6A5O Transcription Rna Dna date Jun 25, 2018
title Rna Polymerase II Elongation Complex Stalled At Shl(-6) Of T Nucleosome
authors T.Kujirai, H.Ehara, Y.Fujino, M.Shirouzu, S.Sekine, H.Kurumizaka
compound source
Molecule: Dna-Directed Rna Polymerase Subunit
Chain: A
Synonym: Dna-Directed Rna Polymerase 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: Dna-Directed Rna Polymerase 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 Third Largest 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

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

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

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: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: H
Synonym: Rna Polymerase Subunit Abc14.5, Common To Rna Poly II, And III;

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: Dna-Directed Rna Polymerase Subunit, Rpb9

Organism_scientific: Komagataella Phaffii (Strain Gs115 A 20864);
Organism_common: Yeast
Organism_taxid: 644223
Strain: Gs115 Atcc 20864

Molecule: Rna Polymerase Subunit Abc10-Beta, Common To Rna Polymerases I, II, And III;
Chain: J

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

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

Organism_scientific: Komagataella Phaffii (Strain Gs115 A 20864);
Organism_common: Yeast
Organism_taxid: 644223
Strain: Gs115 Atcc 20864

Molecule: Rna (5'-R(Pupgpgpgpupgpgpupgpgpc)-3')
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (198-Mer)
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (198-Mer)
Chain: N
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Histone H3.3
Chain: a, e
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H3f3a, H3.3a, H3f3, Pp781, H3f3b, H3.3b
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H4
Chain: b, f
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h4a, H4a, H4fa, Hist1h4b, H4i, H4fi, Hist1h4c, H4fg, Hist1h4d, H4b, H4fb, Hist1h4e, H4j, H4fj, Hist1h4f, H4fc, Hist1h4h, H4h, H4fh, Hist1h4i, H4m, H4fm, Hist1h4j, H4fe, Hist1h4k, H4d, H4fd, Hist1h4l, H4k, H4fk, Hist2h4a, H4f2, H4fn, Hist2h4, Hist2h4b, H4o, H4fo, Hist4h4;
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2a Type 1-Be
Chain: c, g
Synonym: Histone H2a, Histone H2a.2,Histone H2aa,Histone H
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2ab, H2afm, Hist1h2ae, H2afa
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b Type 1-J
Chain: d, h
Synonym: Histone H2b, Histone H2b.1,Histone H2b.R,H2br
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2bj, H2bfr
Expression_system: Escherichia Coli
Expression_system_taxid: 562
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 9.90 Å
ligand 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


    a, e


    d, h


    f, b


    g, c


    Primary referenceStructural basis of the nucleosome transition during RNA polymerase II passage., Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H, Science. 2018 Oct 4. pii: science.aau9904. doi: 10.1126/science.aau9904. PMID:30287617
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (833 Kb) [Save to disk]
  • Biological Unit Coordinates (6a5o.pdb1.gz) 820 Kb
  • LPC: Ligand-Protein Contacts for 6A5O
  • CSU: Contacts of Structural Units for 6A5O
  • Retrieve 6A5O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6A5O from S2C, [Save to disk]
  • View 6A5O 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 6A5O
  • 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 6a5o from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6a5o_h] [6a5o_e] [6a5o_d] [6a5o_K] [6a5o_N] [6a5o_E] [6a5o_I] [6a5o_f] [6a5o_B] [6a5o_D] [6a5o_c] [6a5o_b] [6a5o_G] [6a5o_H] [6a5o_a] [6a5o_P] [6a5o_A] [6a5o_F] [6a5o_T] [6a5o_C] [6a5o_g] [6a5o_L] [6a5o_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6A5O
  • Community annotation for 6A5O at PDBWiki (http://pdbwiki.org)

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