5XOG Transcription date May 28, 2017
title Rna Polymerase II Elongation Complex Bound With Spt5 Kow5 An
authors H.Ehara, M.Shirouzu, S.Sekine
compound source
Molecule: Dna-Directed Rna Polymerase Subunit
Chain: A
Synonym: Rna Polymerase II Subunit Rpb1
Ec: 2.7.7.6
 Organism_scientific: Komagataella Phaffii (Strain Gs115 A 20864);
Organism_common: Yeast
Organism_taxid: 644223
Strain: Gs115 Atcc 20864

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: B
Synonym: Rna Polymerase II Subunit Rpb2
Ec: 2.7.7.6
Organism_scientific: Komagataella Phaffii (Strain Gs115 A 20864);
Organism_common: Yeast
Organism_taxid: 644223
Strain: Gs115 Atcc 20864

Molecule: Rna Polymerase II Third Largest Subunit B44, Part Central Core;
Chain: C
Synonym: Rna Polymerase II Subunit Rpb3
Organism_scientific: Komagataella Phaffii (Strain Gs115 A 20864);
Organism_common: Yeast
Organism_taxid: 644223
Strain: Gs115 Atcc 20864

Molecule: Rna Polymerase II Subunit B32
Chain: D
Synonym: Rna Polymerase II Subunit Rpb4
Organism_scientific: Komagataella Phaffii (Strain Gs115 A 20864);
Organism_common: Yeast
Organism_taxid: 644223
Strain: Gs115 Atcc 20864

Molecule: Rna Polymerase Subunit Abc27, Common To Rna Polym II, And III;
Chain: E
Synonym: Rna Polymerase II Subunit Rpb5
Organism_scientific: Komagataella Phaffii (Strain Gs115 A 20864);
Organism_common: Yeast
Organism_taxid: 644223
Strain: Gs115 Atcc 20864

Molecule: Rna Polymerase Subunit Abc23, Common To Rna Polym II, And III;
Chain: F
Synonym: Rna Polymerase II Subunit Rpb6
Organism_scientific: Komagataella Phaffii (Strain Gs115 A 20864);
Organism_common: Yeast
Organism_taxid: 644223
Strain: Gs115 Atcc 20864

Molecule: Rna Polymerase II Subunit
Chain: G
Synonym: Rna Polymerase II Subunit Rpb7
Organism_scientific: Komagataella Phaffii (Strain Gs115 A 20864);
Organism_common: Yeast
Organism_taxid: 644223
Strain: Gs115 Atcc 20864

Molecule: Rna Polymerase Subunit Abc14.5, Common To Rna Pol I, II, And III;
Chain: H
Synonym: Rna Polymerase II Subunit Rpb8
Organism_scientific: Komagataella Phaffii (Strain Gs115 A 20864);
Organism_common: Yeast
Organism_taxid: 644223
Strain: Gs115 Atcc 20864

Molecule: Dna-Directed Rna Polymerase Subunit
Chain: I
Synonym: Rna Polymerase II Subunit Rpb9
Organism_scientific: Komagataella Phaffii (Strain Atcc 7627 7435 Cect 11047 Nrrl Y-11430 Wegner 21-1);
Organism_common: Yeast
Organism_taxid: 981350
Strain: Atcc 76273 Cbs 7435 Cect 11047 Nrrl Y-11430 21-1;

Molecule: Rna Polymerase Subunit Abc10-Beta, Common To Rna Polymerases I, II, And III;
Chain: J
Synonym: Rna Polymerase II Subunit Rpb10
Organism_scientific: Komagataella Phaffii (Strain Gs115 A 20864);
Organism_common: Yeast
Organism_taxid: 644223
Strain: Gs115 Atcc 20864

Molecule: Rna Polymerase II Subunit B12.5
Chain: K
Synonym: Rna Polymerase II Subunit Rpb11
Organism_scientific: Komagataella Phaffii (Strain Gs115 A 20864);
Organism_common: Yeast
Organism_taxid: 644223
Strain: Gs115 Atcc 20864

Molecule: Rna Polymerase Subunit Abc10-Alpha
Chain: L
Synonym: Rna Polymerase II Subunit Rpb12
Organism_scientific: Komagataella Phaffii (Strain Atcc 7627 7435 Cect 11047 Nrrl Y-11430 Wegner 21-1);
Organism_common: Yeast
Organism_taxid: 981350
Strain: Atcc 76273 Cbs 7435 Cect 11047 Nrrl Y-11430 21-1;

Molecule: Rna (5'- R(Upupupupupupupapupcpgpapgpapgpgpu)-3');
Chain: P
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Molecule: Dna (30-Mer)
Chain: N
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Transcription Elongation Factor 1 Homolog
Chain: M
Fragment: Unp Residues 1-82
Synonym: Transcription Elongation Factor Elf1
Engineered: Yes
Mutation: Yes
Organism_scientific: Komagataella Pastoris
Organism_common: Yeast
Organism_taxid: 4922
Gene: Elf1, Aty40_ba7504229
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Spt45 Complex Component
Chain: W
Fragment: Unp Residues 736-815
Synonym: Transcription Elongation Factor Spt5
Engineered: Yes
Organism_scientific: Komagataella Phaffii
Organism_common: Yeast
Organism_taxid: 981350
Strain: Atcc 76273 Cbs 7435 Cect 11047 Nrrl Y-11430 21-1;
Gene: Spt5, Pp7435_chr3-0027
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.195 R_Free 0.225
crystal
cell
length a length b length c angle alpha angle beta angle gamma
155.250 159.910 268.930 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand APC, MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D
  • RNA-directed 5'-3' RNA polym...


    • E


    F
  • RNA-directed 5'-3' RNA polym...


    • G


    H
  • RNA-directed 5'-3' RNA polym...


    • I


    J
  • RNA-directed 5'-3' RNA polym...


    • K
  • RNA-directed 5'-3' RNA polym...


    • L


    W


    Primary referenceStructure of the complete elongation complex of RNA polymerase II with basal factors., Ehara H, Yokoyama T, Shigematsu H, Yokoyama S, Shirouzu M, Sekine SI, Science. 2017 Aug 3. pii: eaan8552. doi: 10.1126/science.aan8552. PMID:28775211
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (688 Kb) [Save to disk]
  • Biological Unit Coordinates (5xog.pdb1.gz) 677 Kb
  • LPC: Ligand-Protein Contacts for 5XOG
  • CSU: Contacts of Structural Units for 5XOG
  • Structure Factors (3574 Kb)
  • Retrieve 5XOG in mmCIF format [Save to disk]
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    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5xog_H] [5xog_J] [5xog_T] [5xog_C] [5xog_N] [5xog_A] [5xog_F] [5xog_P] [5xog_L] [5xog_M] [5xog_D] [5xog_I] [5xog_E] [5xog_B] [5xog_W] [5xog_K] [5xog_G]
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