5V8F Replication date Mar 21, 2017
title Structural Basis Of Mcm2-7 Replicative Helicase Loading By O And Cdt1
authors Z.Yuan, A.Riera, L.Bai, J.Sun, C.Spanos, Z.A.Chen, M.Barbon, J.Rapp B.Stillman, C.Speck, H.Li
compound source
Molecule: Dna Replication Licensing Factor Mcm2
Chain: 2
Synonym: Minichromosome Maintenance Protein 2
Ec: 3.6.4.12
Engineered: Yes
 Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Mcm2, Ybl023c, Ybl0438
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Dna Replication Licensing Factor Mcm3
Chain: 3
Synonym: Minichromosome Maintenance Protein 3
Ec: 3.6.4.12
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Mcm3, Yel032w, Sygp-Orf23
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Dna Replication Licensing Factor Mcm4
Chain: 4
Synonym: Cell Division Control Protein 54
Ec: 3.6.4.12
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Mcm4, Cdc54, Hcd21, Ypr019w, Yp9531.13
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Minichromosome Maintenance Protein 5
Chain: 5
Synonym: Cell Division Control Protein 46
Ec: 3.6.4.12
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Mcm5, Cdc46, Ylr274w, L9328.1
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Dna Replication Licensing Factor Mcm6
Chain: 6
Synonym: Minichromosome Maintenance Protein 6
Ec: 3.6.4.12
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Mcm6, Ygl201c
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Dna Replication Licensing Factor Mcm7
Chain: 7
Synonym: Cell Division Control Protein 47,Minichromosome Ma Protein 7;
Ec: 3.6.4.12
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Mcm7, Cdc47, Ybr202w, Ybr1441
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Cell Division Cycle Protein Cdt1
Chain: 8
Synonym: Sic1 Indispensable Protein 2,Topoisomerase-A Hyper Protein 11;
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Tah11, Cdt1, Sid2, Yjr046w, J1641
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Cell Division Control Protein 6
Chain: 9
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Cdc6, Yjl194w, J0347
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Origin Recognition Complex Subunit 1
Chain: A
Synonym: Origin Recognition Complex 120 Kda Subunit
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Orc1, Yml065w
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Origin Recognition Complex Subunit 2
Chain: B
Synonym: Origin Recognition Complex 71 Kda Subunit
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Orc2, Rrr1, Sir5, Ybr060c, Ybr0523
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Origin Recognition Complex Subunit 3
Chain: C
Synonym: Origin Recognition Complex 62 Kda Subunit
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Orc3, Oaf1, Oif1, Yll004w, L1365
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Origin Recognition Complex Subunit 5
Chain: E
Synonym: Origin Recognition Complex 53 Kda Subunit
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Orc5, Ynl261w, N0834
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Origin Recognition Complex Subunit 4
Chain: D
Synonym: Origin Recognition Complex 56 Kda Subunit
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Orc4, Ypr162c, P9325.5
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Origin Recognition Complex Subunit 6
Chain: F
Synonym: Acs-Associated Protein 1,Origin Recognition Comple Subunit;
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Orc6, Aap1, Yhr118c
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Dna (39-Mer)
Chain: M
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (39-Mer)
Chain: N
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
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 3.90 Å
ligand AGS enzyme Hydrolase E.C.3.6.4.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
2


3
  • chromatin silencing at telom...

    • 4


    5


    6


    7
  • chromatin silencing at telom...

    • 8


    9


    A


    B
  • chromatin silencing at telom...

    • C


    D


    E


    F


    Primary referenceStructural basis of Mcm2-7 replicative helicase loading by ORC-Cdc6 and Cdt1., Yuan Z, Riera A, Bai L, Sun J, Nandi S, Spanos C, Chen ZA, Barbon M, Rappsilber J, Stillman B, Speck C, Li H, Nat Struct Mol Biol. 2017 Mar;24(3):316-324. doi: 10.1038/nsmb.3372. Epub 2017, Feb 13. PMID:28191893
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1102 Kb) [Save to disk]
  • Biological Unit Coordinates (5v8f.pdb1.gz) 1081 Kb
  • LPC: Ligand-Protein Contacts for 5V8F
  • CSU: Contacts of Structural Units for 5V8F
  • Retrieve 5V8F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5V8F from S2C, [Save to disk]
    • View 5V8F 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 5V8F
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5v8f_3] [5v8f_D] [5v8f_9] [5v8f] [5v8f_2] [5v8f_5] [5v8f_7] [5v8f_A] [5v8f_6] [5v8f_M] [5v8f_4] [5v8f_C] [5v8f_F] [5v8f_N] [5v8f_E] [5v8f_8] [5v8f_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5V8F
  • Community annotation for 5V8F at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science