3K1F	Transcription	date	Sep 27, 2009
title	Crystal Structure Of Rna Polymerase II In Complex With Tfiib
authors	D.Kostrewa, M.E.Zeller, K.J.Armache, M.Seizl, K.Leike, M.Thomm, P
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		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_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		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_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; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb4 Chain: D Synonym: Rna Polymerase II Subunit B4, Dna-Directed Rna Pol 32 Kda Polypeptide, B32; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_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; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_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; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb7 Chain: G Synonym: Rna Polymerase II Subunit B7, B16 Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_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; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_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; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_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 Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_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; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: L Synonym: Rna Polymerases I, II, And III Subunit Abc4, Abc10 Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932
Molecule: Transcription Initiation Factor Iib Chain: M		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932
symmetry	Space Group: C 2 2 21	R_factor 0.220 R_Free 0.255
crystal cell	length a length b length c angle alpha angle beta angle gamma 220.970 408.270 275.240 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	4.30 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... 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
Primary reference	RNA polymerase II-TFIIB structure and mechanism of transcription initiation., Kostrewa D, Zeller ME, Armache KJ, Seizl M, Leike K, Thomm M, Cramer P, Nature. 2009 Oct 9. PMID:19820686

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1362 Kb) [Save to disk] Biological Unit Coordinates (3k1f.pdb1.gz) 1352 Kb LPC: Ligand-Protein Contacts for 3K1F CSU: Contacts of Structural Units for 3K1F Structure Factors (783 Kb) Retrieve 3K1F in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3K1F from S2C, [Save to disk] Re-refined 3k1f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3K1F 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 3K1F

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 3K1F, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3k1f_L] [3k1f_A] [3k1f_B] [3k1f_C] [3k1f_G] [3k1f_K] [3k1f] [3k1f_F] [3k1f_E] [3k1f_J] [3k1f_H] [3k1f_M] [3k1f_D] [3k1f_I] SWISS-PROT database: [P20434] [P20435] [P20436] [P40422] [P22139] [P38902] [P04050] [P08518] [P16370] [P20433] [P34087] [P27999] [P29055] Domain organization of [RPAB1_YEAST] [RPAB2_YEAST] [RPAB3_YEAST] [RPAB4_YEAST] [RPAB5_YEAST] [RPB11_YEAST] [RPB1_YEAST] [RPB2_YEAST] [RPB3_YEAST] [RPB4_YEAST] [RPB7_YEAST] [RPB9_YEAST] [TF2B_YEAST] by SWISSPFAM Domains found in 3K1F: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART

Other resources with information on 3K1F

Community annotation for 3K1F at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---