[English] 日本語
Yorodumi
- PDB-4f9c: Human CDC7 kinase in complex with DBF4 and XL413 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f9c
TitleHuman CDC7 kinase in complex with DBF4 and XL413
Components
  • Cell division cycle 7-related protein kinase
  • Protein DBF4 homolog A
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / SER/THR PROTEIN KINASE / TRANSFERASE / PHOSPHORYLATION / CELL CYCLE / CELL DIVISION / MITOSIS / S PHASE / SERINE/THREONINE-PROTEIN KINASE / DBF4-dependent kinase / DDK / ATP-BINDING / NUCLEOTIDE-BINDING / ZINC-BINDING / NUCLEUS / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / cell cycle phase transition / double-strand break repair via break-induced replication / intercellular bridge / Transcriptional Regulation by E2F6 / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / enzyme activator activity ...Dbf4-dependent protein kinase complex / regulation of cell cycle phase transition / positive regulation of nuclear cell cycle DNA replication / cell cycle phase transition / double-strand break repair via break-induced replication / intercellular bridge / Transcriptional Regulation by E2F6 / Activation of the pre-replicative complex / 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 / mitotic spindle / G1/S transition of mitotic cell cycle / kinase activity / DNA replication / nucleic acid binding / nuclear body / non-specific serine/threonine protein kinase / protein kinase activity / 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 / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Tumor Necrosis Factor Receptor, subunit A; domain 2 - #40 / DBF zinc finger / Zinc finger, DBF-type / DBF-type zinc finger superfamily / : / DBF zinc finger / Zinc finger DBF4-type profile. / Zinc finger in DBF-like proteins / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Tumor Necrosis Factor Receptor, subunit A; domain 2 - #40 / DBF zinc finger / Zinc finger, DBF-type / DBF-type zinc finger superfamily / : / DBF zinc finger / Zinc finger DBF4-type profile. / Zinc finger in DBF-like proteins / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Ribbon / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-0SX / 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: 2.08 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: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen / Item: _diffrn_detector.detector
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)57,9124
Polymers57,5572
Non-polymers3552
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-44 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.270, 61.270, 238.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#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
#3: Chemical ChemComp-0SX / 8-chloro-2-[(2S)-pyrrolidin-2-yl][1]benzofuro[3,2-d]pyrimidin-4(3H)-one


Mass: 289.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12ClN3O2
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.86 %
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 28, 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: 2.08→61.27 Å / Num. all: 28800 / Num. obs: 28512 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 17.6
Reflection shellResolution: 2.08→2.13 Å / Redundancy: 7 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2059 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→59.74 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.524 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24884 1455 5.1 %RANDOM
Rwork0.20352 ---
obs0.20579 28458 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.914 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.08→59.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3177 0 21 81 3279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023270
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.181.9814412
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7635388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3424.276152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92515588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1191518
X-RAY DIFFRACTIONr_chiral_restr0.0880.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212435
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: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 104 -
Rwork0.258 1711 -
obs--99.94 %

+
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