[English] 日本語
Yorodumi
- PDB-4yc6: CDK1/CKS1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yc6
TitleCDK1/CKS1
Components
  • Cyclin-dependent kinase 1
  • Cyclin-dependent kinases regulatory subunit 1
KeywordsCELL CYCLE / CDK1 / Cyclin B1 / CKS2
Function / homology
Function and homology information


regulation of Schwann cell differentiation / cyclin A1-CDK1 complex / regulation of attachment of mitotic spindle microtubules to kinetochore / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / histone kinase activity / Golgi disassembly ...regulation of Schwann cell differentiation / cyclin A1-CDK1 complex / regulation of attachment of mitotic spindle microtubules to kinetochore / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / histone kinase activity / Golgi disassembly / microtubule cytoskeleton organization involved in mitosis / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / MASTL Facilitates Mitotic Progression / Activation of NIMA Kinases NEK9, NEK6, NEK7 / mitotic nuclear membrane disassembly / : / cyclin A2-CDK1 complex / Phosphorylation of Emi1 / Transcriptional regulation by RUNX2 / Phosphorylation of the APC/C / Nuclear Pore Complex (NPC) Disassembly / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / protein localization to kinetochore / Initiation of Nuclear Envelope (NE) Reformation / cyclin-dependent protein serine/threonine kinase activator activity / Golgi Cisternae Pericentriolar Stack Reorganization / response to copper ion / Condensation of Prometaphase Chromosomes / centrosome cycle / chromosome condensation / [RNA-polymerase]-subunit kinase / SCF ubiquitin ligase complex / cyclin-dependent protein kinase activity / MAPK3 (ERK1) activation / response to amine / G1/S-Specific Transcription / mitotic G2 DNA damage checkpoint signaling / Regulation of APC/C activators between G1/S and early anaphase / regulation of embryonic development / peptidyl-threonine phosphorylation / protein deubiquitination / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / response to axon injury / APC/C:Cdc20 mediated degradation of Cyclin B / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / response to cadmium ion / Cyclin A/B1/B2 associated events during G2/M transition / cyclin-dependent protein kinase holoenzyme complex / positive regulation of cardiac muscle cell proliferation / positive regulation of G2/M transition of mitotic cell cycle / ERK1 and ERK2 cascade / epithelial cell differentiation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / RNA polymerase II CTD heptapeptide repeat kinase activity / Hsp70 protein binding / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / cyclin binding / regulation of mitotic cell cycle / Resolution of Sister Chromatid Cohesion / Condensation of Prophase Chromosomes / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / AURKA Activation by TPX2 / positive regulation of DNA replication / ubiquitin binding / response to activity / spindle microtubule / MAPK6/MAPK4 signaling / G1/S transition of mitotic cell cycle / SCF(Skp2)-mediated degradation of p27/p21 / regulation of circadian rhythm / PKR-mediated signaling / response to toxic substance / positive regulation of protein import into nucleus / positive regulation of protein localization to nucleus / microtubule cytoskeleton organization / Cyclin D associated events in G1 / cellular response to hydrogen peroxide / The role of GTSE1 in G2/M progression after G2 checkpoint / Ovarian tumor domain proteases / Regulation of TP53 Degradation / Regulation of PLK1 Activity at G2/M Transition / G2/M transition of mitotic cell cycle / mitotic spindle / peptidyl-serine phosphorylation / kinase activity / rhythmic process / cell migration / virus receptor activity / protein-containing complex assembly / midbody / fibroblast proliferation / response to ethanol
Similarity search - Function
Cyclin-Dependent Kinase Subunit Type 2 / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / : / Phosphorylase Kinase; domain 1 ...Cyclin-Dependent Kinase Subunit Type 2 / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 Alpha / Alpha Beta
Similarity search - Domain/homology
Cyclin-dependent kinase 1 / Cyclin-dependent kinases regulatory subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsBrown, N.R. / Korolchuk, S. / Martin, M.P. / Stanley, W. / Moukhametzianov, R. / Noble, M.E.M. / Endicott, J.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G0901526 United Kingdom
Cancer Research UKC240/A15751 United Kingdom
Astex PharmaceuticalsNICR-Alliance United Kingdom
CitationJournal: Nat Commun / Year: 2015
Title: CDK1 structures reveal conserved and unique features of the essential cell cycle CDK.
Authors: Brown, N.R. / Korolchuk, S. / Martin, M.P. / Stanley, W.A. / Moukhametzianov, R. / Noble, M.E. / Endicott, J.A.
History
DepositionFeb 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model / Author supporting evidence
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_validate_close_contact
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_2
Revision 2.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclin-dependent kinase 1
B: Cyclin-dependent kinases regulatory subunit 1
C: Cyclin-dependent kinase 1
D: Cyclin-dependent kinases regulatory subunit 1
E: Cyclin-dependent kinase 1
F: Cyclin-dependent kinases regulatory subunit 1
G: Cyclin-dependent kinase 1
H: Cyclin-dependent kinases regulatory subunit 1


Theoretical massNumber of molelcules
Total (without water)178,6028
Polymers178,6028
Non-polymers00
Water11,512639
1
A: Cyclin-dependent kinase 1
B: Cyclin-dependent kinases regulatory subunit 1


Theoretical massNumber of molelcules
Total (without water)44,6512
Polymers44,6512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-6 kcal/mol
Surface area18210 Å2
MethodPISA
2
C: Cyclin-dependent kinase 1
D: Cyclin-dependent kinases regulatory subunit 1


Theoretical massNumber of molelcules
Total (without water)44,6512
Polymers44,6512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-6 kcal/mol
Surface area18180 Å2
MethodPISA
3
E: Cyclin-dependent kinase 1
F: Cyclin-dependent kinases regulatory subunit 1


Theoretical massNumber of molelcules
Total (without water)44,6512
Polymers44,6512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-6 kcal/mol
Surface area18170 Å2
MethodPISA
4
G: Cyclin-dependent kinase 1
H: Cyclin-dependent kinases regulatory subunit 1


Theoretical massNumber of molelcules
Total (without water)44,6512
Polymers44,6512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-6 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.817, 147.531, 87.297
Angle α, β, γ (deg.)90.000, 92.060, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

-
Components

#1: Protein
Cyclin-dependent kinase 1 / CDK1 / Cell division control protein 2 homolog / Cell division protein kinase 1 / p34 protein kinase


Mass: 34142.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK1, CDC2, CDC28A, CDKN1, P34CDC2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P06493, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#2: Protein
Cyclin-dependent kinases regulatory subunit 1 / CKS-1


Mass: 10508.093 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CKS1B, CKS1, PNAS-143, PNAS-16 / Production host: Escherichia coli (E. coli) / References: UniProt: P61024
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / 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: 2.6 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.3 / Details: 16-18% PEG 10 000, 0.1M imidazole pH 8.2 -8.4 / PH range: 8.2-8.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→75.09 Å / Num. all: 50462 / Num. obs: 50462 / % possible obs: 97 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.094 / Rsym value: 0.084 / Net I/σ(I): 16.6
Reflection shellResolution: 2.6→2.68 Å / Redundancy: 3.7 % / Rmerge(I) obs: 2.08 / Mean I/σ(I) obs: 1.97 / % possible all: 80.6

-
Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
REFMAC5.8.0103refinement
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.6→75.09 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1787 3.5 %RANDOM
Rwork0.2248 48643 --
obs0.2268 50430 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 218.11 Å2 / Biso mean: 95.396 Å2 / Biso min: 39.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å2-2.01 Å2
2--4.54 Å20 Å2
3----2.67 Å2
Refinement stepCycle: LAST / Resolution: 2.6→75.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11632 0 0 639 12271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01911998
X-RAY DIFFRACTIONr_bond_other_d00.0211516
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.9716234
X-RAY DIFFRACTIONr_angle_other_deg3.625326586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0551418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.94323.83564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.959152168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7581572
X-RAY DIFFRACTIONr_chiral_restr0.1080.21752
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02113234
X-RAY DIFFRACTIONr_gen_planes_other0.0120.022734
X-RAY DIFFRACTIONr_mcbond_it2.2963.2455702
X-RAY DIFFRACTIONr_mcbond_other2.2933.2445701
X-RAY DIFFRACTIONr_mcangle_it3.9434.8437110
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.391 3068 -
obs--79.71 %
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)
17.11431.8715-0.867.3283-0.30916.23930.29660.59510.0656-0.1403-0.05870.8259-0.0012-0.2544-0.23790.33560.09190.00310.0852-0.08670.66-30.47820.323-8.335
27.47591.25931.96058.4019-0.38077.1468-0.06540.3388-0.212-0.251-0.2116-0.7360.0990.2930.2770.31580.0330.03910.03420.0570.50191.0267.154-6.925
38.7432-2.12251.5173.914-1.01618.1139-0.5183-1.01751.0106-0.03050.14640.95610.0344-0.8990.3720.9955-0.1209-0.21940.2549-0.33771.4835-31.21211.779-37.256
47.93320.2738-2.96449.35060.48247.7061-0.5512-0.4404-0.3769-0.02440.4193-0.6783-0.25550.67190.13180.8674-0.1540.23740.1083-0.04510.48863.16110.173-35.953
53.3471-0.7259-0.97614.89511.99351.9985-0.51060.06990.0055-1.90450.27540.8446-0.9919-0.04150.23511.8946-0.2148-0.30320.07270.15490.7128-16.31634.791-43.65
65.6995-1.4623.18062.8678-1.63929.9060.27010.9214-0.4019-0.9453-0.328-0.26860.36620.78210.05780.79650.0650.11460.1603-0.06790.80239.78634.961-21.55
74.61191.1687-1.04314.7014-0.6081.50020.2198-0.48670.35470.5691-0.24370.0959-0.34790.09280.02390.6513-0.01020.04730.0719-0.11270.3965-6.9135.136-0.077
86.2846-1.0554-2.42460.98982.82368.3134-0.20831.01480.295-0.1197-0.21510.1155-0.0458-0.66130.42350.7187-0.1461-0.00680.394-0.02910.8816-39.132-9.704-16.837
95.96710.5212-0.56363.9647-0.17091.20690.0589-0.0841-0.06930.4888-0.19240.13680.1715-0.20630.13340.6154-0.04550.04580.05760.00950.3335-22.508-5.4764.34
105.6917-2.0101-5.53871.7213-0.439711.4434-0.35-0.65720.3437-0.0680.1345-0.21170.9980.63250.21551.2505-0.1204-0.05730.2427-0.17740.8434-1.904-18.366-21.834
114.5911-0.1962.52885.39260.313.56650.1360.0971-0.0384-1.0008-0.01680.48510.6956-0.1129-0.11921.2465-0.259-0.02580.0742-0.06760.4541-15.603-11.613-44.33
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B5 - 73
2X-RAY DIFFRACTION2D5 - 73
3X-RAY DIFFRACTION3F5 - 73
4X-RAY DIFFRACTION4H5 - 73
5X-RAY DIFFRACTION5G1 - 290
6X-RAY DIFFRACTION6A1 - 80
7X-RAY DIFFRACTION7A81 - 289
8X-RAY DIFFRACTION8C1 - 80
9X-RAY DIFFRACTION9C81 - 289
10X-RAY DIFFRACTION10E1 - 80
11X-RAY DIFFRACTION11E81 - 289

+
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