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- PDB-6ya7: Cdc7-Dbf4 bound to an Mcm2-S40 derived bivalent substrate -

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Basic information

Entry
Database: PDB / ID: 6ya7
TitleCdc7-Dbf4 bound to an Mcm2-S40 derived bivalent substrate
Components
  • Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase
  • DNA replication licensing factor MCM2
  • Protein DBF4 homolog A
KeywordsCELL CYCLE / kinase / cdc7 / dbf4 / bivalent substrate / transferase
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 / Switching of origins to a post-replicative state / cell cycle phase transition / Unwinding of DNA / nuclear origin of replication recognition complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / CMG complex / MCM complex ...Dbf4-dependent protein kinase complex / positive regulation of nuclear cell cycle DNA replication / regulation of cell cycle phase transition / Switching of origins to a post-replicative state / cell cycle phase transition / Unwinding of DNA / nuclear origin of replication recognition complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / CMG complex / MCM complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / regulation of DNA-templated DNA replication initiation / Transcriptional Regulation by E2F6 / DNA replication origin binding / cochlea development / DNA replication initiation / Activation of the pre-replicative complex / positive regulation of G2/M transition of mitotic cell cycle / Activation of ATR in response to replication stress / intercellular bridge / cellular response to interleukin-4 / DNA helicase activity / protein serine/threonine kinase activator activity / Assembly of the pre-replicative complex / enzyme activator activity / G1/S transition of mitotic cell cycle / Orc1 removal from chromatin / mitotic spindle / kinase activity / nucleosome assembly / single-stranded DNA binding / histone binding / DNA helicase / nucleic acid binding / chromosome, telomeric region / DNA replication / non-specific serine/threonine protein kinase / protein kinase activity / nuclear body / cilium / cell division / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / chromatin / enzyme binding / signal transduction / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm / cytosol
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 / DNA replication licensing factor MCM2-like, winged-helix domain / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site ...Zinc finger, DBF-type / DBF-type zinc finger superfamily / : / DBF zinc finger / Zinc finger DBF4-type profile. / Zinc finger in DBF-like proteins / DNA replication licensing factor MCM2-like, winged-helix domain / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site / MCM family signature. / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Nucleic acid-binding, OB-fold / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Cell division cycle 7-related protein kinase / DNA replication licensing factor MCM2 / Protein DBF4 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsDick, S.D. / Cherepanov, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick InstituteFC10061 United Kingdom
CitationJournal: Structure / Year: 2020
Title: Structural Basis for the Activation and Target Site Specificity of CDC7 Kinase.
Authors: Dick, S.D. / Federico, S. / Hughes, S.M. / Pye, V.E. / O'Reilly, N. / Cherepanov, P.
History
DepositionMar 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 19, 2020Group: Database references / Derived calculations
Category: citation / pdbx_struct_conn_angle ...citation / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Jan 24, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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,Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase
B: Protein DBF4 homolog A
C: DNA replication licensing factor MCM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5098
Polymers58,8213
Non-polymers6895
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-142 kcal/mol
Surface area22170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.280, 62.280, 234.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 40099.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC7, CDC7L1 / Production host: Homo sapiens (human)
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
Source: (gene. exp.) Homo sapiens (human) / Gene: DBF4, ASK, DBF4A, ZDBF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBU7

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide DNA replication licensing factor MCM2 / Minichromosome maintenance protein 2 homolog / Nuclear protein BM28


Mass: 1797.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49736, DNA helicase

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Non-polymers , 3 types, 371 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M PCTP pH7, 18% PEG 1500, 8% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.67→60.2 Å / Num. obs: 54941 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 17.27 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.098 / Net I/σ(I): 19.4
Reflection shellResolution: 1.67→1.71 Å / Rmerge(I) obs: 0.724 / Num. unique obs: 5401 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
PHENIXdev_3707refinement
PHENIXdev_3707refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MH9

5mh9
PDB Unreleased entry


Resolution: 1.67→60.2 Å / SU ML: 0.144 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.1672
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1852 2739 4.99 %
Rwork0.1562 52179 -
obs0.1577 54918 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.91 Å2
Refinement stepCycle: LAST / Resolution: 1.67→60.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3710 0 36 366 4112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00983838
X-RAY DIFFRACTIONf_angle_d1.15085191
X-RAY DIFFRACTIONf_chiral_restr0.0669576
X-RAY DIFFRACTIONf_plane_restr0.0074664
X-RAY DIFFRACTIONf_dihedral_angle_d20.18421461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.70.231190.22122585X-RAY DIFFRACTION99.96
1.7-1.730.26521120.1962585X-RAY DIFFRACTION99.67
1.73-1.760.24311200.18692559X-RAY DIFFRACTION100
1.76-1.80.18661260.17082544X-RAY DIFFRACTION99.89
1.8-1.840.21841290.16512591X-RAY DIFFRACTION99.93
1.84-1.880.20261230.16422574X-RAY DIFFRACTION99.96
1.88-1.930.19631390.15692549X-RAY DIFFRACTION99.96
1.93-1.980.20071590.1562535X-RAY DIFFRACTION99.93
1.98-2.040.17661550.15152554X-RAY DIFFRACTION100
2.04-2.10.1821430.15112573X-RAY DIFFRACTION99.96
2.1-2.180.16851520.14562563X-RAY DIFFRACTION100
2.18-2.270.18781320.15142601X-RAY DIFFRACTION100
2.27-2.370.17451230.15142607X-RAY DIFFRACTION100
2.37-2.490.17711410.15662623X-RAY DIFFRACTION100
2.49-2.650.15821260.15952604X-RAY DIFFRACTION100
2.65-2.860.18751560.16162621X-RAY DIFFRACTION100
2.86-3.140.19571610.15852621X-RAY DIFFRACTION100
3.14-3.60.15821440.14732650X-RAY DIFFRACTION100
3.6-4.530.16121350.13342731X-RAY DIFFRACTION100
4.53-60.20.21341440.16712909X-RAY DIFFRACTION99.93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.467712606631-0.006308016375650.06851240824270.153757649772-0.09479133144090.961749457423-0.00163557921479-0.00407309860970.05695920517690.0408000954962-0.045420583494-0.003383310389070.000438981322188-0.020290288248-0.07403329524440.10616166883-0.003615873128080.009602087515230.0563502134256-0.004123478364440.0861145820234-16.766243354311.2238845635-0.234377833171
20.09845109336920.1099083528560.0284496572850.616415618584-0.06802765541370.0597763578064-0.0314663213914-0.02286466495780.0440676183698-0.01201893974110.03006676683630.0162646821146-0.02119465718740.002514338144675.25439896174E-50.1052933154430.0003695834141870.0003769785725460.0776657847039-0.006508086194670.0979908125196-12.761285125226.4893830128-22.4442517485
30.186942201117-0.04258857380450.1862348020890.256867058691-0.2139531401850.2627897747260.02350252211320.0916905803818-0.0699232972731-0.217660492846-0.03769491739860.06632526474130.1187950090320.00132476579904-0.0128071216520.13433716084-0.00477630942573-0.00262505695880.0909606900418-0.01015838647170.109039523384-19.64544424137.51945644728-26.1357781761
40.07851790379790.0848725675934-0.02977250716640.172062879669-0.005665640820140.0777784329907-0.133905845518-0.0193831218853-0.0728106227228-0.1472879072520.06161120759640.0151062536734-0.07674168267930.0564652895158-0.004840489483490.146888223920.0127660953590.01000137905060.124572855805-0.02653403012090.177804018627-9.0118542399342.0290401383-22.2938517699
50.103562380365-0.00909062224251-0.02786054575060.0211699246002-0.02681427845930.03228269586240.0153020487878-0.1173980804030.128742197940.0570130017405-0.0374677093677-0.11940703322-0.03970291014710.189828074824-0.007870093509590.1304512771840.008123918399690.02879941388910.138988566523-0.01255250791930.173718047042.2929245446817.5742935655-24.1033172178
60.255921775702-0.3687693500260.1242478310390.365354334313-0.14684524120.190338324930.0095356757068-0.03357170298680.03383429048830.399359733795-0.0139291719179-0.10677716654-0.1261945395120.0277876968185-0.0001669136259290.199728131361-0.00955893911542-0.01079797991210.158186620735-0.02412659810680.161393406334-15.223703720519.869862198215.7434487697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 39:349)
2X-RAY DIFFRACTION2(chain A and resid 350:467)
3X-RAY DIFFRACTION3(chain A and resid 468:573)
4X-RAY DIFFRACTION4(chain B and resid 207:238)
5X-RAY DIFFRACTION5(chain B and resid 239:256)
6X-RAY DIFFRACTION6(chain B and resid 291:348)

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