[English] 日本語
Yorodumi
- PDB-4ggd: Structural analysis of human Cdc20 supports multisite degron reco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ggd
TitleStructural analysis of human Cdc20 supports multisite degron recognition by APC/C.
Components
  • Cell division cycle protein 20 homolog
  • Mitotic checkpoint serine/threonine-protein kinase BUB1 beta
KeywordsCELL CYCLE / mitosis / securin / ubiquitination / WD40
Function / homology
Function and homology information


metaphase/anaphase transition of cell cycle / metaphase/anaphase transition of meiosis I / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / regulation of meiotic nuclear division / meiotic sister chromatid cohesion, centromeric / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of synapse maturation / Inactivation of APC/C via direct inhibition of the APC/C complex ...metaphase/anaphase transition of cell cycle / metaphase/anaphase transition of meiosis I / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / regulation of meiotic nuclear division / meiotic sister chromatid cohesion, centromeric / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of synapse maturation / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Phosphorylation of Emi1 / anaphase-promoting complex / regulation of meiotic cell cycle / metaphase/anaphase transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / positive regulation of synaptic plasticity / anaphase-promoting complex binding / outer kinetochore / protein localization to chromosome, centromeric region / ubiquitin ligase activator activity / positive regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin protein ligase activity / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / Regulation of APC/C activators between G1/S and early anaphase / ubiquitin-like ligase-substrate adaptor activity / mitotic spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / regulation of mitotic cell cycle / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / RHO GTPases Activate Formins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / kinetochore / spindle pole / spindle / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / cell differentiation / non-specific serine/threonine protein kinase / Ub-specific processing proteases / protein kinase activity / protein ubiquitination / phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / perinuclear region of cytoplasm / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Mad3/Bub1 homology region 1 / Mitotic spindle checkpoint protein Bub1/Mad3 / Mad3/BUB1 homology region 1 / BUB1 N-terminal domain profile. / Mad3/BUB1 hoMad3/BUB1 homology region 1 / The WD repeat Cdc20/Fizzy family / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller ...Mad3/Bub1 homology region 1 / Mitotic spindle checkpoint protein Bub1/Mad3 / Mad3/BUB1 homology region 1 / BUB1 N-terminal domain profile. / Mad3/BUB1 hoMad3/BUB1 homology region 1 / The WD repeat Cdc20/Fizzy family / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Mitotic checkpoint serine/threonine-protein kinase BUB1 beta / Cell division cycle protein 20 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.435 Å
AuthorsLuo, X. / Tian, W. / Tomchick, D.R.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural analysis of human Cdc20 supports multisite degron recognition by APC/C.
Authors: Tian, W. / Li, B. / Warrington, R. / Tomchick, D.R. / Yu, H. / Luo, X.
#1: Journal: Mol.Cell / Year: 2007
Title: Cdc20: a WD40 activator for a cell cycle degradation machine
Authors: Yu, H.
#2: Journal: J.Biol.Chem. / Year: 2007
Title: KEN-box-dependent degradation of Bub1 spindle checkpoint kinase by the anaphase-promoting complex/cyclosome
Authors: Qi, W. / Yu, H.
#3: Journal: Dev.Cell / Year: 2001
Title: Mad2-independent inhibition of APC-Cdc20 by the mitotic checkpoint protein BubR1
Authors: Tang, Z. / Bharadwaj, R. / Li, B. / Yu, H.
History
DepositionAug 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Oct 26, 2016Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.5Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cell division cycle protein 20 homolog
B: Cell division cycle protein 20 homolog
C: Mitotic checkpoint serine/threonine-protein kinase BUB1 beta
D: Mitotic checkpoint serine/threonine-protein kinase BUB1 beta


Theoretical massNumber of molelcules
Total (without water)100,5134
Polymers100,5134
Non-polymers00
Water3,333185
1
A: Cell division cycle protein 20 homolog
C: Mitotic checkpoint serine/threonine-protein kinase BUB1 beta


Theoretical massNumber of molelcules
Total (without water)50,2562
Polymers50,2562
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell division cycle protein 20 homolog
D: Mitotic checkpoint serine/threonine-protein kinase BUB1 beta


Theoretical massNumber of molelcules
Total (without water)50,2562
Polymers50,2562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.826, 88.129, 118.351
Angle α, β, γ (deg.)90.000, 99.660, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cell division cycle protein 20 homolog / p55CDC


Mass: 47495.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC20 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q12834
#2: Protein/peptide Mitotic checkpoint serine/threonine-protein kinase BUB1 beta / MAD3/BUB1-related protein kinase / hBUBR1 / Mitotic checkpoint kinase MAD3L / Protein SSK1


Mass: 2761.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: O60566, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 293 K / Method: sitting-drop vapor diffusion / pH: 9.3
Details: 50 mM CAPSO, 5% (w/v) PEG 6000, and 15.5 % MPD, pH 9.3, sitting-drop vapor diffusion, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2010 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.435→48.6 Å / Num. all: 36956 / Num. obs: 36910 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 39.4 Å2 / Limit h max: 19 / Limit h min: -20 / Limit k max: 35 / Limit k min: 0 / Limit l max: 47 / Limit l min: 0 / Rmerge(I) obs: 0.104 / Net I/σ(I): 14.7
Reflection scaleGroup code: 1
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 3.9 % / Num. unique all: 1762 / % possible all: 93.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1062refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.435→29.168 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.83 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2012 1835 4.97 %RANDOM
Rwork0.1541 ---
all0.1565 36910 --
obs0.1565 36910 97.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.68 Å2 / Biso mean: 43.9021 Å2 / Biso min: 8.96 Å2
Refine analyzeLuzzati sigma a obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.435→29.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4949 0 0 185 5134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135079
X-RAY DIFFRACTIONf_angle_d1.4176928
X-RAY DIFFRACTIONf_chiral_restr0.077757
X-RAY DIFFRACTIONf_plane_restr0.006888
X-RAY DIFFRACTIONf_dihedral_angle_d14.4241766
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.4346-2.50040.261110.215922412352224180
2.5004-2.57390.30071460.205827142860271499
2.5739-2.65690.24461490.195726932842269397
2.6569-2.75180.26271400.18827142854271498
2.7518-2.86190.26761410.184726942835269499
2.8619-2.9920.24581420.180327002842270098
2.992-3.14960.22521470.169627462893274698
3.1496-3.34670.2091330.166627282861272899
3.3467-3.60460.21941410.149627492890274999
3.6046-3.96660.18511460.141827442890274499
3.9666-4.53870.16881440.119127712915277199
4.5387-5.71130.15521510.119727542905275499
5.7113-29.170.17571440.161328272971282799
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)
10.49950.39220.13560.76630.19520.3115-0.0590.30760.43310.0775-0.00660.0443-0.08220.0917-0.31620.19620.0542-0.03410.31810.18150.2692-12.146312.2023-55.5632
20.1266-0.3356-0.01950.92890.05720.4171-0.00440.3202-0.110.01120.07590.30670.1944-0.22-0.01090.1338-0.0132-0.05650.3386-0.02150.1469-21.9958-1.6915-54.7155
30.16920.0239-0.01940.0698-0.0830.09610.0698-0.0833-0.26560.10890.0220.04440.0378-0.02760.00030.18830.0069-0.00270.1357-0.00210.169-8.7197-8.182-41.4999
40.32010.1116-0.07630.2671-0.08510.1264-0.10090.26550.42440.1764-0.0919-0.1818-0.07880.1791-0.01510.21080.0103-0.03260.21830.10680.3259-0.846810.1311-49.1967
50.4101-0.2844-0.14390.81510.31270.680.0185-0.4593-0.2651-0.0274-0.08270.1015-0.037-0.1553-0.44010.1071-0.05880.05460.28580.14010.1575-3.5612-8.4054-2.3752
60.34540.1409-0.0940.2031-0.17250.1968-0.0639-0.05380.1114-0.0525-0.03390.066-0.0542-0.01-00.1256-0.01610.00210.1075-0.03180.13474.77183.8902-13.63
70.1803-0.0147-0.05750.1173-0.07030.3430.0113-0.2729-0.521-0.0903-0.0941-0.21930.13680.27070.05990.193-0.03820.05240.21070.25230.369113.5664-14.0262-8.1723
80.0009-0.00010.00140.0020.00120.00250.0255-0.0077-0.00220.01340.02750.02830.02380.012500.48670.1405-0.02360.4271-0.16190.3447-14.91310.6371-33.9571
90.00360.0012-0.00160.0004-0.00030.00060.01630.03580.02810.00720.09430.02760.04510.0032-00.2912-0.06990.00550.1836-0.01920.2185-1.4582-12.5557-24.7615
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 165 through 202 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 203 through 285 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 286 through 359 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 360 through 476 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 165 through 254 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 255 through 380 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 381 through 476 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 5 through 11 )C0
9X-RAY DIFFRACTION9chain 'D' and (resid 4 through 11 )D0

+
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://pdbjlvh1.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