[English] 日本語
Yorodumi
- PDB-6ya8: Cdc7-Dbf4 bound to ADP-BeF3 -

+
Open data


ID or keywords:

Loading...

-
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 / regulation of cell cycle phase transition / positive regulation of nuclear cell cycle DNA replication / mitotic DNA damage checkpoint signaling / cell cycle phase transition / double-strand break repair via break-induced replication / intercellular bridge / Transcriptional Regulation by E2F6 / Activation of the pre-replicative complex / enzyme activator activity ...Dbf4-dependent protein kinase complex / regulation of cell cycle phase transition / positive regulation of nuclear cell cycle DNA replication / mitotic DNA damage checkpoint signaling / cell cycle phase transition / double-strand break repair via break-induced replication / intercellular bridge / Transcriptional Regulation by E2F6 / Activation of the pre-replicative complex / enzyme activator activity / Activation of ATR in response to replication stress / positive regulation of G2/M transition of mitotic cell cycle / protein serine/threonine kinase activator activity / G1/S transition of mitotic cell cycle / mitotic spindle / kinase activity / DNA replication / nucleic acid binding / nuclear body / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / 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 / 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 ...Zinc finger, DBF-type / DBF-type zinc finger superfamily / DBF zinc finger / Zinc finger DBF4-type profile. / Zinc finger in DBF-like proteins / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 5 types, 308 molecules

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


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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more