5FYW	Transcription	date	Mar 10, 2016
title	Transcription Initiation Complex Structures Elucidate Dna Op
authors	C.Plaschka, M.Hantsche, C.Dienemann, C.Burzinski, J.Plitzko, P.Cr
compound		source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1 Chain: A Synonym: Rna Polymerase II Subunit 1, Rna Polymerase II Sub Dna-Directed Rna Polymerase III Largest Subunit, Rna Polyme Subunit B220, Rpb1; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Bj5464 Rpb3 His-Bio
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb2 Chain: B Synonym: Rna Polymerase II Subunit 2, B150, Dna-Directed Rn Polymerase II 140 Kda Polypeptide, Rpb2; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Bj5464 Rpb3 His-Bio
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb3 Chain: C Synonym: Rna Polymerase II Subunit 3, Rna Polymerase II Sub B44.5, Dna-Directed Rna Polymerase II 45 Kda Polypeptide, R		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Bj5464 Rpb3 His-Bio
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb4 Chain: D Synonym: Rna Polymerase II Subunit B4, B32, Dna-Directed Rn Polymerase II 32 Kda Polypeptide, Rpb4;		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Bj5464 Rpb3 His-Bio
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 1; Chain: E Synonym: Rna Polymerases I, II, And III Subunit Abc1, Abc27 Directed Rna Polymerases I, II, And III 27 Kda Polypeptide,		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Bj5464 Rpb3 His-Bio
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 2; Chain: F Synonym: Rna Polymerases I, II, And III Subunit Abc2, Abc23 Directed Rna Polymerases I, II, And III 23 Kda Polypeptide,		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Bj5464 Rpb3 His-Bio
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb7 Chain: G Synonym: Rna Polymerase II Subunit B7, B16, Rpb7		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Bj5464 Rpb3 His-Bio
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 3; Chain: H Synonym: Rna Polymerases I, II, And III Subunit Abc3, Abc14 .5, Dna-Directed Rna Polymerases I, II, And III 14.5 Kda Po Rpb8;		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Bj5464 Rpb3 His-Bio
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb9 Chain: I Synonym: Rna Polymerase II Subunit B9, B12.6, Dna-Directed Polymerase II 14.2 Kda Polypeptide, Dna-Directed Rna Polyme Subunit 9, Rpb9;		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Bj5464 Rpb3 His-Bio
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 5; Chain: J Synonym: Rna Polymerases I, II, And III Subunit Abc5, Abc10 C8, Dna-Directed Rna Polymerases I, II, And III 8.3 Kda Pol Rpb10;		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Bj5464 Rpb3 His-Bio
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb11 Chain: K Synonym: Rna Polymerase II Subunit B11, B13.6, Dna-Directed Polymerase II 13.6 Kda Polypeptide, Rpb11;		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Bj5464 Rpb3 His-Bio
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 4; Chain: L Synonym: Rna Polymerases I, II, And III Subunit Abc4, Abc10 Pb12;		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Bj5464 Rpb3 His-Bio
Molecule: Transcription Initiation Factor Iib Chain: M Synonym: General Transcription Factor Tfiib, Transcription Tfiib; Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_variant: Ril Expression_system_vector_type: Plasmid Expression_system_vector: Pet21b
Molecule: Nontemplate Dna Chain: N Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: Tata-Box-Binding Protein Chain: O Synonym: Tata Sequence-Binding Protein, Tbp, Tata-Binding F Ta-Box Factor, Transcription Factor D, Transcription Initia Factor Tfiid Tbp Subunit; Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_variant: Ril Expression_system_vector_type: Plasmid Expression_system_vector: Popine
Molecule: Transcription Initiation Factor Iif Subunit Alpha Chain: Q Synonym: Tfiif-Alpha, Tfiif Large Subunit, Transcription Fa Kda Subunit, P105, Tfg1; Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_variant: Ril Expression_system_vector_type: Plasmid Expression_system_vector: Petduet-1
Molecule: Transcription Initiation Factor Iif Subunit Beta Chain: R Synonym: Atp-Dependent Helicase Tfg2, Tfiif Medium Subunit, Beta, Transcription Factor G 54 Kda Subunit, Tfg2; Ec: 3.6.4.12 Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_variant: Ril Expression_system_vector_type: Plasmid Expression_system_vector: Petduet-1
Molecule: Nontemplate Dna Chain: T Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: Transcription Initiation Factor Iia Large Subunit Chain: U Synonym: Tfiia Large Subunit, Tfiia 32 Kda Subunit, Toa1 Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_variant: Ril Expression_system_vector_type: Plasmid Expression_system_vector: Popine
Molecule: Transcription Initiation Factor Iia Subunit 2 Chain: V Synonym: General Transcription Factor Iia Subunit 2, Tfiia Subunit, Transcription Initiation Factor Iia Small Chain, Transcription Initiation Factor Iia Small Subunit, Toa2; Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_variant: Ril Expression_system_vector_type: Plasmid Expression_system_vector: Popine
Molecule: Transcription Initiation Factor Iie Subunit Alpha Chain: W Synonym: Tfiie-Alpha, Factor A 66 Kda Subunit, Transcriptio Large Subunit, Tfa1; Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_variant: Ril Expression_system_vector_type: Plasmid Expression_system_vector: Pet21
Molecule: Transcription Initiation Factor Iie Subunit Beta Chain: X Synonym: Tfiie-Beta, Factor A 43 Kda Subunit, Transcription Small Subunit, Tfa2; Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_variant: Ril Expression_system_vector_type: Plasmid Expression_system_vector: Pet21
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 Microscopy	resolution	4.35 Å
ligand	MG, 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... D RNA-directed 5'-3' RNA polym... E RNA-directed 5'-3' RNA polym... F RNA-directed 5'-3' RNA polym... G 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 O Q transcription factor TFIIF c... R transcription factor TFIIF c... U transcription cofactor activ... V W X
Primary reference	Transcription initiation complex structures elucidate DNA opening., Plaschka C, Hantsche M, Dienemann C, Burzinski C, Plitzko J, Cramer P, Nature. 2016 May 11;533(7603):353-8. doi: 10.1038/nature17990. PMID:27193681

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (866 Kb) [Save to disk] Biological Unit Coordinates (5fyw.pdb1.gz) 842 Kb LPC: Ligand-Protein Contacts for 5FYW CSU: Contacts of Structural Units for 5FYW Retrieve 5FYW in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5FYW from S2C, [Save to disk]

View 5FYW in 3D

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Visual 3D analysis of 5FYW

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5fyw_D] [5fyw_Q] [5fyw_R] [5fyw_C] [5fyw_E] [5fyw_U] [5fyw_N] [5fyw_B] [5fyw_X] [5fyw_I] [5fyw_M] [5fyw_G] [5fyw_V] [5fyw_W] [5fyw_H] [5fyw_F] [5fyw] [5fyw_A] [5fyw_O] [5fyw_T] [5fyw_K] [5fyw_J] [5fyw_L] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 5FYW: [CYCLIN] [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [TFIIA] [TFIIE] [ZnF_C2C2 ] by SMART

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