1I6H Transcription Dna-Rna Hybrid date Mar 02, 2001
title Rna Polymerase II Elongation Complex
authors A.L.Gnatt, P.Cramer, R.D.Kornberg
compound source
Molecule: 5'-D(Papapaptpgpcpcptpgpgptpcpt)-3'
Chain: D
Engineered: Yes
Other_details: Template
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: 5'-R(Pgpapcpcpapgpgpcpa)-3'
Chain: R
Engineered: Yes
Other_details: Transcript

Synthetic: Yes
Other_details: The Rna Was Synthesized By The Polymerase Be Crystal Was Formed.;

Molecule: Dna-Directed Rna Polymerase II Largest Subunit
Chain: A
Synonym: Rpb1
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4

Molecule: Dna-Directed Rna Polymerase II 140kd Polypeptide
Chain: B
Synonym: Rpb2
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4

Molecule: Dna-Directed Rna Polymerase II 45kd Polypeptide
Chain: C
Synonym: Rpb3
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4

Molecule: Dna-Directed Rna Polymerase II 27kd Polypeptide
Chain: E
Synonym: Rpb5
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4

Molecule: Dna-Directed Rna Polymerase II 23kd Polypeptide
Chain: F
Synonym: Rpb6
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4

Molecule: Dna-Directed Rna Polymerase II 14.5kd Polypeptide
Chain: H
Synonym: Rpb8
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4

Molecule: Dna-Directed Rna Polymerase II 14.2kd Polypeptide
Chain: I
Synonym: Rpb9
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4

Molecule: Dna-Directed Rna Polymerase II 8.3kd Polypeptide
Chain: J
Synonym: Rpb10
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4

Molecule: Dna-Directed Rna Polymerase II 13.6kd Polypeptide
Chain: K
Synonym: Rpb11
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4

Molecule: Dna-Directed Rna Polymerase II 7.7kd Polypeptide
Chain: L
Synonym: Rpb12
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4
symmetry Space Group: C 1 2 1
R_factor 0.250 R_Free 0.298
crystal
cell
length a length b length c angle alpha angle beta angle gamma
157.300 220.700 191.300 90.00 97.50 90.00
method X-Ray Diffractionresolution 3.30 Å
ligand MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
note 1I6H (Molecule of the Month:pdb40)
Gene
Ontology
ChainFunctionProcessComponent
A
  • RNA-directed 5'-3' RNA polym...


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


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


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


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


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


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


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

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


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


  • Primary referenceStructural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution., Gnatt AL, Cramer P, Fu J, Bushnell DA, Kornberg RD, Science 2001 Jun 8;292(5523):1876-82. PMID:11313499
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (587 Kb) [Save to disk]
  • Biological Unit Coordinates (1i6h.pdb1.gz) 576 Kb
  • LPC: Ligand-Protein Contacts for 1I6H
  • CSU: Contacts of Structural Units for 1I6H
  • Likely Quarternary Molecular Structure file(s) for 1I6H
  • Retrieve 1I6H in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1I6H from S2C, [Save to disk]
  • View 1I6H 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 1I6H
  • 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
  • 3D motif for 1I6H, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1i6ha_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1i6hb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1i6hc1, region C:3-41,C:173-268 [Jmol] [rasmolscript] [script source]
        - Domain d1i6hc2, region C:42-172 [Jmol] [rasmolscript] [script source]
        - Domain d1i6he2, region E:144-215 [Jmol] [rasmolscript] [script source]
        - Domain d1i6he1, region E:2-143 [Jmol] [rasmolscript] [script source]
        - Domain d1i6hf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1i6hh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1i6hi1, region I:2-49 [Jmol] [rasmolscript] [script source]
        - Domain d1i6hi2, region I:50-120 [Jmol] [rasmolscript] [script source]
        - Domain d1i6hj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1i6hk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1i6hl_, region L [Jmol] [rasmolscript] [script source]
  • Fold representative 1i6h from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1i6h_B] [1i6h_F] [1i6h_J] [1i6h_R] [1i6h_C] [1i6h_D] [1i6h_H] [1i6h_K] [1i6h_I] [1i6h_L] [1i6h_E] [1i6h] [1i6h_A]
  • SWISS-PROT database: [P20434] [P20435] [P20436] [P40422] [P22139] [P38902] [P04050] [P08518] [P16370] [P27999]
  • Domain organization of [RPAB1_YEAST] [RPAB2_YEAST] [RPAB3_YEAST] [RPAB4_YEAST] [RPAB5_YEAST] [RPB11_YEAST] [RPB1_YEAST] [RPB2_YEAST] [RPB3_YEAST] [RPB9_YEAST] by SWISSPFAM
  • Domains found in 1I6H: [RNA_pol_Rpb6] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [ZnF_C2C2 ] by SMART
  • Other resources with information on 1I6H
  • Community annotation for 1I6H at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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