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 Diffraction	resolution	3.30 Å
ligand	MG, ZN	enzyme	Transferase E.C.2.7.7.6 BRENDA
note	1I6H (Molecule of the Month:pdb40)
Gene Ontology	Chain Function Process Component 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 reference	Structural 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)

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