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- PDB-4f99: Human CDC7 kinase in complex with DBF4 and nucleotide -

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Basic information

Entry
Database: PDB / ID: 4f99
TitleHuman CDC7 kinase in complex with DBF4 and nucleotide
Components
  • Cell division cycle 7-related protein kinase
  • Protein DBF4 homolog A
KeywordsTRANSFERASE / SER/THR PROTEIN KINASE / PHOSPHORYLATION / CELL CYCLE / CELL DIVISION / MITOSIS / S PHASE / SERINE/THREONINE-PROTEIN KINASE / DBF4-dependent kinase / DDK / ATP-BINDING / NUCLEOTIDE-BINDING / ZINC-BINDING / NUCLEUS
Function / homology
Function and homology information


Dbf4-dependent protein kinase complex / positive regulation of nuclear cell cycle DNA replication / regulation of cell cycle phase transition / cell cycle phase transition / double-strand break repair via break-induced replication / Transcriptional Regulation by E2F6 / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / intercellular bridge / positive regulation of G2/M transition of mitotic cell cycle ...Dbf4-dependent protein kinase complex / positive regulation of nuclear cell cycle DNA replication / regulation of cell cycle phase transition / cell cycle phase transition / double-strand break repair via break-induced replication / Transcriptional Regulation by E2F6 / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / intercellular bridge / positive regulation of G2/M transition of mitotic cell cycle / enzyme activator activity / protein serine/threonine kinase activator activity / G1/S transition of mitotic cell cycle / mitotic spindle / kinase activity / nucleic acid binding / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / DNA replication / non-specific serine/threonine protein kinase / protein kinase activity / nuclear body / cell division / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / signal transduction / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Zinc finger, DBF-type / DBF-type zinc finger superfamily / : / DBF zinc finger / Zinc finger DBF4-type profile. / Zinc finger in DBF-like proteins / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...Zinc finger, DBF-type / DBF-type zinc finger superfamily / : / DBF zinc finger / Zinc finger DBF4-type profile. / Zinc finger in DBF-like proteins / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Cell division cycle 7-related protein kinase / Protein DBF4 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsHughes, S. / Cherepanov, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Crystal structure of human CDC7 kinase in complex with its activator DBF4.
Authors: Hughes, S. / Elustondo, F. / Di Fonzo, A. / Leroux, F.G. / Wong, A.C. / Snijders, A.P. / Matthews, S.J. / Cherepanov, P.
History
DepositionMay 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division cycle 7-related protein kinase
B: Protein DBF4 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0745
Polymers57,5572
Non-polymers5173
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-63 kcal/mol
Surface area18540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.480, 61.480, 237.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Cell division cycle 7-related protein kinase / CDC7-related kinase / HsCdc7 / huCdc7


Mass: 40633.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC7, CDC7L1 / Plasmid: pRSF-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2(DE3)
References: UniProt: O00311, non-specific serine/threonine protein kinase
#2: Protein Protein DBF4 homolog A / Activator of S phase kinase / Chiffon homolog A / DBF4-type zinc finger-containing protein 1


Mass: 16923.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: coexpression / Source: (gene. exp.) Homo sapiens (human) / Gene: ASK, DBF4, DBF4A, ZDBF1 / Plasmid: pCDF-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2(DE3) / References: UniProt: Q9UBU7

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Non-polymers , 4 types, 51 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG-1500, 15% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 16, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.33→79.14 Å / Num. all: 20628 / Num. obs: 20628 / % possible obs: 100 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 15.4
Reflection shellResolution: 2.33→2.39 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1470 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PVG (Automatic molecular replacement with BALBES).

3pvg


Resolution: 2.33→59.52 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.57 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.331 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24148 1051 5.1 %RANDOM
Rwork0.1915 ---
obs0.19396 20540 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.608 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.33→59.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3237 0 29 48 3314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023338
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9824510
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7595397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22224.487156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34315596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8641517
X-RAY DIFFRACTIONr_chiral_restr0.0840.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212485
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.327→2.388 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 55 -
Rwork0.238 1218 -
obs--100 %

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