5L9T Cell Cycle date Jun 11, 2016
title Model Of Human Anaphase-Promoting Complexcyclosome (Apcc-C E2 Ube2s Poised For Polyubiquitination Where Ube2s, Apc2, A Are Modeled Into Low Resolution Density
authors N.G.Brown, R.Vanderlinden, P.Dube, D.Haselbach, J.M.Peters, H.Sta B.A.Schulman
compound source
Molecule: Anaphase-Promoting Complex Subunit 1
Chain: A
Synonym: Apc1,Cyclosome Subunit 1,Mitotic Checkpoint Regula Testis-Specific Gene 24 Protein;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc1, Tsg24
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Anaphase-Promoting Complex Subunit 11
Chain: B
Synonym: Apc11,Cyclosome Subunit 11,Hepatocellular Carcinom Associated Ring Finger Protein;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc11, Hspc214
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Cell Division Cycle Protein 23 Homolog
Chain: C, P
Synonym: Anaphase-Promoting Complex Subunit 8,Apc8,Cyclosom 8;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdc23, Anapc8
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Anaphase-Promoting Complex Subunit 15
Chain: D
Synonym: Apc15
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc15, C11orf51, Hspc020
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Anaphase-Promoting Complex Subunit 16
Chain: E
Synonym: Apc16,Cyclosome Subunit 16
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc16, C10orf104, Cenp-27
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Cell Division Cycle Protein 27 Homolog
Chain: F, H
Synonym: Anaphase-Promoting Complex Subunit 3,Apc3,Cdc27 Ho Cdc27hs,H-Nuc;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdc27, Anapc3, D0s1430e, D17s978e
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Anaphase-Promoting Complex Subunit Cdc26
Chain: G, W
Synonym: Anaphase-Promoting Complex Subunit 12,Apc12,Cell D Cycle Protein 26 Homolog;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdc26, Anapc12, C9orf17
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Anaphase-Promoting Complex Subunit 4
Chain: I
Synonym: Apc4,Cyclosome Subunit 4
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc4, Apc4
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Cell Division Cycle Protein 16 Homolog
Chain: J, K
Synonym: Anaphase-Promoting Complex Subunit 6,Apc6,Cdc16 Ho Cdc16hs,Cyclosome Subunit 6;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdc16, Anapc6
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Anaphase-Promoting Complex Subunit 10
Chain: L
Synonym: Apc10,Cyclosome Subunit 10
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc10, Apc10
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Anaphase-Promoting Complex Subunit 13
Chain: M
Synonym: Apc13,Cyclosome Subunit 13
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc13
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Anaphase-Promoting Complex Subunit 2
Chain: N
Synonym: Apc2,Cyclosome Subunit 2
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc2, Apc2, Kiaa1406
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Anaphase-Promoting Complex Subunit 5
Chain: O
Synonym: Apc5,Cyclosome Subunit 5
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc5, Apc5
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Fizzy-Related Protein Homolog
Chain: R
Synonym: Fzr,Cdc20-Like Protein 1,Cdh1hct1 Homolog,Hcdh1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fzr1, Cdh1, Fyr, Fzr, Kiaa1242
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Ubiquitin_variant-Hsl1(Substrate) Fusion
Chain: S
Ec: 2.7.11.1
Engineered: Yes
Other_details: This Construct Comprises A Ubiquitin Variant Fused To Apcc Substrate Hsl1 Residues 818-842;

Organism_scientific: Homo Sapiens, Saccharomyces Cerevisiae Atcc 204508 S288c);
Organism_common: Human, Baker'S Yeast
Organism_taxid: 9606, 559292
Strain: Atcc 204508 S288c
Gene: Ubb, Hsl1, Ykl101w, Ykl453
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ubiquitin-Conjugating Enzyme E2 S
Chain: T
Synonym: E2 Ubiquitin-Conjugating Enzyme S,E2-Epf,Ubiquitin Protein S,Ubiquitin-Conjugating Enzyme E2-24 Kda,Ubiquitin- Conjugating Enzyme E2-Epf5,Ubiquitin-Protein Ligase S;
Ec: 2.3.2.23
Engineered: Yes
Mutation: Yes
Other_details: This Construct As An N-Terminal Remnant Of C Site And Linker. C95 Of This Construct Is Cross-Linked To U And Ub G75c Via Tmea.;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ube2s, E2epf, Oksw-Cl.73
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Anaphase-Promoting Complex Subunit 7
Chain: X, Y
Synonym: Apc7,Cyclosome Subunit 7
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Anapc7, Apc7
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 6.40 Å
ligand
enzyme Transferase E.C.2.7.11.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


C, P


D


E


F, H


I


K, J


L


M


N


R


W, G


Y, O, X


Primary referenceDual RING E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC/C., Brown NG, VanderLinden R, Watson ER, Weissmann F, Ordureau A, Wu KP, Zhang W, Yu S, Mercredi PY, Harrison JS, Davidson IF, Qiao R, Lu Y, Dube P, Brunner MR, Grace CR, Miller DJ, Haselbach D, Jarvis MA, Yamaguchi M, Yanishevski D, Petzold G, Sidhu SS, Kuhlman B, Kirschner MW, Harper JW, Peters JM, Stark H, Schulman BA, Cell. 2016 Jun 2;165(6):1440-53. doi: 10.1016/j.cell.2016.05.037. PMID:27259151
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (211 Kb) [Save to disk]
  • Biological Unit Coordinates (5l9t.pdb1.gz) 192 Kb
  • CSU: Contacts of Structural Units for 5L9T
  • Retrieve 5L9T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5L9T from S2C, [Save to disk]
  • View 5L9T in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5L9T
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5l9t from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5l9t_P] [5l9t_E] [5l9t] [5l9t_R] [5l9t_G] [5l9t_Y] [5l9t_H] [5l9t_K] [5l9t_W] [5l9t_M] [5l9t_A] [5l9t_N] [5l9t_T] [5l9t_J] [5l9t_O] [5l9t_S] [5l9t_D] [5l9t_F] [5l9t_L] [5l9t_X] [5l9t_I] [5l9t_C] [5l9t_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5L9T: [APC10] [APC2] [CULLIN] [RING] [TPR] [UBCc] [UBQ] [WD40 ] by SMART
  • Other resources with information on 5L9T
  • Community annotation for 5L9T at PDBWiki (http://pdbwiki.org)

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