[English] 日本語
Yorodumi
- PDB-1bd8: STRUCTURE OF CDK INHIBITOR P19INK4D -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bd8
TitleSTRUCTURE OF CDK INHIBITOR P19INK4D
ComponentsP19INK4D CDK4/6 INHIBITOR
KeywordsTUMOR SUPPRESSOR / CDK4/6 INHIBITOR / ANKYRIN MOTIF
Function / homology
Function and homology information


cyclin D2-CDK4 complex / autophagic cell death / negative regulation of cell cycle G1/S phase transition / negative regulation of phosphorylation / response to vitamin D / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cyclin-dependent protein serine/threonine kinase inhibitor activity / DNA synthesis involved in DNA repair / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of G1/S transition of mitotic cell cycle ...cyclin D2-CDK4 complex / autophagic cell death / negative regulation of cell cycle G1/S phase transition / negative regulation of phosphorylation / response to vitamin D / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cyclin-dependent protein serine/threonine kinase inhibitor activity / DNA synthesis involved in DNA repair / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of G1/S transition of mitotic cell cycle / response to retinoic acid / response to UV / sensory perception of sound / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Oncogene Induced Senescence / negative regulation of cell growth / Cyclin D associated events in G1 / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / cell cycle / negative regulation of cell population proliferation / protein kinase binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
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 / Mainly Alpha
Similarity search - Domain/homology
Cyclin-dependent kinase 4 inhibitor D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.8 Å
AuthorsBaumgartner, R. / Fernandez-Catalan, C. / Winoto, A. / Huber, R. / Engh, R. / Holak, T.A.
Citation
Journal: Structure / Year: 1998
Title: Structure of human cyclin-dependent kinase inhibitor p19INK4d: comparison to known ankyrin-repeat-containing structures and implications for the dysfunction of tumor suppressor p16INK4a.
Authors: Baumgartner, R. / Fernandez-Catalan, C. / Winoto, A. / Huber, R. / Engh, R.A. / Holak, T.A.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal Structure of the Cdk4/6 Inhibitory Protein P18Ink4C Provides Insights Into Ankyrin-Like Repeat Structure/Function and Tumor-Derived P16Ink4 Mutations
Authors: Venkataramani, R. / Swaminathan, K. / Marmorstein, R.
History
DepositionMay 12, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: P19INK4D CDK4/6 INHIBITOR


Theoretical massNumber of molelcules
Total (without water)16,6281
Polymers16,6281
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.470, 54.560, 45.590
Angle α, β, γ (deg.)90.00, 90.16, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein P19INK4D CDK4/6 INHIBITOR


Mass: 16627.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Cellular location: CYTOPLASM / Plasmid: PET-15B / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P55273
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 1.86 Å3/Da / Density % sol: 34 % / Description: DATA COLLECTED IN THE OSCILLATION MODE.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 35% PEG 4000, 200 MM MGSO4 AND 200 MM TRIS/HCL PH 8.5, SITTING DROP METHOD, AT 4 DEG. C., vapor diffusion - sitting drop, temperature 277K
Crystal
*PLUS
Density % sol: 35 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
230 %PEG40001reservoir
30.1 MTris-HCl1reservoir
40.2 M1reservoirMgCl2

-
Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 13017 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.7
Reflection
*PLUS
% possible obs: 99.4 %

-
Processing

Software
NameVersionClassification
CCP4SUITEmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Highest resolution: 1.8 Å /
Rfactor% reflection
Rfree0.26 5 %
Rwork0.19 -
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1167 0 0 198 1365
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.0058
X-RAY DIFFRACTIONp_angle_deg0.96

+
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