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- PDB-2m1l: Solution NMR Structure of Cyclin-dependent kinase 2-associated pr... -

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Basic information

Entry
Database: PDB / ID: 2m1l
TitleSolution NMR Structure of Cyclin-dependent kinase 2-associated protein 2 (CDK2AP2, DOC-1R) from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR8910C
ComponentsCyclin-dependent kinase 2-associated protein 2
KeywordsCELL CYCLE / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


regulation of stem cell division / NuRD complex / negative regulation of G1/S transition of mitotic cell cycle / regulation of microtubule cytoskeleton organization / microtubule / nucleus / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsErtekin, A. / Janjua, H. / Kohan, E. / Shastry, R. / Pederson, K. / Prestegard, J.H. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of CDK2-associated protein 2 (CDK2AP2, Deleted in Oral Cancer 1 Related protein, DOC-1R)
Authors: Ertekin, A. / Janjua, H. / Shastry, R. / Pederson, K. / Prestegard, J.H. / Montelione, G.T.
History
DepositionNov 30, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
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: Cyclin-dependent kinase 2-associated protein 2
B: Cyclin-dependent kinase 2-associated protein 2


Theoretical massNumber of molelcules
Total (without water)15,2902
Polymers15,2902
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 2 / CDK2-associated protein 2 / DOC-1-related protein / DOC-1R


Mass: 7644.793 Da / Num. of mol.: 2 / Fragment: UNP residues 61-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2AP2, DOC1R / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: O75956

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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 CBCA(CO)NH
1713D HBHA(CO)NH
1813D HN(CA)CO
1913D 1H-13C NOESY aliphatic
11013D 1H-15N NOESY
11123D 13C-filtered NOESY aliphatic
11222D 13C-filtered NOESY aromatic
11342D 1H-13C high res (L/V methyl stereospecific assignment)
11413D (H)CCH-TOCSY
11513D (H)CCH-COSY
11613D (H)CCH-TOCSY
11713D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
15.0 mg/mL [U-100% 13C; U-100% 15N] HR8910C.003, 1 x Proteinase Inhibitors, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 200 mM NaCL, 20 mM MES pH 6.5, 5 % D2O, 95% H2O/5% D2O95% H2O/5% D2O
25.0 mg/mL [U-100% 13C; U-100% 15N] HR8910C, 15.0 mg/mL HR8910C, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 200 mM NaCL, 20 mM MES pH 6.5, 5 % D2O, 1 x Proteinase Inhibitors, 95% H2O/5% D2O95% H2O/5% D2O
30.3 mM [U-100% 15N] HR8910C, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 200 mM NaCL, 20 mM MES pH 6.5, 5 % D2O, 1 x Proteinase Inhibitors, 4.2 % PEG, 95% H2O/5% D2O95% H2O/5% D2O
45.0 mg/mL [U-5% 13C; U-100% 15N] HR8910C.005, 1 x Proteinase Inhibitors, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 200 mM NaCL, 20 mM MES pH 6.5, 5 % D2O, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5.0 mg/mLHR8910C.003-1[U-100% 13C; U-100% 15N]1
1 %Proteinase Inhibitors-21
0.02 %NaN3-31
10 mMDTT-41
5 mMCaCL2-51
200 mMNaCL-61
20 mMMES pH 6.5-71
5 %D2O-81
5.0 mg/mLHR8910C-9[U-100% 13C; U-100% 15N]2
15.0 mg/mLHR8910C-102
0.02 %NaN3-112
10 mMDTT-122
5 mMCaCL2-132
200 mMNaCL-142
20 mMMES pH 6.5-152
5 %D2O-162
1 %Proteinase Inhibitors-172
0.3 mMHR8910C-18[U-100% 15N]3
0.02 %NaN3-193
10 mMDTT-203
5 mMCaCL2-213
200 mMNaCL-223
20 mMMES pH 6.5-233
5 %D2O-243
1 %Proteinase Inhibitors-253
4.2 %PEG-263
5.0 mg/mLHR8910C.005-27[U-5% 13C; U-100% 15N]4
1 %Proteinase Inhibitors-284
0.02 %NaN3-294
10 mMDTT-304
5 mMCaCL2-314
200 mMNaCL-324
20 mMMES pH 6.5-334
5 %D2O-344
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement,structure solution,geometry optimization
CYANA3.02Guntert, Mumenthaler and Wuthrichrefinement,geometry optimization,structure solution
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis,chemical shift assignment
NMRPipe2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin2.1Bruker Biospincollection
PINE1Bahrami, Markley, Assadi, and Eghbalniachemical shift assignment
Sparky3.112Goddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALESPALES (Zweckstetter, Bax)geometry optimization
PSVS1.4Bhattacharya, Montelionestructure validation
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination of this symmetric homodimer was performed iteratively using CYANA 3.02. 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 CYANA 3.02. The 20 structures out of 100 with lowest target function were further refined by restrained molecular dynamics/energy minimization in explicit water using CNS 1.3. Residual dipolar couplings and backbone dihedral angle constraints for the ordered regions were applied at all stages of the structure determination
NMR constraintsNOE constraints total: 1914 / NOE intraresidue total count: 437 / NOE long range total count: 476 / NOE medium range total count: 523 / NOE sequential total count: 478 / Protein phi angle constraints total count: 50 / Protein psi angle constraints total count: 51
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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