[English] 日本語
Yorodumi
- PDB-6ya7: Cdc7-Dbf4 bound to an Mcm2-S40 derived bivalent substrate -

+
Open data


ID or keywords:

Loading...

-
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 / regulation of cell cycle phase transition / positive regulation of nuclear cell cycle DNA replication / Switching of origins to a post-replicative state / Unwinding of DNA / cell cycle phase transition / nuclear origin of replication recognition complex / CMG complex / MCM complex / double-strand break repair via break-induced replication ...Dbf4-dependent protein kinase complex / regulation of cell cycle phase transition / positive regulation of nuclear cell cycle DNA replication / Switching of origins to a post-replicative state / Unwinding of DNA / cell cycle phase transition / nuclear origin of replication recognition complex / CMG complex / MCM complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / regulation of DNA-templated DNA replication initiation / intercellular bridge / cochlea development / DNA unwinding involved in DNA replication / Transcriptional Regulation by E2F6 / DNA replication origin binding / DNA replication initiation / Activation of the pre-replicative complex / cellular response to interleukin-4 / Activation of ATR in response to replication stress / enzyme activator activity / positive regulation of G2/M transition of mitotic cell cycle / protein serine/threonine kinase activator activity / helicase activity / Assembly of the pre-replicative complex / mitotic spindle / Orc1 removal from chromatin / G1/S transition of mitotic cell cycle / nucleosome assembly / kinase activity / single-stranded DNA binding / histone binding / DNA helicase / DNA replication / nucleic acid binding / chromosome, telomeric region / non-specific serine/threonine protein kinase / nuclear body / protein kinase activity / cell division / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / chromatin / apoptotic process / enzyme binding / signal transduction / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / 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 / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site / MCM family signature. ...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 / 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 / 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
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

-
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
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

-
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: 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

-
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

-
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

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
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

-
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

-
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)

+
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