1I3Q	Transcription	date	Feb 15, 2001
title	Rna Polymerase II Crystal Form I At 3.1 A Resolution
authors	P.Cramer, D.A.Bushnell, R.D.Kornberg
compound		source
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: I 2 2 2	R_factor 0.229 R_Free 0.283
crystal cell	length a length b length c angle alpha angle beta angle gamma 130.700 224.800 369.400 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.10 Å
ligand	MG, ZN	enzyme	Transferase E.C.2.7.7.6 BRENDA
note	1I3Q supersedes 1EN0
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: RNA polymerase II at 2.8 angstrom resolution., Cramer P, Bushnell DA, Kornberg RD, Science. 2001 Jun 8;292(5523):1863-76. Epub 2001 Apr 19. PMID:11313498

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (569 Kb) [Save to disk] Biological Unit Coordinates (1i3q.pdb1.gz) 560 Kb LPC: Ligand-Protein Contacts for 1I3Q CSU: Contacts of Structural Units for 1I3Q Likely Quarternary Molecular Structure file(s) for 1I3Q Retrieve 1I3Q in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1I3Q from S2C, [Save to disk]

View 1I3Q 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 1I3Q

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1I3Q, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1i3qa_, region A [Jmol] [rasmolscript] [script source]     - Domain d1i3qb_, region B [Jmol] [rasmolscript] [script source]     - Domain d1i3qc1, region C:3-41,C:173-268 [Jmol] [rasmolscript] [script source]     - Domain d1i3qc2, region C:42-172 [Jmol] [rasmolscript] [script source]     - Domain d1i3qe1, region E:1-143 [Jmol] [rasmolscript] [script source]     - Domain d1i3qe2, region E:144-215 [Jmol] [rasmolscript] [script source]     - Domain d1i3qf_, region F [Jmol] [rasmolscript] [script source]     - Domain d1i3qh_, region H [Jmol] [rasmolscript] [script source]     - Domain d1i3qi1, region I:1-49 [Jmol] [rasmolscript] [script source]     - Domain d1i3qi2, region I:50-122 [Jmol] [rasmolscript] [script source]     - Domain d1i3qj_, region J [Jmol] [rasmolscript] [script source]     - Domain d1i3qk_, region K [Jmol] [rasmolscript] [script source]     - Domain d1i3ql_, region L [Jmol] [rasmolscript] [script source] 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: [1i3q_H] [1i3q_B] [1i3q_K] [1i3q_L] [1i3q_A] [1i3q_J] [1i3q_I] [1i3q] [1i3q_E] [1i3q_C] [1i3q_F] 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 1I3Q: [RNA_pol_Rpb6] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [ZnF_C2C2 ] by SMART

Other resources with information on 1I3Q

Community annotation for 1I3Q at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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