[English] 日本語
Yorodumi
- PDB-2w99: Crystal Structure of CDK4 in complex with a D-type cyclin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2w99
TitleCrystal Structure of CDK4 in complex with a D-type cyclin
Components
  • CELL DIVISION PROTEIN KINASE 4
  • G1/S-SPECIFIC CYCLIN-D1
KeywordsCELL CYCLE / SERINE/THREONINE-PROTEIN KINASE / CHROMOSOMAL REARRANGEMENT / ATP-BINDING / TRANSFERASE / POLYMORPHISM / CELL DIVISION / PROTO-ONCOGENE / PHOSPHOPROTEIN / DISEASE MUTATION / NUCLEOTIDE-BINDING / CYCLIN DEPENDENT KINASE / KINASE / CYCLIN / ONCOLOGY / DRUG DESGN
Function / homology
Function and homology information


cyclin D3-CDK4 complex / cyclin D1-CDK4 complex / cyclin D2-CDK4 complex / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 / re-entry into mitotic cell cycle / cyclin D1-CDK6 complex / cellular response to ionomycin / regulation of transcription initiation by RNA polymerase II / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 ...cyclin D3-CDK4 complex / cyclin D1-CDK4 complex / cyclin D2-CDK4 complex / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 / re-entry into mitotic cell cycle / cyclin D1-CDK6 complex / cellular response to ionomycin / regulation of transcription initiation by RNA polymerase II / 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 / regulation of type B pancreatic cell proliferation / RUNX3 regulates WNT signaling / response to leptin / positive regulation of mammary gland epithelial cell proliferation / Transcriptional regulation by RUNX2 / cellular response to phorbol 13-acetate 12-myristate / positive regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein serine/threonine kinase activator activity / proline-rich region binding / Regulation of RUNX1 Expression and Activity / cyclin-dependent protein serine/threonine kinase regulator activity / mammary gland epithelial cell proliferation / response to UV-A / negative regulation of epithelial cell differentiation / PTK6 Regulates Cell Cycle / fat cell differentiation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / microtubule organizing center / RUNX3 regulates p14-ARF / Transcriptional Regulation by VENTX / mammary gland alveolus development / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of G1/S transition of mitotic cell cycle / bicellular tight junction / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / endoplasmic reticulum unfolded protein response / cyclin-dependent protein kinase holoenzyme complex / regulation of G2/M transition of mitotic cell cycle / positive regulation of G2/M transition of mitotic cell cycle / mitotic G1 DNA damage checkpoint signaling / lactation / transcription repressor complex / cellular response to interleukin-4 / cyclin binding / liver regeneration / Ubiquitin-dependent degradation of Cyclin D / Oncogene Induced Senescence / Meiotic recombination / Transcriptional regulation of white adipocyte differentiation / Pre-NOTCH Transcription and Translation / SCF(Skp2)-mediated degradation of p27/p21 / Wnt signaling pathway / G1/S transition of mitotic cell cycle / RMTs methylate histone arginines / histone deacetylase binding / Transcriptional regulation of granulopoiesis / positive regulation of fibroblast proliferation / neuron differentiation / transcription corepressor activity / Cyclin D associated events in G1 / positive regulation of protein phosphorylation / regulation of gene expression / cellular response to lipopolysaccharide / Senescence-Associated Secretory Phenotype (SASP) / Interleukin-4 and Interleukin-13 signaling / Oxidative Stress Induced Senescence / nuclear membrane / transcription regulator complex / Estrogen-dependent gene expression / negative regulation of neuron apoptotic process / protein kinase activity / regulation of cell cycle / protein phosphorylation / response to xenobiotic stimulus / cell division / protein serine kinase activity / positive regulation of cell population proliferation / DNA damage response / protein kinase binding / chromatin / nucleolus / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain ...Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / 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 4 / G1/S-specific cyclin-D1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDay, P.J. / Cleasby, A. / Tickle, I.J. / Reilly, M.O. / Coyle, J.E. / Holding, F.P. / McMenamin, R.L. / Yon, J. / Chopra, R. / Lengauer, C. / Jhoti, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Crystal Structure of Human Cdk4 in Complex with a D-Type Cyclin.
Authors: Day, P.J. / Cleasby, A. / Tickle, I.J. / O'Reilly, M. / Coyle, J.E. / Holding, F.P. / Mcmenamin, R.L. / Yon, J. / Chopra, R. / Lengauer, C. / Jhoti, H.
History
DepositionJan 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 24, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: G1/S-SPECIFIC CYCLIN-D1
B: CELL DIVISION PROTEIN KINASE 4


Theoretical massNumber of molelcules
Total (without water)65,5352
Polymers65,5352
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-11.9 kcal/mol
Surface area30860 Å2
MethodPQS
Unit cell
Length a, b, c (Å)57.023, 64.684, 188.747
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein G1/S-SPECIFIC CYCLIN-D1 / D-TYPE CYCLIN / PRAD1 ONCOGENE


Mass: 30990.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P24385
#2: Protein CELL DIVISION PROTEIN KINASE 4 / CDK4 / CYCLIN-DEPENDENT KINASE 4 / PSK-J3


Mass: 34544.625 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 1-44,48-303 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P11802, cyclin-dependent kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN B, GLY 43 TO GLU ENGINEERED RESIDUE IN CHAIN B, GLY 44 TO GLU ...ENGINEERED RESIDUE IN CHAIN B, GLY 43 TO GLU ENGINEERED RESIDUE IN CHAIN B, GLY 44 TO GLU ENGINEERED RESIDUE IN CHAIN B, THR 172 TO ALA
Sequence detailsRESIDUES 1-271 WERE EXPRESSED, BUT THE N AND C-TERMINAL WERE DISORDERED AND THEREFORE NOT COMPLETE ...RESIDUES 1-271 WERE EXPRESSED, BUT THE N AND C-TERMINAL WERE DISORDERED AND THEREFORE NOT COMPLETE IN THE MODEL. HIS TAG WAS ADDED AT THE C-TERMINAL. RESIDUES 45, 46, 47 IN CHAIN B WERE DELETED.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.28 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.94
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 2.8→94.5 Å / Num. obs: 17640 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 78.76 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6
Reflection shellResolution: 2.8→2.91 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.5 / % possible all: 94.8

-
Processing

Software
NameVersionClassification
BUSTER-TNT2.1.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BLX

1blx


Resolution: 2.8→94.49 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELLED STEREOCHEMICALLY WHERE THE DENSITY WAS NOT CLEAR. IN REGIONS WHERE THE DENSITY WAS UNINTERPRETABLE OR ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELLED STEREOCHEMICALLY WHERE THE DENSITY WAS NOT CLEAR. IN REGIONS WHERE THE DENSITY WAS UNINTERPRETABLE OR ABSENT, RESIDUES WERE OMITTED.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 845 4.79 %RANDOM
Rwork0.213 ---
obs0.216 17640 98.3 %-
Displacement parametersBiso mean: 86.21 Å2
Baniso -1Baniso -2Baniso -3
1--4.53183 Å20 Å20 Å2
2--10.1525 Å20 Å2
3----5.62067 Å2
Refinement stepCycle: LAST / Resolution: 2.8→94.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4259 0 0 126 4385
LS refinement shellResolution: 2.8→2.97 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2633 132 4.97 %
Rwork0.2142 2524 -
all0.2166 2656 -
obs--98.27 %

+
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