5EXR Replication date Nov 24, 2015
title Crystal Structure Of Human Primosome
authors T.H.Tahirov, A.G.Baranovskiy, N.D.Babayeva
compound source
Molecule: Dna Primase Small Subunit
Chain: A, E
Synonym: Dna Primase 49 Kda Subunit,P49
Ec: 2.7.7.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Prim1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna Primase Large Subunit
Chain: B, F
Synonym: Dna Primase 58 Kda Subunit,P58
Ec: 2.7.7.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Prim2, Prim2a
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna Polymerase Alpha Catalytic Subunit
Chain: C, G
Synonym: Dna Polymerase Alpha Catalytic Subunit P180
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pola1, Pola
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

Molecule: Dna Polymerase Alpha Subunit B
Chain: D, H
Synonym: Dna Polymerase Alpha 70 Kda Subunit
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pola2
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
symmetry Space Group: P 1 21 1
R_factor 0.268 R_Free 0.326
crystal
cell
length a length b length c angle alpha angle beta angle gamma
113.096 210.164 172.565 90.00 93.56 90.00
method X-Ray Diffractionresolution 3.60 Å
ligand SF4, ZN enzyme Transferase E.C.2.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceMECHANISM OF CONCERTED RNA-DNA PRIMER SYNTHESIS BY THE HUMAN PRIMOSOME., Baranovskiy AG, Babayeva ND, Zhang Y, Gu J, Suwa Y, Pavlov YI, Tahirov TH, J Biol Chem. 2016 Mar 14. pii: jbc.M116.717405. PMID:26975377
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (776 Kb) [Save to disk]
  • Biological Unit Coordinates (5exr.pdb1.gz) 388 Kb
  • Biological Unit Coordinates (5exr.pdb2.gz) 389 Kb
  • LPC: Ligand-Protein Contacts for 5EXR
  • CSU: Contacts of Structural Units for 5EXR
  • Structure Factors (1097 Kb)
  • Retrieve 5EXR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EXR from S2C, [Save to disk]
  • Re-refined 5exr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5EXR 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 5EXR
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5exr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5exr_A] [5exr] [5exr_E] [5exr_D] [5exr_B] [5exr_H] [5exr_C] [5exr_G] [5exr_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5EXR: [POLBc ] by SMART
  • Other resources with information on 5EXR
  • Community annotation for 5EXR at PDBWiki (http://pdbwiki.org)

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