Cyclin-dependent kinase 2-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsErtekin, A. / Aramini, J.M. / Rossi, P. / Lee, A.B. / Jiang, M. / Ciccosanti, C.T. / Xiao, R. / Swapna, G.V.T. / Rost, B. / Everett, J.K. ...Ertekin, A. / Aramini, J.M. / Rossi, P. / Lee, A.B. / Jiang, M. / Ciccosanti, C.T. / Xiao, R. / Swapna, G.V.T. / Rost, B. / Everett, J.K. / Acton, T.B. / Prestegard, J.H. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Human cyclin-dependent kinase 2-associated protein 1 (CDK2AP1) is dimeric in its disulfide-reduced state, with natively disordered N-terminal region.
Authors: Ertekin, A. / Aramini, J.M. / Rossi, P. / Leonard, P.G. / Janjua, H. / Xiao, R. / Maglaqui, M. / Lee, H.W. / Prestegard, J.H. / Montelione, G.T.
History
DepositionMar 31, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 2, 2013Group: Database references
Revision 1.3Feb 5, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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 1.5May 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: Cyclin-dependent kinase 2-associated protein 1
B: Cyclin-dependent kinase 2-associated protein 1


Theoretical massNumber of molelcules
Total (without water)14,8812
Polymers14,8812
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 Cyclin-dependent kinase 2-associated protein 1 / CDK2-associated protein 1 / Putative oral cancer suppressor / Deleted in oral cancer 1 / DOC-1


Mass: 7440.539 Da / Num. of mol.: 2 / Fragment: sequence database residues 61-115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2AP1, CDKAP1, DOC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O14519

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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 simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1413D HNCO
1513D HBHA(CO)NH
1612D 1H-13C arom NOESY
1713D (H)CCH-TOCSY
1813D HNCA
1913D HN(CO)CA
11013D (H)CCH-TOCSY
11113D (H)CCH-COSY
11212D 1H-15N hetNOE
11313D HN(CA)CB
11413D HN(CA)CO
11513D CBCA(CO)NH
11613D HN(CA)CB
11722D 1H-13C HSQC high res. (L/V methyl stereospecific assignment)
11822D 1H-15N T1 relaxation
11922D 1H-15N T2 relaxation
12022D 1H-15N hetNOE
1213X-filtered 13C NOESY
12242D 1H-15N TROSY
12353D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM [U-100% 13C; U-100% 15N] HR3057H, 20 mM MES, 50 uM DSS, 200 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.68 mM [U-5% 13C; U-100% 15N] HR3057H, 20 mM MES, 50 uM DSS, 200 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
30.92 mM [U-100% 13C; U-100% 15N] + unlabeled HR3057H, 20 mM MES, 50 uM DSS, 200 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
40.68 mM [U-5% 13C; U-100% 15N] + unlabeled HR3057H, 20 mM MES, 50 uM DSS, 200 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02 % sodium azide, 7 % Polyacrylamide Gel, 95% H2O/5% D2O95% H2O/5% D2O
50.9 mM [U-100% 13C; U-100% 15N] + unlabeled HR3057H, 20 mM MES, 50 uM DSS, 200 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02 % sodium azide, 4.2 % PEG, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMHR3057H-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
50 uMDSS-31
200 mMNaCl-41
10 mMDTT-51
5 mMCaCl2-61
0.02 %sodium azide-71
0.68 mMHR3057H-8[U-5% 13C; U-100% 15N]2
20 mMMES-92
50 uMDSS-102
200 mMNaCl-112
10 mMDTT-122
5 mMCaCl2-132
0.02 %sodium azide-142
0.92 mMHR3057H-15[U-100% 13C; U-100% 15N] + unlabeled3
20 mMMES-163
50 uMDSS-173
200 mMNaCl-183
10 mMDTT-193
5 mMCaCl2-203
0.02 %sodium azide-213
0.68 mMHR3057H-22[U-5% 13C; U-100% 15N] + unlabeled4
20 mMMES-234
50 uMDSS-244
200 mMNaCl-254
10 mMDTT-264
5 mMCaCl2-274
0.02 %sodium azide-284
7 %Polyacrylamide Gel-294
0.9 mMHR3057H-30[U-100% 13C; U-100% 15N] + unlabeled5
20 mMMES-315
50 uMDSS-325
200 mMNaCl-335
10 mMDTT-345
5 mMCaCl2-355
0.02 %sodium azide-365
4.2 %PEG-375
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis,refinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
VnmrJVariancollection
Sparky3Goddardpeak picking
Sparky3Goddarddata analysis
PINE1Bahrami, Markley, Assadi, and Eghbalniachemical shift assignment
PSVS1.4Bhattacharya and Montelionestructure quality analysis
TALOS+Cornilescu, Delaglio and Baxdihedral angle constraints
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination of this symmetric homodimer was performed iteratively using CYANA3.0. The 20 structures out of 100 with lowest target function were further refined by restrained ...Details: Structure determination of this symmetric homodimer was performed iteratively using CYANA3.0. The 20 structures out of 100 with lowest target function were further refined by restrained molecular dynamics/energy minimization in explicit water using CNS 1.1. Residual dipolar couplings were applied at all stages of the structure determination.
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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