3K7A	Transcription	date	Oct 12, 2009
title	Crystal Structure Of An Rna Polymerase II-Tfiib Complex
authors	X.Liu, D.A.Bushnell, D.Wang, G.Calero, R.D.Kornberg
compound		source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1 Chain: A Synonym: Rna Polymerase II Subunit B1, Rna Polymerase II Su Dna-Directed Rna Polymerase III Largest Subunit, Rna Polyme Subunit B220; Ec: 2.7.7.6 Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932 Gene: D2150, Rpb1, Rpb220, Rpo21, Sua8, Ydl140c Expression_system: Saccharomyces Cerevisiae Expression_system_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb2 Chain: B Synonym: Rna Polymerase II Subunit 2, Dna-Directed Rna Poly 140 Kda Polypeptide, B150; Ec: 2.7.7.6 Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932 Gene: Rpb150, Rpb2, Rpo22, Yor151c Expression_system: Saccharomyces Cerevisiae Expression_system_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb3 Chain: C Synonym: Rna Polymerase II Subunit B3, Rna Polymerase II Su Dna-Directed Rna Polymerase II 45 Kda Polypeptide, B44.5; Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932 Gene: Rpb3, Yil021w Expression_system: Saccharomyces Cerevisiae Expression_system_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: E Synonym: Rna Polymerases I, II, And III Subunit Abc1, Dna-D Rna Polymerases I, II, And III 27 Kda Polypeptide, Abc27; Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932 Gene: Rpa7, Rpb5, Rpc9, Ybr1204, Ybr154c Expression_system: Saccharomyces Cerevisiae Expression_system_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: F Synonym: Rna Polymerases I, II, And III Subunit Abc2, Dna-D Rna Polymerases I, II, And III 23 Kda Polypeptide, Abc23; Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932 Gene: P9677.8, Rpb6, Rpo26, Ypr187w Expression_system: Saccharomyces Cerevisiae Expression_system_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: H Synonym: Rna Polymerases I, II, And III Subunit Abc3, Dna-D Rna Polymerases I, II, And III 14.5 Kda Polypeptide, Abc14. Abc14.4; Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932 Gene: Rpb8, Yor224c, Yor50-14 Expression_system: Saccharomyces Cerevisiae Expression_system_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb9 Chain: I Synonym: Rna Polymerase II Subunit B9, Dna-Directed Rna Pol Subunit 9, Dna-Directed Rna Polymerase II 14.2 Kda Polypept B12.6; Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932 Gene: Rpb9, Ygl070c Expression_system: Saccharomyces Cerevisiae Expression_system_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: J Synonym: Rna Polymerases I, II, And III Subunit Abc5, Dna-D Rna Polymerases I, II, And III 8.3 Kda Polypeptide, Abc10-B Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932 Gene: Rpb10, Yor210w Expression_system: Saccharomyces Cerevisiae Expression_system_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb11 Chain: K Synonym: Rna Polymerase II Subunit B11, Dna-Directed Rna Po II 13.6 Kda Polypeptide, B13.6; Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932 Gene: Rpb11, Yol005c Expression_system: Saccharomyces Cerevisiae Expression_system_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: L Synonym: Rna Polymerases I, II, And III Subunit Abc4, Abc10 Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932 Gene: Rpb12, Rpc10, Yhr143bw, Yhr143w-A Expression_system: Saccharomyces Cerevisiae Expression_system_taxid: 4932
Molecule: Transcription Initiation Factor Iib Chain: M Synonym: General Transcription Factor Tfiib, Transcription Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932 Gene: P9513.4, Sua7, Ypr086w Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Rosetta 2 Expression_system_vector_type: Plasmid Expression_system_plasmid: Ptyb2
symmetry	Space Group: I 2 2 2	R_factor 0.263 R_Free 0.313
crystal cell	length a length b length c angle alpha angle beta angle gamma 204.150 216.210 420.980 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.80 Å
ligand	ZN	enzyme	Transferase E.C.2.7.7.6 BRENDA
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... M
Primary reference	Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism., Liu X, Bushnell DA, Wang D, Calero G, Kornberg RD, Science. 2010 Jan 8;327(5962):206-9. Epub 2009 Nov 12. PMID:19965383

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (603 Kb) [Save to disk] Biological Unit Coordinates (3k7a.pdb1.gz) 591 Kb LPC: Ligand-Protein Contacts for 3K7A CSU: Contacts of Structural Units for 3K7A Structure Factors (1582 Kb) Retrieve 3K7A in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3K7A from S2C, [Save to disk] Re-refined 3k7a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3K7A 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 3K7A

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 3K7A, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3k7a_C] [3k7a_K] [3k7a] [3k7a_H] [3k7a_B] [3k7a_A] [3k7a_L] [3k7a_M] [3k7a_F] [3k7a_I] [3k7a_E] [3k7a_J] SWISS-PROT database: [P20434] [P20435] [P20436] [P40422] [P22139] [P38902] [P04050] [P08518] [P16370] [P27999] [P29055] Domain organization of [RPAB1_YEAST] [RPAB2_YEAST] [RPAB3_YEAST] [RPAB4_YEAST] [RPAB5_YEAST] [RPB11_YEAST] [RPB1_YEAST] [RPB2_YEAST] [RPB3_YEAST] [RPB9_YEAST] [TF2B_YEAST] by SWISSPFAM Domains found in 3K7A: [CYCLIN] [RNA_pol_Rpb6] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [ZnF_C2C2 ] by SMART

Other resources with information on 3K7A

Community annotation for 3K7A at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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