[English] 日本語
Yorodumi
- PDB-1blx: P19INK4D/CDK6 COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1blx
TitleP19INK4D/CDK6 COMPLEX
Components
  • CYCLIN-DEPENDENT KINASE 6
  • P19INK4D
KeywordsCOMPLEX (INHIBITOR PROTEIN/KINASE) / INHIBITOR PROTEIN / CYCLIN-DEPENDENT KINASE / CELL CYCLE CONTROL / ALPHA/BETA / COMPLEX (INHIBITOR PROTEIN-KINASE) / COMPLEX (INHIBITOR PROTEIN-KINASE) complex
Function / homology
Function and homology information


cyclin D2-CDK6 complex / cyclin D3-CDK6 complex / cyclin D2-CDK4 complex / cyclin D1-CDK6 complex / cell dedifferentiation / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Drug-mediated inhibition of CDK4/CDK6 activity / FBXO family protein binding / lateral ventricle development ...cyclin D2-CDK6 complex / cyclin D3-CDK6 complex / cyclin D2-CDK4 complex / cyclin D1-CDK6 complex / cell dedifferentiation / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Drug-mediated inhibition of CDK4/CDK6 activity / FBXO family protein binding / lateral ventricle development / autophagic cell death / negative regulation of cell cycle G1/S phase transition / negative regulation of myeloid cell differentiation / type B pancreatic cell development / negative regulation of monocyte differentiation / astrocyte development / dentate gyrus development / regulation of cell motility / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cyclin-dependent protein serine/threonine kinase inhibitor activity / gliogenesis / Regulation of RUNX1 Expression and Activity / regulation of hematopoietic stem cell differentiation / response to vitamin D / positive regulation of cell-matrix adhesion / generation of neurons / DNA synthesis involved in DNA repair / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of cell cycle / regulation of G1/S transition of mitotic cell cycle / negative regulation of cellular senescence / negative regulation of cell differentiation / hematopoietic stem cell differentiation / response to retinoic acid / negative regulation of osteoblast differentiation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / response to UV / cyclin-dependent protein kinase holoenzyme complex / regulation of G2/M transition of mitotic cell cycle / ruffle / Notch signaling pathway / cyclin binding / sensory perception of sound / regulation of erythrocyte differentiation / G1/S transition of mitotic cell cycle / negative regulation of cell growth / Oncogene Induced Senescence / response to virus / positive regulation of fibroblast proliferation / negative regulation of epithelial cell proliferation / Cyclin D associated events in G1 / T cell differentiation in thymus / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / regulation of cell cycle / negative regulation of cell population proliferation / cell division / protein serine kinase activity / DNA damage response / centrosome / positive regulation of gene expression / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Cyclin-dependent kinase 6 / Ankyrin repeat-containing domain / : / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat ...: / Cyclin-dependent kinase 6 / Ankyrin repeat-containing domain / : / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 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 6 / Cyclin-dependent kinase 4 inhibitor D
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBrotherton, D.H. / Dhanaraj, V. / Wick, S. / Brizuela, L. / Domaille, P.J. / Volyanik, E. / Xu, X. / Parisini, E. / Smith, B.O. / Archer, S.J. ...Brotherton, D.H. / Dhanaraj, V. / Wick, S. / Brizuela, L. / Domaille, P.J. / Volyanik, E. / Xu, X. / Parisini, E. / Smith, B.O. / Archer, S.J. / Serrano, M. / Brenner, S.L. / Blundell, T.L. / Laue, E.D.
Citation
Journal: Nature / Year: 1998
Title: Crystal structure of the complex of the cyclin D-dependent kinase Cdk6 bound to the cell-cycle inhibitor p19INK4d.
Authors: Brotherton, D.H. / Dhanaraj, V. / Wick, S. / Brizuela, L. / Domaille, P.J. / Volyanik, E. / Xu, X. / Parisini, E. / Smith, B.O. / Archer, S.J. / Serrano, M. / Brenner, S.L. / Blundell, T.L. / Laue, E.D.
#1: Journal: Nature / Year: 1998
Title: Erratum. Crystal Structure of the Complex of the Cyclin D-Dependent Kinase Cdk6 Bound to the Cell-Cycle Inhibitor P19Ink4D
Authors: Brotherton, D.H. / Dhanaraj, V. / Wick, S. / Brizuela, L. / Domaille, P.J. / Volyanik, E. / Xu, X. / Parisini, E. / Smith, B.O. / Archer, S.J. / Serrano, M. / Brenner, S.L. / Blundell, T.L. / Laue, E.D.
History
DepositionJul 21, 1998Processing site: BNL
Revision 1.0Jun 1, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYCLIN-DEPENDENT KINASE 6
B: P19INK4D
A: CALCIUM ION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8603
Polymers54,8202
Non-polymers401
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-15 kcal/mol
Surface area21750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.210, 76.410, 93.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein CYCLIN-DEPENDENT KINASE 6


Mass: 36987.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Plasmid: GST FUSION PLASMID / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): BL21 (DE3) / References: UniProt: Q00534
#2: Protein P19INK4D


Mass: 17832.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: SF9 / Plasmid: GST FUSION PLASMID / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q60773
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 %PEG80001reservoir
20.1 MMES1reservoir
30.1 Mcadmium acetate1reservoir

-
Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9475
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 1, 1998 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9475 Å / Relative weight: 1
ReflectionResolution: 1.9→18.54 Å / Num. obs: 41965 / % possible obs: 98.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 8.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.327 / % possible all: 97.7
Reflection
*PLUS
Num. measured all: 166218

-
Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1HCK AND 1AP7

1hck

1ap7


Resolution: 1.9→18.54 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.253 -5 %
Rwork0.2 --
obs-41965 98.5 %
Refinement stepCycle: LAST / Resolution: 1.9→18.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3565 0 1 294 3860
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.024
X-RAY DIFFRACTIONp_angle_deg2.3

+
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