[English] 日本語
Yorodumi
- PDB-6ath: Cdk2/cyclin A/p27-KID-deltaC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ath
TitleCdk2/cyclin A/p27-KID-deltaC
Components
  • Cyclin-A2
  • Cyclin-dependent kinase 2
  • Cyclin-dependent kinase inhibitor 1B
KeywordsTRANSFERASE / Inhibitor / Complex / IDP / CDK / Cyclin / kinase / Phosphortlation
Function / homology
Function and homology information


cyclin-dependent protein kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / autophagic cell death / FOXO-mediated transcription of cell cycle genes / negative regulation of epithelial cell proliferation involved in prostate gland development / cyclin A2-CDK1 complex / regulation of cell cycle G1/S phase transition / epithelial cell proliferation involved in prostate gland development / cell cycle G1/S phase transition ...cyclin-dependent protein kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / autophagic cell death / FOXO-mediated transcription of cell cycle genes / negative regulation of epithelial cell proliferation involved in prostate gland development / cyclin A2-CDK1 complex / regulation of cell cycle G1/S phase transition / epithelial cell proliferation involved in prostate gland development / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / negative regulation of epithelial cell apoptotic process / regulation of exit from mitosis / G2/M DNA replication checkpoint / cyclin-dependent protein serine/threonine kinase inhibitor activity / negative regulation of mitotic cell cycle / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / regulation of cyclin-dependent protein serine/threonine kinase activity / male pronucleus / female pronucleus / nuclear export / RHO GTPases activate CIT / cellular response to cocaine / epithelial cell apoptotic process / AKT phosphorylates targets in the cytosol / response to glucagon / ubiquitin ligase activator activity / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to lithium ion / molecular function inhibitor activity / positive regulation of DNA biosynthetic process / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cellular response to insulin-like growth factor stimulus / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / Y chromosome / cyclin-dependent protein kinase activity / regulation of heterochromatin organization / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / X chromosome / PTK6 Regulates Cell Cycle / Constitutive Signaling by AKT1 E17K in Cancer / inner ear development / regulation of anaphase-promoting complex-dependent catabolic process / cellular response to antibiotic / Cul4A-RING E3 ubiquitin ligase complex / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / protein kinase inhibitor activity / telomere maintenance in response to DNA damage / ciliary transition zone / regulation of DNA replication / centrosome duplication / animal organ regeneration / microtubule organizing center / G0 and Early G1 / negative regulation of vascular associated smooth muscle cell proliferation / cochlea development / Telomere Extension By Telomerase / Activation of the pre-replicative complex / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Notch signaling pathway / Activation of ATR in response to replication stress / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cajal body / Cyclin E associated events during G1/S transition / regulation of G2/M transition of mitotic cell cycle / Cyclin A:Cdk2-associated events at S phase entry / cellular response to platelet-derived growth factor stimulus / Cyclin A/B1/B2 associated events during G2/M transition / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / cyclin-dependent protein kinase holoenzyme complex / positive regulation of microtubule polymerization / regulation of G1/S transition of mitotic cell cycle / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / cellular response to nitric oxide / negative regulation of protein localization to chromatin / FLT3 Signaling / regulation of mitotic cell cycle / post-translational protein modification / placenta development / regulation of cell migration / cyclin binding / positive regulation of DNA replication / male germ cell nucleus / potassium ion transport / peptidyl-serine phosphorylation / DNA damage response, signal transduction by p53 class mediator / cellular response to estradiol stimulus
Similarity search - Function
Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin ...Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin-like / Cyclin, C-terminal domain / Cyclin_C / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cyclin-A2 / Cyclin-dependent kinase 2 / Cyclin-dependent kinase inhibitor 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsWhite, S.W. / Yun, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA82491, P30 CA21765 United States
CitationJournal: Nat Commun / Year: 2019
Title: Dynamic anticipation by Cdk2/Cyclin A-bound p27 mediates signal integration in cell cycle regulation.
Authors: Tsytlonok, M. / Sanabria, H. / Wang, Y. / Felekyan, S. / Hemmen, K. / Phillips, A.H. / Yun, M.K. / Waddell, M.B. / Park, C.G. / Vaithiyalingam, S. / Iconaru, L. / White, S.W. / Tompa, P. / ...Authors: Tsytlonok, M. / Sanabria, H. / Wang, Y. / Felekyan, S. / Hemmen, K. / Phillips, A.H. / Yun, M.K. / Waddell, M.B. / Park, C.G. / Vaithiyalingam, S. / Iconaru, L. / White, S.W. / Tompa, P. / Seidel, C.A.M. / Kriwacki, R.
History
DepositionAug 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.3Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclin-dependent kinase 2
B: Cyclin-A2
C: Cyclin-dependent kinase inhibitor 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5454
Polymers72,4493
Non-polymers961
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-54 kcal/mol
Surface area24910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.191, 77.645, 137.511
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 2 / Cell division protein kinase 2 / p33 protein kinase


Mass: 34200.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Phosphorylated / Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, cyclin-dependent kinase
#2: Protein Cyclin-A2 / Cyclin-A / Cyclin A


Mass: 30142.834 Da / Num. of mol.: 1 / Fragment: UNP residues 173-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNA2, CCN1, CCNA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P20248
#3: Protein Cyclin-dependent kinase inhibitor 1B / Cyclin-dependent kinase inhibitor p27 / p27Kip1


Mass: 8105.980 Da / Num. of mol.: 1 / Fragment: UNP residues 22-85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDKN1B, KIP1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P46527
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: HEPES, Lithium Sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 30, 2007
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 71452 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 26.6
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6848 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPv9.2.10phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JSU

1jsu


Resolution: 1.82→29.625 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.44
RfactorNum. reflection% reflection
Rfree0.1873 3582 5.02 %
Rwork0.1711 --
obs0.1719 71378 98.61 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 42.912 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--0.1949 Å20 Å2-0 Å2
2--1.6979 Å2-0 Å2
3----1.503 Å2
Refinement stepCycle: LAST / Resolution: 1.82→29.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 5 399 5160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054903
X-RAY DIFFRACTIONf_angle_d0.946661
X-RAY DIFFRACTIONf_dihedral_angle_d14.0821830
X-RAY DIFFRACTIONf_chiral_restr0.068746
X-RAY DIFFRACTIONf_plane_restr0.005840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8158-1.83970.27721200.29142071X-RAY DIFFRACTION80
1.8397-1.86490.28921470.25962484X-RAY DIFFRACTION96
1.8649-1.89150.23991210.22862560X-RAY DIFFRACTION98
1.8915-1.91970.22251520.2172509X-RAY DIFFRACTION97
1.9197-1.94970.25811510.19152533X-RAY DIFFRACTION97
1.9497-1.98170.22141390.17872541X-RAY DIFFRACTION98
1.9817-2.01580.20511390.16212579X-RAY DIFFRACTION100
2.0158-2.05250.18361380.15732652X-RAY DIFFRACTION100
2.0525-2.0920.17721390.15462587X-RAY DIFFRACTION100
2.092-2.13460.17791350.15312603X-RAY DIFFRACTION100
2.1346-2.1810.16791700.14842629X-RAY DIFFRACTION100
2.181-2.23180.16681240.15312618X-RAY DIFFRACTION100
2.2318-2.28760.17491320.15862641X-RAY DIFFRACTION100
2.2876-2.34940.19381290.16132610X-RAY DIFFRACTION100
2.3494-2.41850.19161280.16092662X-RAY DIFFRACTION100
2.4185-2.49650.16661350.1612644X-RAY DIFFRACTION100
2.4965-2.58570.23781110.16152638X-RAY DIFFRACTION100
2.5857-2.68910.17811450.16832663X-RAY DIFFRACTION100
2.6891-2.81140.17221460.16982623X-RAY DIFFRACTION100
2.8114-2.95950.1771190.18082670X-RAY DIFFRACTION100
2.9595-3.14480.21121310.18272684X-RAY DIFFRACTION100
3.1448-3.38730.19031460.17722657X-RAY DIFFRACTION100
3.3873-3.72750.17661440.15852681X-RAY DIFFRACTION100
3.7275-4.26560.15251480.15092681X-RAY DIFFRACTION100
4.2656-5.36890.1691460.15812728X-RAY DIFFRACTION100
5.3689-29.62860.20111470.20012848X-RAY DIFFRACTION100
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)
11.2434-0.4186-0.17760.95920.40751.1998-0.0896-0.14580.01120.11930.00570.0630.2019-0.05120.03140.0761-0.01950.03790.1253-0.03490.096317.19389.272171.8809
20.98570.1627-0.20981.41350.37421.1638-0.04010.02050.0272-0.0243-0.00160.07530.1071-0.0280.02540.08610.00180.01390.0636-0.01540.070831.8965-5.551445.743
30.1466-0.1567-0.09790.1956-0.0711.4249-0.2282-0.3142-0.56080.78550.03520.1470.4297-0.025-0.17440.9315-0.07110.1370.23070.17620.260723.0649-23.980267.163
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

+
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