+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50416 | |||||||||
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Title | Structure of human APC3loop 375-381 bound to the NCP | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Arginine anchor / NCP / APC3 / Complex / CELL CYCLE | |||||||||
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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
Authors | Young RVC / Muhammad R / Alfieri C | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: To be published Title: Spatial control of the APC/C ensures the rapid degradation of Cyclin B1 Authors: Cirillo L / Young RVC / Veerapathiran S / Roberti A / Martin M / Abubacar A / Perosa C / Coates C / Muhammad R / Roumeliotis TI / Choudhary JS / Alfieri C / Pines J | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_50416.map.gz | 4.8 MB | EMDB map data format | |
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Header (meta data) | emd-50416-v30.xml emd-50416.xml | 24.2 KB 24.2 KB | Display Display | EMDB header |
Images | emd_50416.png | 126.8 KB | ||
Filedesc metadata | emd-50416.cif.gz | 7.6 KB | ||
Others | emd_50416_half_map_1.map.gz emd_50416_half_map_2.map.gz | 29.7 MB 29.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50416 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50416 | HTTPS FTP |
-Validation report
Summary document | emd_50416_validation.pdf.gz | 733.6 KB | Display | EMDB validaton report |
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Full document | emd_50416_full_validation.pdf.gz | 733.2 KB | Display | |
Data in XML | emd_50416_validation.xml.gz | 11 KB | Display | |
Data in CIF | emd_50416_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50416 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50416 | HTTPS FTP |
-Related structure data
Related structure data | 9fgqMC 9fh9C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_50416.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_50416_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_50416_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : APC3 motif bound to the NCP acidic patch
Entire | Name: APC3 motif bound to the NCP acidic patch |
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Components |
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-Supramolecule #1: APC3 motif bound to the NCP acidic patch
Supramolecule | Name: APC3 motif bound to the NCP acidic patch / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3, #6-#7 Details: Recombinant protein sample of residues 375-381 of APC3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Cell division cycle protein 27 homolog
Macromolecule | Name: Cell division cycle protein 27 homolog / type: protein_or_peptide / ID: 1 Details: This is a disorder loop of human APC3 residues 177-446 fused to a SpyTag via a 27 residue GSA linker. Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 32.788488 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: GGSASNCLPN SCTTQVPNHS LSHRQPETVL TETPQDTIEL NRLNLESSNS KYSLNTDSSV SYIDSAVISP DTVPLGTGTS ILSKQVQNK PKTGRSLLGG PAALSPLTPS FGILPLETPS PGDGSYLQNY TNTPPVIDVP STGAPSKKSV ARIGQTGTKS V FSQSGNSR ...String: GGSASNCLPN SCTTQVPNHS LSHRQPETVL TETPQDTIEL NRLNLESSNS KYSLNTDSSV SYIDSAVISP DTVPLGTGTS ILSKQVQNK PKTGRSLLGG PAALSPLTPS FGILPLETPS PGDGSYLQNY TNTPPVIDVP STGAPSKKSV ARIGQTGTKS V FSQSGNSR EVTPILAQTQ SSGPQTSTTP QVLSPTITSP PNALPRRSSR LFTSDSSTTK ENSKKLKMKF PPKIPNRKTK SK TNKGGIT QPNINDSLEI TKLDSSIISE GKISTITGSA GSAGSAGSAG SAGSAGSAGS AGSARGVPHI VMVDAYKRYK UniProtKB: Cell division cycle protein 27 homolog |
-Macromolecule #2: Histone H3.1
Macromolecule | Name: Histone H3.1 / type: protein_or_peptide / ID: 2 / Details: Human histone H3.1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 15.437167 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA UniProtKB: Histone H3.1 |
-Macromolecule #3: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 3 / Details: Human histone H4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.394426 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG UniProtKB: Histone H4 |
-Macromolecule #4: Histone H2A type 2-A
Macromolecule | Name: Histone H2A type 2-A / type: protein_or_peptide / ID: 4 Details: This is a H2A/H2B fusion protein with a SpyCatcher tag attached Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 14.125549 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSGRGKQGGK ARAKAKSRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YMAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHHKAKG K UniProtKB: Histone H2A type 2-A |
-Macromolecule #5: Histone H2B type 1-B
Macromolecule | Name: Histone H2B type 1-B / type: protein_or_peptide / ID: 5 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 Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 29.445771 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: VTTLSGLSGE QGPSGDMTTE EDSATHIKFS KRDEDGRELA GATMELRDSS GKTISTWISD GHVKDFYLYP GKYTFVETAA PDGYEVATP IEFTVNEDGQ VTVDGEATEG DAHTGSAWSH PQFEKGSAGS AAGSGAGWSH PQFEKGSAMP EPSKSAPAPK K GSKKAITK ...String: VTTLSGLSGE QGPSGDMTTE EDSATHIKFS KRDEDGRELA GATMELRDSS GKTISTWISD GHVKDFYLYP GKYTFVETAA PDGYEVATP IEFTVNEDGQ VTVDGEATEG DAHTGSAWSH PQFEKGSAGS AAGSGAGWSH PQFEKGSAMP EPSKSAPAPK K GSKKAITK AQKKDGKKRK RSRKESYSIY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTIT SR EIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK UniProtKB: Histone H2B type 1-B |
-Macromolecule #6: DNA (132-MER)
Macromolecule | Name: DNA (132-MER) / type: dna / ID: 6 Details: The Widom 147 bp sequence with 32 nucleotides of DNA on either side Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 64.911336 KDa |
Sequence | String: (DA)(DT)(DC)(DT)(DT)(DA)(DG)(DC)(DG)(DC) (DG)(DG)(DT)(DG)(DA)(DG)(DT)(DT)(DC)(DA) (DA)(DA)(DT)(DA)(DC)(DC)(DC)(DG)(DG) (DC)(DA)(DA)(DA)(DT)(DC)(DG)(DA)(DG)(DA) (DA) (DT)(DC)(DC)(DC)(DG)(DG) ...String: (DA)(DT)(DC)(DT)(DT)(DA)(DG)(DC)(DG)(DC) (DG)(DG)(DT)(DG)(DA)(DG)(DT)(DT)(DC)(DA) (DA)(DA)(DT)(DA)(DC)(DC)(DC)(DG)(DG) (DC)(DA)(DA)(DA)(DT)(DC)(DG)(DA)(DG)(DA) (DA) (DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG) (DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC) (DT)(DC) (DA)(DA)(DT)(DT)(DG)(DG)(DT) (DC)(DG)(DT)(DA)(DG)(DA)(DC)(DA)(DG)(DC) (DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC) (DG)(DC)(DT)(DT)(DA)(DA)(DA)(DC)(DG)(DC) (DA)(DC)(DG)(DT) (DA)(DC)(DG)(DC)(DG) (DC)(DT)(DG)(DT)(DC)(DC)(DC)(DC)(DC)(DG) (DC)(DG)(DT)(DT)(DT) (DT)(DA)(DA)(DC) (DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG)(DG)(DG) (DA)(DT)(DT)(DA)(DC)(DT) (DC)(DC)(DC) (DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC)(DG)(DT)(DG) (DT)(DC) (DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC)(DC)(DG)(DA)(DT)(DT) (DT) (DG)(DC)(DC)(DG)(DG)(DG)(DT)(DA)(DT)(DT) (DT)(DG)(DA)(DA)(DC)(DT)(DC)(DA)(DC) (DC)(DG)(DC)(DG)(DC)(DT)(DA)(DA)(DG)(DA) (DT) |
-Macromolecule #7: DNA (131-MER)
Macromolecule | Name: DNA (131-MER) / type: dna / ID: 7 Details: Widom 147 DNA sequence flanked with 32 nucleotides on either side Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 65.382633 KDa |
Sequence | String: (DA)(DT)(DC)(DT)(DT)(DA)(DG)(DC)(DG)(DC) (DG)(DG)(DT)(DG)(DA)(DG)(DT)(DT)(DC)(DA) (DA)(DA)(DT)(DA)(DC)(DC)(DC)(DG)(DG) (DC)(DA)(DA)(DA)(DT)(DC)(DG)(DG)(DA)(DT) (DG) (DT)(DA)(DT)(DA)(DT)(DA) ...String: (DA)(DT)(DC)(DT)(DT)(DA)(DG)(DC)(DG)(DC) (DG)(DG)(DT)(DG)(DA)(DG)(DT)(DT)(DC)(DA) (DA)(DA)(DT)(DA)(DC)(DC)(DC)(DG)(DG) (DC)(DA)(DA)(DA)(DT)(DC)(DG)(DG)(DA)(DT) (DG) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC) (DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC) (DC)(DT) (DG)(DG)(DA)(DG)(DA)(DC)(DT) (DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT) (DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC) (DG)(DG)(DT)(DT)(DA)(DA)(DA)(DA)(DC)(DG) (DC)(DG)(DG)(DG) (DG)(DG)(DA)(DC)(DA) (DG)(DC)(DG)(DC)(DG)(DT)(DA)(DC)(DG)(DT) (DG)(DC)(DG)(DT)(DT) (DT)(DA)(DA)(DG) (DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA)(DG)(DA) (DG)(DC)(DT)(DG)(DT)(DC) (DT)(DA)(DC) (DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG)(DC)(DC)(DT) (DC)(DG) (DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT)(DC)(DG)(DA)(DT)(DT) (DT) (DG)(DC)(DC)(DG)(DG)(DG)(DT)(DA)(DT)(DT) (DT)(DG)(DA)(DA)(DC)(DT)(DC)(DA)(DC) (DC)(DG)(DC)(DG)(DC)(DT)(DA)(DA)(DG)(DA) (DT) |
-Macromolecule #8: water
Macromolecule | Name: water / type: ligand / ID: 8 / Number of copies: 75 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
Details: 20 mM HEPEs pH8.0, 50 mM NaCl, 0.5 mM TCEP | ||||||||||||
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 62.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |