Supplementary Information

Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity

Fuensanta W. Martinez-Rucobo, Sarah Sainsbury, Alan C.M. Cheung, and Patrick Cramer*

Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.*Corresponding author: Tel.: +49-89-2180-76965, Fax: +49-89-2180-76998, Email:

Supplementary Information comprises:

Supplementary text and references

Supplementary model coordinate files

Building of three-dimensional models of RNAP complexes with Spt4/5 or NusG

To obtain a model of the archaeal RNAP-Spt4/5 complex (model 2; Archaeal-RNAP-Spt45.pdb), we superimposed the clamp domain in the Pfu RNAP clamp-Spt4/5structure with the clamp in the structure of free S. solfataricus RNAP(Hirata et al, 2008). To obtain models of the bacterial RNAP-NusG complex (model 3; Bacterial-RNAP-NusG.pdb) and the eukaryotic RNAP II-Spt4/5 complex (model 1; Yeast-PolII-Spt45-ElongationComplex.pdb), we repeated the superposition with the structures of T. thermophilus RNAP (Vassylyev et al, 2007) and S. cerevisiae RNAP II (Armache et al, 2005), respectively, and then replaced the archaeal Spt4/5 by T. thermophilus NusG (Reay et al, 2004) or yeast Spt4/5 (Guo et al, 2008) via superposition of their NGN domains. All domains (clamp, Spt5 or NusG NGN) superposed with an RMSD of 2.0 Å or less. For the yeast RNAP II-Spt4/5 model we included the nucleic acids from the complete elongation complex (Andrecka et al, 2009; Kettenberger et al, 2004) and slightly moved the upstream DNA duplex to avoid a clash with the Spt5 NGN domain. All resulting models were free of steric clashes.

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Vassylyev DG, Vassylyeva MN, Perederina A, Tahirov TH, Artsimovitch I (2007)Structural basis for transcription elongation by bacterial RNA polymerase. Nature448: 157-162

Armache K-J, Mitterweger S, Meinhart A, Cramer P (2005) Structures of complete RNA polymerase II and its subcomplex Rpb4/7. J Biol Chem280: 7131-7134

Reay P, Yamasaki K, Terada T, Kuramitsu S, Shirouzu M, Yokoyama S (2004) Structural and sequence comparisons arising from the solution structure of the transcription elongation factor NusG from Thermus thermophilus. Proteins56: 40-51

Guo M, Xu F, Yamada J, Egelhofer T, Gao Y, Hartzog GA, Teng M, Niu L (2008) Core structure of the yeast spt4-spt5 complex: a conserved module for regulation of transcription elongation. Structure16: 1649-1658

Andrecka J, Treutlein B, Arcusa MA, Muschielok A, Lewis R, Cheung AC, Cramer P, Michaelis J (2009) Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex. Nucleic Acids Res37: 5803-5809

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Coordinate files for models of RNAP complexes with Spt4/5 or NusG

Model 1: coordinate file: Yeast-PolII-Spt45-ElongationComplex.pdb

The model contains the following chains:

Subunit / Chain
RPB1 / A
RPB2 / B
RPB3 / C
RPB4 / D
RPB5 / E
RPB6 / F
RPB7 / G
RPB8 / H
RPB9 / I
RPB10 / J
RPB11 / K
RPB12 / L
Spt4 / X
Spt5 / Y
Non-Template DNA / N
Template DNA / T
Product RNA / P

Model 2: coordinate file: Archaeal-RNAP-Spt45.pdb

The model contains the following chains:

Subunit / Chain
RNAP A' / A
RNAP A'' / C
RNAP B / B
RNAP D / D
RNAP E’ / E
RNAP F / F
RNAP G / G
RNAP H / H
RNAP K / K
RNAP L / L
RNAP N / N
RNAP P / P
RNAP 13 / X
Spt4 / J
SPT5 / I

Model 3: coordinate file: Bacterial-RNAP-Spt45.pdb

The model contains the following chains:

Subunit / Chain
RNAP alpha I / A
RNAP alpha II / B
RNAP beta / C
RNAP beta’ / D
RNAP omega / E
NusG / F