6HV9 Dna Binding Protein date Oct 10, 2018
title S. Cerevisiae Cmg-Pol Epsilon-Dna
authors F.Abid Ali, A.G.Purkiss, A.Cheung, A.Costa
compound source
Molecule: Dna Replication Licensing Factor Mcm3
Chain: 3
Synonym: Minichromosome Maintenance Protein 3
Ec: 3.6.4.12
Engineered: Yes
 Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
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
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Mcm4, Cdc54, Hcd21, Ypr019w, Yp9531.13
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Dna Replication Licensing Factor Mcm5
Chain: 5
Ec: 3.6.4.12
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Pacbioseq_locus4112, Pacbioseq_locus4129, Pacbioseq_l Pacbioseq_locus4202, Scnyr20_0004029000, Scp684_0004028600;
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
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Mcm6, Ygl201c
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Dna Replication Licensing Factor Mcm2
Chain: 2
Synonym: Minichromosome Maintenance Protein 2
Ec: 3.6.4.12
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Pacbioseq_locus187, Pacbioseq_locus193, Pacbioseq_loc Pacbioseq_locus196, Scnyr20_0007007400, Scp684_0007007100;
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
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Mcm7, Cdc47, Ybr202w, Ybr1441
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Dna Replication Complex Gins Protein Psf1
Chain: C
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Pacbioseq_locus944, Pacbioseq_locus956, Pacbioseq_loc Scnyr20_0001022500, Scp684_0001022000;
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Dna Replication Complex Gins Protein Psf2
Chain: D
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Pacbioseq_locus3163, Pacbioseq_locus3191, Pacbioseq_l Pacbioseq_locus3231, Pacbioseq_locus3255, Scnyr20_000901230 Scp684_0009011800;
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Dna Replication Complex Gins Protein Psf3
Chain: E
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Psf3, Gi527_g0005213
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Dna Replication Complex Gins Protein Sld5
Chain: F
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Sld5, Ydr489w
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Cell Division Control Protein 45
Chain: G
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Cdc45, Sld4, Ylr103c, L8004.11
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Dna (5'- D(Gpcpapgpcpcpapcpgpcptpgpgpcpcpgptptptp 3');
Chain: X
Engineered: Yes
Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: Dna (5'- D(Ptpapapapapcpgpgpcpcpapgpcpgptpgpgpcpt 3');
Chain: Y
Engineered: Yes
Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: Dna (5'-D(Ptptptptptptpt)-3')
Chain: J
Engineered: Yes
Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: Dna Polymerase Epsilon Subunit B
Chain: B
Synonym: Dna Polymerase II Subunit 2
Engineered: Yes
Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna Polymerase Epsilon Catalytic Subunit
Chain: A
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Pol2, Gi527_g0004851
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932
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 4.98 Å
ligand AGS, ZN 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...

    • A


    B

  • epsilon DNA polymerase compl...
    • C


    D
  • 3'-5' DNA helicase activity


    • E


    F
  • 3'-5' DNA helicase activity


    • G


    Primary referenceStructure of DNA-CMG-Pol epsilon elucidates the roles of the non-catalytic polymerase modules in the eukaryotic replisome., Goswami P, Abid Ali F, Douglas ME, Locke J, Purkiss A, Janska A, Eickhoff P, Early A, Nans A, Cheung AMC, Diffley JFX, Costa A, Nat Commun. 2018 Nov 29;9(1):5061. doi: 10.1038/s41467-018-07417-1. PMID:30498216
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (879 Kb) [Save to disk]
  • Biological Unit Coordinates (6hv9.pdb1.gz) 858 Kb
  • LPC: Ligand-Protein Contacts for 6HV9
  • CSU: Contacts of Structural Units for 6HV9
  • Retrieve 6HV9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6HV9 from S2C, [Save to disk]
    • View 6HV9 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 6HV9
  • 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: [6hv9_X] [6hv9_J] [6hv9_E] [6hv9_D] [6hv9_C] [6hv9_4] [6hv9_A] [6hv9_7] [6hv9_B] [6hv9_F] [6hv9_6] [6hv9_2] [6hv9_G] [6hv9_3] [6hv9_Y] [6hv9_5]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6HV9
  • Community annotation for 6HV9 at PDBWiki (http://pdbwiki.org)

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