P38902 (RPB11_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA-directed RNA polymerase II subunit RPB11
Short name=RNA polymerase II subunit B11

Alternative name(s):
B13.6
DNA-directed RNA polymerase II 13.6 kDa polypeptide

Gene names

Name:	RPB11
Ordered Locus Names:	YOL005C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	120 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB11 is part of the core element with the central large cleft. Seems to be involved transcript termination. Ref.6
Subunit structure	Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits.
Subcellular location	Nucleus.
Miscellaneous	Present with 4280 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the archaeal RpoL/eukaryotic RPB11/RPC19 RNA polymerase subunit family.

Ontologies

Keywords
Biological process	Transcription
Cellular component	DNA-directed RNA polymerase Nucleus
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	termination of RNA polymerase II transcription Inferred from mutant phenotype Ref.6. Source: SGD transcription from RNA polymerase II promoter Inferred from mutant phenotype PubMed 17179178. Source: SGD transcription, RNA-templated Inferred from direct assay PubMed 18004386. Source: GOC
Cellular_component	DNA-directed RNA polymerase II, core complex Inferred from direct assay PubMed 1331084. Source: SGD
Molecular_function	DNA binding Inferred from electronic annotation. Source: InterPro DNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
RPB3	P16370	4	EBI-15806,EBI-15773

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 120

120

DNA-directed RNA polymerase II subunit RPB11

PRO_0000149315

Experimental info

Mutagenesis

108

1

E → G or V: Transcript termination readthrough. Ref.6

Mutagenesis

108

1

E → K: Transcript termination readthrough. Lethal. Ref.6

Mutagenesis

111

1

L → P: Transcript termination readthrough. Ref.6

Mutagenesis

114

1

L → P: Transcript termination readthrough. Ref.6

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

120

Helix Strand Turn

Details...

Helix

7 – 9

3

Beta strand

18 – 20

3

Beta strand

21 – 23

3

Beta strand

25 – 27

3

Beta strand

30 – 37

8

Helix

40 – 50

11

Beta strand

51 – 53

3

Beta strand

56 – 62

7

Beta strand

66 – 68

3

Beta strand

70 – 77

8

Helix

83 – 108

26

Turn

109 – 111

3

Sequences

	Sequence		Length	Mass (Da)
	P38902 [UniParc]. Last modified February 1, 1995. Version 1. Checksum: A98D109C5FF8E356	FASTA	120	13,616
	10 20 30 40 50 60 MNAPDRFELF LLGEGESKLK IDPDTKAPNA VVITFEKEDH TLGNLIRAEL LNDRKVLFAA 70 80 90 100 110 120 YKVEHPFFAR FKLRIQTTEG YDPKDALKNA CNSIINKLGA LKTNFETEWN LQTLAADDAF

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Yeast RNA polymerase II subunit RPB11 is related to a subunit shared by RNA polymerase I and III." Woychik N.A., McKune K., Lane W.S., Young R.A. Gene Expr. 3:77-82(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 27-37; 75-84; 98-102 AND 103-116. Strain: X2180-2.
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV." Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D. , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K. Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[5]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[6]	"cis- and trans-Acting determinants of transcription termination by yeast RNA polymerase II." Steinmetz E.J., Ng S.B., Cloute J.P., Brow D.A. Mol. Cell. Biol. 26:2688-2696(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF GLU-108; LEU-111 AND LEU-114.
[7]	"RNA polymerase II/TFIIF structure and conserved organization of the initiation complex." Chung W.H., Craighead J.L., Chang W.H., Ezeokonkwo C., Bareket-Samish A., Kornberg R.D., Asturias F.J. Mol. Cell 12:1003-1013(2003) [PubMed] [Europe PMC] [Abstract] Cited for: ELECTRON MICROSCOPY OF THE RNA POL II/TFIIF COMPLEX.
[8]	"Structural basis of transcription: RNA polymerase II at 2.8 A resolution." Cramer P., Bushnell D.A., Kornberg R.D. Science 292:1863-1876(2001) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
[9]	"Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution." Gnatt A.L., Cramer P., Fu J., Bushnell D.A., Kornberg R.D. Science 292:1876-1882(2001) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
[10]	"Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution." Bushnell D.A., Cramer P., Kornberg R.D. Proc. Natl. Acad. Sci. U.S.A. 99:1218-1222(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF THE RNA POL II CORE COMPLEX IN COMPLEX WITH ALPHA-AMANITIN.
[11]	"Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage." Kettenberger H., Armache K.J., Cramer P. Cell 114:347-357(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX IN COMPLEX WITH DST1.
[12]	"Architecture of initiation-competent 12-subunit RNA polymerase II." Armache K.J., Kettenberger H., Cramer P. Proc. Natl. Acad. Sci. U.S.A. 100:6964-6968(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (4.2 ANGSTROMS) OF THE RNA POL II COMPLEX.
[13]	"Complete, 12-subunit RNA polymerase II at 4.1-A resolution: implications for the initiation of transcription." Bushnell D.A., Kornberg R.D. Proc. Natl. Acad. Sci. U.S.A. 100:6969-6973(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (4.1 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
[14]	"Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center." Westover K.D., Bushnell D.A., Kornberg R.D. Cell 119:481-489(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
[15]	"Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS." Kettenberger H., Armache K.J., Cramer P. Mol. Cell 16:955-965(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (4.5 ANGSTROMS).
[16]	"Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms." Bushnell D.A., Westover K.D., Davis R.E., Kornberg R.D. Science 303:983-988(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (4.5 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
[17]	"Structures of complete RNA polymerase II and its subcomplex, Rpb4/7." Armache K.J., Mitterweger S., Meinhart A., Cramer P. J. Biol. Chem. 280:7131-7134(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX.
[18]	"Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs." Kettenberger H., Eisenfuhr A., Brueckner F., Theis M., Famulok M., Cramer P. Nat. Struct. Mol. Biol. 13:44-48(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX IN COMPLEX WITH INHIBITING NON-CODING RNA.
[19]	"Phasing RNA polymerase II using intrinsically bound Zn atoms: an updated structural model." Meyer P.A., Ye P., Zhang M., Suh M.H., Fu J. Structure 14:973-982(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (4.15 ANGSTROMS) OF THE RNA POL II COMPLEX.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

S62624 Genomic DNA. Translation: AAB27135.1.
Z74747 Genomic DNA. Translation: CAA99004.1.
AY557998 Genomic DNA. Translation: AAS56324.1.
BK006948 Genomic DNA. Translation: DAA10778.1.

PIR

S58933.

RefSeq

NP_014638.1. NM_001183259.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1I3Q	X-ray	3.10	K	1-120	[»]
1I50	X-ray	2.80	K	1-120	[»]
1I6H	X-ray	3.30	K	1-120	[»]
1K83	X-ray	2.80	K	1-120	[»]
1NIK	X-ray	4.10	K	1-120	[»]
1NT9	X-ray	4.20	K	1-120	[»]
1PQV	X-ray	3.80	K	1-120	[»]
1R5U	X-ray	4.50	K	1-120	[»]
1R9S	X-ray	4.25	K	1-120	[»]
1R9T	X-ray	3.50	K	1-120	[»]
1SFO	X-ray	3.61	K	1-120	[»]
1TWA	X-ray	3.20	K	1-120	[»]
1TWC	X-ray	3.00	K	1-120	[»]
1TWF	X-ray	2.30	K	1-120	[»]
1TWG	X-ray	3.30	K	1-120	[»]
1TWH	X-ray	3.40	K	1-120	[»]
1WCM	X-ray	3.80	K	1-120	[»]
1Y1V	X-ray	3.80	K	1-120	[»]
1Y1W	X-ray	4.00	K	1-120	[»]
1Y1Y	X-ray	4.00	K	1-120	[»]
1Y77	X-ray	4.50	K	1-120	[»]
2B63	X-ray	3.80	K	1-120	[»]
2B8K	X-ray	4.15	K	1-120	[»]
2E2H	X-ray	3.95	K	1-120	[»]
2E2I	X-ray	3.41	K	1-120	[»]
2E2J	X-ray	3.50	K	1-120	[»]
2JA5	X-ray	3.80	K	1-120	[»]
2JA6	X-ray	4.00	K	1-120	[»]
2JA7	X-ray	3.80	K/W	1-120	[»]
2JA8	X-ray	3.80	K	1-120	[»]
2NVQ	X-ray	2.90	K	1-120	[»]
2NVT	X-ray	3.36	K	1-120	[»]
2NVX	X-ray	3.60	K	1-120	[»]
2NVY	X-ray	3.40	K	1-120	[»]
2NVZ	X-ray	4.30	K	1-120	[»]
2R7Z	X-ray	3.80	K	1-120	[»]
2R92	X-ray	3.80	K	1-120	[»]
2R93	X-ray	4.00	K	1-120	[»]
2VUM	X-ray	3.40	K	1-120	[»]
2YU9	X-ray	3.40	K	1-120	[»]
3CQZ	X-ray	2.80	K	1-120	[»]
3FKI	X-ray	3.88	K	1-120	[»]
3GTG	X-ray	3.78	K	1-120	[»]
3GTJ	X-ray	3.42	K	1-120	[»]
3GTK	X-ray	3.80	K	1-120	[»]
3GTL	X-ray	3.38	K	1-120	[»]
3GTM	X-ray	3.80	K	1-120	[»]
3GTO	X-ray	4.00	K	1-120	[»]
3GTP	X-ray	3.90	K	1-120	[»]
3GTQ	X-ray	3.80	K	1-120	[»]
3H3V	X-ray	4.00	L	1-120	[»]
3HOU	X-ray	3.20	K/W	1-120	[»]
3HOV	X-ray	3.50	K	1-120	[»]
3HOW	X-ray	3.60	K	1-120	[»]
3HOX	X-ray	3.65	K	1-120	[»]
3HOY	X-ray	3.40	K	1-120	[»]
3HOZ	X-ray	3.65	K	1-120	[»]
3I4M	X-ray	3.70	K	1-120	[»]
3I4N	X-ray	3.90	K	1-120	[»]
3J1N	electron microscopy	16.00	K	1-120	[»]
3K1F	X-ray	4.30	K	1-120	[»]
3K7A	X-ray	3.80	K	1-120	[»]
3M3Y	X-ray	3.18	K	1-120	[»]
3M4O	X-ray	3.57	K	1-120	[»]
3PO2	X-ray	3.30	K	1-120	[»]
3PO3	X-ray	3.30	K	1-120	[»]
3QT1	X-ray	4.30	K	1-120	[»]
3RZD	X-ray	3.30	K	1-120	[»]
3RZO	X-ray	3.00	K	1-120	[»]
3S14	X-ray	2.85	K	1-120	[»]
3S15	X-ray	3.30	K	1-120	[»]
3S16	X-ray	3.24	K	1-120	[»]
3S17	X-ray	3.20	K	1-120	[»]
3S1M	X-ray	3.13	K	1-120	[»]
3S1N	X-ray	3.10	K	1-120	[»]
3S1Q	X-ray	3.30	K	1-120	[»]
3S1R	X-ray	3.20	K	1-120	[»]
3S2D	X-ray	3.20	K	1-120	[»]
3S2H	X-ray	3.30	K	1-120	[»]
4A3B	X-ray	3.50	K	1-120	[»]
4A3C	X-ray	3.50	K	1-120	[»]
4A3D	X-ray	3.40	K	1-120	[»]
4A3E	X-ray	3.40	K	1-120	[»]
4A3F	X-ray	3.50	K	1-120	[»]
4A3G	X-ray	3.50	K	1-120	[»]
4A3I	X-ray	3.80	K	1-120	[»]
4A3J	X-ray	3.70	K	1-120	[»]
4A3K	X-ray	3.50	K	1-120	[»]
4A3L	X-ray	3.50	K	1-120	[»]
4A3M	X-ray	3.90	K	1-120	[»]
4A93	X-ray	3.40	K	1-120	[»]
4BBR	X-ray	3.40	K	1-120	[»]
4BBS	X-ray	3.60	K	1-120	[»]
4BXX	X-ray	3.28	K	1-120	[»]
4BXZ	X-ray	4.80	K	1-120	[»]
4BY1	X-ray	3.60	K	1-120	[»]
4BY7	X-ray	3.15	K	1-120	[»]

ProteinModelPortal

P38902.

SMR

P38902. Positions 1-114.

ModBase

Search...

MobiDB

Search...

Protein-protein interaction databases

BioGrid

34399. 50 interactions.

DIP

DIP-937N.

IntAct

P38902. 15 interactions.

MINT

MINT-618340.

STRING

4932.YOL005C.

Proteomic databases

PaxDb

P38902.

PeptideAtlas

P38902.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YOL005C; YOL005C; YOL005C.

GeneID

854157.

KEGG

sce:YOL005C.

Organism-specific databases

CYGD

YOL005c.

SGD

S000005365. RPB11.

Phylogenomic databases

eggNOG

COG1761.

GeneTree

ENSGT00550000074975.

HOGENOM

HOG000179862.

KO

K03008.

OMA

FAAYKVE.

OrthoDB

EOG7T4MZH.

Enzyme and pathway databases

BioCyc

YEAST:G3O-33422-MONOMER.

Gene expression databases

Genevestigator

P38902.

Family and domain databases

InterPro

IPR009025. RBP11-like_dimer.
IPR008193. RNA_pol_Rpb11_13-16kDa_CS.
[Graphical view]

SUPFAM

SSF55257. SSF55257. 1 hit.

PROSITE

PS01154. RNA_POL_L_13KD. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P38902.

NextBio

975923.

PRO

P38902.

Entry information

Entry name

RPB11_YEAST

Accession

Primary (citable) accession number: P38902
Secondary accession number(s): D6W262

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	April 16, 2014
This is version 135 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program