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- PDB-9fgq: Structure of human APC3loop 375-381 bound to the NCP -

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Basic information

Entry
Database: PDB / ID: 9fgq
TitleStructure of human APC3loop 375-381 bound to the NCP
Components
  • Cell division cycle protein 27 homolog
  • DNA (131-MER)
  • DNA (132-MER)
  • Histone H2A type 2-A
  • Histone H2B type 1-B
  • Histone H3.1
  • Histone H4
KeywordsCELL CYCLE / Arginine anchor / NCP / APC3 / Complex
Function / homology
Function and homology information


Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of meiotic cell cycle / metaphase/anaphase transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / Phosphorylation of the APC/C / protein K11-linked ubiquitination ...Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of meiotic cell cycle / metaphase/anaphase transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / Phosphorylation of the APC/C / protein K11-linked ubiquitination / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / heterochromatin organization / epigenetic regulation of gene expression / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / regulation of mitotic cell cycle / Inhibition of DNA recombination at telomere / APC/C:Cdc20 mediated degradation of Cyclin B / Meiotic synapsis / APC-Cdc20 mediated degradation of Nek2A / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Defective pyroptosis / Assembly of the pre-replicative complex / HDACs deacetylate histones / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / CDK-mediated phosphorylation and removal of Cdc6 / mitotic spindle / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / spindle / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / Separation of Sister Chromatids / UCH proteinases / nucleosome / nucleosome assembly / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / protein phosphatase binding / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / Ub-specific processing proteases / protein ubiquitination / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / cell division / centrosome / protein-containing complex / DNA binding
Similarity search - Function
Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histone H2B signature. / Histone H2B ...Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Cell division cycle protein 27 homolog / Histone H2B type 1-B / Histone H4 / Histone H3.1 / Histone H2A type 2-A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsYoung, R.V.C. / Muhammad, R. / Alfieri, C.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
The Institute of Cancer Research (ICR) United Kingdom
CitationJournal: To be published
Title: Spatial control of the APC/C ensures the rapid degradation of Cyclin B1
Authors: Cirillo, L. / Young, R.V.C. / Veerapathiran, S. / Roberti, A. / Martin, M. / Abubacar, A. / Perosa, C. / Coates, C. / Muhammad, R. / Roumeliotis, T.I. / Choudhary, J.S. / Alfieri, C. / Pines, J.
History
DepositionMay 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
K: Cell division cycle protein 27 homolog
L: Cell division cycle protein 27 homolog
A: Histone H3.1
B: Histone H4
C: Histone H2A type 2-A
D: Histone H2B type 1-B
E: Histone H3.1
F: Histone H4
G: Histone H2A type 2-A
H: Histone H2B type 1-B
I: DNA (132-MER)
J: DNA (131-MER)


Theoretical massNumber of molelcules
Total (without water)336,67712
Polymers336,67712
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 10 molecules KLAEBFCGDH

#1: Protein Cell division cycle protein 27 homolog / Anaphase-promoting complex subunit 3 / APC3 / CDC27 homolog / CDC27Hs / H-NUC


Mass: 32788.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This is a disorder loop of human APC3 residues 177-446 fused to a SpyTag via a 27 residue GSA linker.
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC27, ANAPC3, D0S1430E, D17S978E / Plasmid: pFastBac1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P30260
#2: Protein Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 15437.167 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Human histone H3.1 / Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
Production host: Escherichia coli (E. coli) / References: UniProt: P68431
#3: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Human histone H4 / Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#4: Protein Histone H2A type 2-A / H2A-clustered histone 18 / H2A-clustered histone 19 / Histone H2A.2 / Histone H2A/o


Mass: 14125.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This is a H2A/H2B fusion protein with a SpyCatcher tag attached
Source: (gene. exp.) Homo sapiens (human)
Gene: H2AC18, H2AFO, HIST2H2AA, HIST2H2AA3, H2AC19, HIST2H2AA4
Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / References: UniProt: Q6FI13
#5: Protein Histone H2B type 1-B / H2B-clustered histone 3 / Histone H2B.1 / Histone H2B.f / H2B/f


Mass: 29445.771 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This is a H2A/H2B fusion protein with a SpyCatcher tag attached,This is a H2A/H2B fusion protein with a SpyCatcher tag attached
Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC3, H2BFF, HIST1H2BB / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / References: UniProt: P33778

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DNA chain , 2 types, 2 molecules IJ

#6: DNA chain DNA (132-MER)


Mass: 64911.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The Widom 147 bp sequence with 32 nucleotides of DNA on either side
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#7: DNA chain DNA (131-MER)


Mass: 65382.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Widom 147 DNA sequence flanked with 32 nucleotides on either side
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 1 types, 75 molecules

#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: APC3 motif bound to the NCP acidic patch / Type: COMPLEX
Details: Recombinant protein sample of residues 375-381 of APC3
Entity ID: #1-#3, #6-#7 / Source: RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8 / Details: 20 mM HEPEs pH8.0, 50 mM NaCl, 0.5 mM TCEP
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPEsC8H18N2O4S1
250 mMSodium chlorideNaCl1
30.5 mMTCEPC9H15O6P1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Image recordingElectron dose: 62 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
13RELION5.0-beta-latest3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2698450
Details: Template base particel picking and Topaz trained particle picking
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 414277 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 50.81 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003412177
ELECTRON MICROSCOPYf_angle_d0.561717554
ELECTRON MICROSCOPYf_chiral_restr0.0351995
ELECTRON MICROSCOPYf_plane_restr0.00411308
ELECTRON MICROSCOPYf_dihedral_angle_d30.59653494

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