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- PDB-6ya8: Cdc7-Dbf4 bound to ADP-BeF3 -

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Basic information

Entry
Database: PDB / ID: 6ya8
TitleCdc7-Dbf4 bound to ADP-BeF3
Components
  • Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase
  • Protein DBF4 homolog A
KeywordsCELL CYCLE / kinase / cdc7 / dbf4 / 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 / cell cycle phase transition / double-strand break repair via break-induced replication / Transcriptional Regulation by E2F6 / 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 ...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 / positive regulation of G2/M transition of mitotic cell cycle / Activation of ATR in response to replication stress / intercellular bridge / protein serine/threonine kinase activator activity / enzyme activator activity / G1/S transition of mitotic cell cycle / mitotic spindle / kinase activity / nucleic acid binding / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...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 / 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 / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / 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: 1.79 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9068
Polymers57,2342
Non-polymers6736
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-69 kcal/mol
Surface area21460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.150, 61.150, 235.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw

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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: 40230.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC7, CDC7L1 / Production host: Escherichia coli (E. coli)
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: 17003.393 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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Non-polymers , 5 types, 308 molecules

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


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.57
Details: 0.1M MMT pH 6.57, 21% PEG 1500, 15% v/v Acetonitrile, 20mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97957 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.79→58.86 Å / Num. obs: 42930 / % possible obs: 98.98 % / Redundancy: 11.5 % / Biso Wilson estimate: 21.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0698 / Net I/σ(I): 23.66
Reflection shellResolution: 1.79→1.854 Å / Redundancy: 11.5 % / Num. unique obs: 4056 / CC1/2: 0.827 / % possible all: 91.15

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Processing

Software
NameVersionClassification
PHENIX1.18rc4_3812refinement
PHENIX1.18rc4_3812refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4f99

4f99


Resolution: 1.79→58.86 Å / SU ML: 0.1855 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.5996
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.197 2208 5.14 %
Rwork0.1656 40722 -
obs0.1672 42930 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.29 Å2
Refinement stepCycle: LAST / Resolution: 1.79→58.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3536 0 35 302 3873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00633693
X-RAY DIFFRACTIONf_angle_d0.93365004
X-RAY DIFFRACTIONf_chiral_restr0.0539556
X-RAY DIFFRACTIONf_plane_restr0.0053638
X-RAY DIFFRACTIONf_dihedral_angle_d18.63381408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.28881160.2352231X-RAY DIFFRACTION89.21
1.83-1.870.25421140.21982429X-RAY DIFFRACTION95.46
1.87-1.920.24511450.19242506X-RAY DIFFRACTION99.4
1.92-1.970.22151460.18132524X-RAY DIFFRACTION99.89
1.97-2.030.17631490.16362474X-RAY DIFFRACTION100
2.03-2.090.21241580.16482501X-RAY DIFFRACTION100
2.09-2.170.19851450.16312544X-RAY DIFFRACTION99.93
2.17-2.260.19011280.16192539X-RAY DIFFRACTION100
2.26-2.360.16931210.1612580X-RAY DIFFRACTION100
2.36-2.480.2151330.16762549X-RAY DIFFRACTION100
2.48-2.640.22091220.17272573X-RAY DIFFRACTION99.96
2.64-2.840.21011570.17142551X-RAY DIFFRACTION99.96
2.84-3.130.19891590.17192572X-RAY DIFFRACTION99.89
3.13-3.580.19241440.16242632X-RAY DIFFRACTION99.86
3.58-4.510.16321260.13762664X-RAY DIFFRACTION99.96
4.51-58.860.18941450.16812853X-RAY DIFFRACTION99.83
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)
10.4689641358490.06684432724470.06304697837720.4639495387670.2710834527381.14496775486-0.00287546474716-0.0180311980940.03517171863840.119499051141-0.0195277154947-0.0324964540565-0.01522643124-0.0572803109216-0.006160076977290.1351000021620.00831364311574-0.004705703856470.1080579037621.34543239704E-50.123491984498-16.624486647218.00840502910.575000797676
20.2999562681940.1581120182880.008521323051070.594537213345-0.066993784485-0.00449464543168-0.0195964924073-0.0217880087392-0.017657883503-0.03251476392950.00875120167852-0.05448105444410.01833366896960.01368879029050.0003146691911610.1344413186540.009915123945570.004099278352520.1272133188150.02097577465110.105351526808-21.91344106893.19102823043-22.9021824424
30.4029158707330.1577873208790.02871817996190.3596742256710.1421678450180.2693308601140.01665213947590.2735529124280.0897774540522-0.2432079791710.0139845547269-0.0992715911036-0.148391413950.02515945255240.05970734460730.1621497344910.006611930395630.01167340433750.1564177650880.03556388991350.160009274677-16.171659832722.5126501958-26.1053915584
40.3094349127640.135340098896-0.1368875406370.4405771135490.2400620910.661949892325-0.2120480170050.06695244935880.0905123332295-0.06378381123640.0123098871420.03631199139520.1211255832410.0799393196515-0.211053945590.1670840584220.00879683626617-0.01303729917030.1461204929970.04775567031120.225735536293-25.5755264739-11.5714062207-23.4996130605
50.0291150625263-0.07779732354740.02351535027530.1791723662750.07125007498490.1325221100950.0715892073135-0.00365673967595-0.196371816061-0.006129895431280.04573705317870.1449878155120.138634444353-0.09033325995020.003055989107290.185186852155-0.000322610597084-0.009370472156010.1587822524620.02241783892780.232832508132-30.24638071756.39768063503-12.2723897363
60.246122839233-0.16373038111-0.2137557014210.1964113273430.05813805069860.1408002152340.0257647883429-0.157372442288-0.1036945977940.228543184653-0.07895933034140.06457643679090.09651872243630.0465161542674-0.01146351219020.2513800763030.0131432364632-0.003061126455770.1661466555630.03649838601670.246683960392-14.61834057767.8680991708716.1413239932
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 38:348)AA38 - 3481 - 189
22(chain A and resid 349:465)AA349 - 465190 - 310
33(chain A and resid 466:572)AA466 - 572311 - 353
44(chain B and resid 207:238)BD207 - 2381 - 34
55(chain B and resid 239:301)BD239 - 30135 - 60
66(chain B and resid 302:346)BD302 - 34661 - 105

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