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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "YDR311W"

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Search Summary

This query matches 19 Structures.

Refinements

Structure Determination Methodology

experimental (19)

Scientific Name of Source Organism

	Saccharomyces cerevisiae S288C (15)
	synthetic construct (10)
	Saccharomyces cerevisiae (5)
	Homo sapiens (3)
	Xenopus laevis (3)
	Human herpesvirus 1 (strain F) (1)
	Human herpesvirus 4 strain B95-8 (1)
	Rift valley fever virus (STRAIN ZH-548 M12) (1)

Taxonomy

	Eukaryota (19)
	other sequences (10)
	Duplodnaviria (2)
	Riboviria (1)

Experimental Method

	ELECTRON MICROSCOPY (11)
	SOLUTION NMR (8)

Polymer Entity Type

	Protein (19)
	DNA (11)

Refinement Resolution (Å)

	2.5 - 3.0 (1)
	3.0 - 3.5 (4)
	3.5 - 4.0 (1)
	4.0 - 4.5 (1)
	> 4.5 (4)

Release Date

	2005 - 2009 (1)
	2010 - 2014 (4)
	2015 - 2019 (6)
	2020 - 2024 (8)

Enzyme Classification Name

	Hydrolases (12)
	Isomerases (11)
	Transferases (11)

Symmetry Type

Asymmetric (19)

SCOP Classification

	All beta proteins (8)
	Artifacts (5)

AllSelected

1 to 19 of 19 Structures

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2K2U \| pdb_00002k2u	Download File View File

NMR Structure of the complex between Tfb1 subunit of TFIIH and the activation domain of VP16

Langlois, C., Mas, C., Di Lello, P., Miller Jenkins, P.M., Legault, J., Omichinski, J.G.

(2008) J Am Chem Soc 130: 10596-10604

Released	2008-08-12
Method	SOLUTION NMR
Organisms	Human herpesvirus 1 (strain F) Saccharomyces cerevisiae
Macromolecule	Alpha trans-inducing protein (protein) RNA polymerase II transcription factor B subunit 1 (protein)

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2L2I \| pdb_00002l2i	Download File View File

NMR Structure of the complex between the Tfb1 subunit of TFIIH and the activation domain of EKLF

Mas, C., Di Lello, P., Lafrance-Vanasse, J., Omichinski, J.G.

To be published

Released	2011-07-06
Method	SOLUTION NMR
Organisms	Homo sapiens Saccharomyces cerevisiae S288C
Macromolecule	Krueppel-like factor 1 (protein) RNA polymerase II transcription factor B subunit 1 (protein)

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2LOX \| pdb_00002lox	Download File View File

NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad2

Lafrance-Vanasse, J., Legault, P., Omichinski, J.

(2012) Nucleic Acids Res 40: 5739-5750

Released	2012-02-15
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	DNA repair protein RAD2 (protein) RNA polymerase II transcription factor B subunit 1 (protein)

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2M14 \| pdb_00002m14	Download File View File

NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad4

Lafrance-Vanasse, J., Arseneault, G., Cappadocia, L., Legault, P., Omichinski, J.G.

(2013) Nucleic Acids Res 41: 2736-2745

Released	2013-01-23
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	DNA repair protein RAD4 (protein) RNA polymerase II transcription factor B subunit 1 (protein)

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2MKR \| pdb_00002mkr	Download File View File

Structural Characterization of a Complex Between the Acidic Transactivation Domain of EBNA2 and the Tfb1/p62 subunit of TFIIH.

Chabot, P.R., Raiola, L., Lussier-Price, M., Morse, T., Arseneault, G., Archambault, J., Omichinski, J.

(2014) PLoS Pathog 10: e1004042-e1004042

Released	2014-03-05
Method	SOLUTION NMR
Organisms	Human herpesvirus 4 strain B95-8 Saccharomyces cerevisiae S288C
Macromolecule	Epstein-Barr nuclear antigen 2 (protein) RNA polymerase II transcription factor B subunit 1 (protein)

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2N0Y \| pdb_00002n0y	Download File View File

NMR structure of the complex between the C-terminal domain of the Rift Valley fever virus protein NSs and the PH domain of the Tfb1 subunit of TFIIH

Cyr, N., de la Fuente, C., Lecoq, L., Guendel, I., Chabot, P.R., Kehn-Hall, K., Omichinski, J.G.

(2015) Proc Natl Acad Sci U S A 112: 6021-6026

Released	2015-04-22
Method	SOLUTION NMR
Organisms	Rift valley fever virus (STRAIN ZH-548 M12) Saccharomyces cerevisiae S288C
Macromolecule	Non-structural protein NS-S (protein) RNA polymerase II transcription factor B subunit 1 (protein)

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2N23 \| pdb_00002n23	Download File View File

NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the N-terminal activation domain of EKLF (TAD1)

Lecoq, L., Morse, T., Raiola, L., Arseneault, G., Omichinski, J.

To be published

Released	2016-04-27
Method	SOLUTION NMR
Organisms	Homo sapiens Saccharomyces cerevisiae S288C
Macromolecule	Krueppel-like factor 1 (protein) RNA polymerase II transcription factor B subunit 1 (protein)

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5OQJ \| pdb_00005oqj	Download File View File

STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH

Schilbach, S., Hantsche, M., Tegunov, D., Dienemann, C., Wigge, C., Henning, U., Cramer, P.

(2017) Nature 551: 204-209

Released	2018-04-25
Method	ELECTRON MICROSCOPY 4.7 Å
Organisms	Saccharomyces cerevisiae S288C synthetic construct
Macromolecule	Unique protein chains: 29 Unique nucleic acid chains: 2
Unique Ligands	MG, SF4, ZN

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5OQM \| pdb_00005oqm	Download File View File

STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR

Schilbach, S., Hantsche, M., Tegunov, D., Dienemann, C., Wigge, C., Urlaub, H., Cramer, P.

(2017) Nature 551: 204-209

Released	2018-05-09
Method	ELECTRON MICROSCOPY 5.8 Å
Organisms	Saccharomyces cerevisiae Saccharomyces cerevisiae S288C synthetic construct
Macromolecule	Unique protein chains: 44 Unique nucleic acid chains: 2
Unique Ligands	MG, SF4, ZN

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5URN \| pdb_00005urn	Download File View File

NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the transactivation domain 1 of p65

Lecoq, L., Omichinski, J.G., Raiola, L., Cyr, N., Chabot, P., Arseneault, G., Legault, P.

(2017) Nucleic Acids Res 45: 5564-5576

Released	2017-03-08
Method	SOLUTION NMR
Organisms	Homo sapiens Saccharomyces cerevisiae S288C
Macromolecule	RNA polymerase II transcription factor B subunit 1 (protein) Transcription factor p65 (protein)

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6GYM \| pdb_00006gym	Download File View File

Structure of a yeast closed complex with distorted DNA (CCdist)

Dienemann, C., Schwalb, B., Schilbach, S., Cramer, P.

(2019) Mol Cell 73: 97-106.e4

Released	2018-12-05
Method	ELECTRON MICROSCOPY 6.7 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 29 Unique nucleic acid chains: 2
Unique Ligands	MG, SF4, ZN

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7O4I \| pdb_00007o4i	Download File View File

Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble

Schilbach, S., Aibara, S., Dienemann, C., Grabbe, F., Cramer, P.

(2021) Cell 184: 4064-4072.e28

Released	2021-06-16
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Saccharomyces cerevisiae S288C synthetic construct
Macromolecule	Unique protein chains: 28 Unique nucleic acid chains: 2
Unique Ligands	ADP, BEF, MG, SF4, ZN

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7O4J \| pdb_00007o4j	Download File View File

Yeast RNA polymerase II transcription pre-initiation complex (consensus)

Schilbach, S., Aibara, S., Dienemann, C., Grabbe, F., Cramer, P.

(2021) Cell 184: 4064-4072.e28

Released	2021-06-16
Method	ELECTRON MICROSCOPY 2.9 Å
Organisms	Saccharomyces cerevisiae S288C synthetic construct
Macromolecule	Unique protein chains: 28 Unique nucleic acid chains: 2
Unique Ligands	ADP, BEF, MG, SF4, ZN

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7O4K \| pdb_00007o4k	Download File View File

Yeast TFIIH in the contracted state within the pre-initiation complex

Schilbach, S., Aibara, S., Dienemann, C., Grabbe, F., Cramer, P.

(2021) Cell 184: 4064-4072.e28

Released	2021-06-16
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Saccharomyces cerevisiae S288C synthetic construct
Macromolecule	Unique protein chains: 15 Unique nucleic acid chains: 2
Unique Ligands	ADP, BEF, MG, SF4, ZN

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7O4L \| pdb_00007o4l	Download File View File

Yeast TFIIH in the expanded state within the pre-initiation complex

Schilbach, S., Aibara, S., Dienemann, C., Grabbe, F., Cramer, P.

(2021) Cell 184: 4064-4072.e28

Released	2021-06-16
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Saccharomyces cerevisiae S288C synthetic construct
Macromolecule	Unique protein chains: 15 Unique nucleic acid chains: 2
Unique Ligands	ADP, BEF, MG, SF4, ZN

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7O73 \| pdb_00007o73	Download File View File

Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA

Schilbach, S., Aibara, S., Dienemann, C., Grabbe, F., Cramer, P.

(2021) Cell 184: 4064-4072.e28

Released	2021-06-16
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Saccharomyces cerevisiae S288C synthetic construct
Macromolecule	Unique protein chains: 28 Unique nucleic acid chains: 2
Unique Ligands	ADP, BEF, MG, SF4, ZN

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7ZS9 \| pdb_00007zs9	Download File View File

Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A)

Wang, H., Cramer, P.

(2023) Nat Struct Mol Biol 30: 226-232

Released	2022-11-16
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Saccharomyces cerevisiae Xenopus laevis synthetic construct
Macromolecule	Unique protein chains: 32 Unique nucleic acid chains: 2
Unique Ligands	MG, SF4, ZN

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7ZSA \| pdb_00007zsa	Download File View File

Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B)

Wang, H., Cramer, P.

(2023) Nat Struct Mol Biol 30: 226-232

Released	2022-11-16
Method	ELECTRON MICROSCOPY 4 Å
Organisms	Saccharomyces cerevisiae Xenopus laevis synthetic construct
Macromolecule	Unique protein chains: 32 Unique nucleic acid chains: 2
Unique Ligands	MG, SF4, ZN

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7ZSB \| pdb_00007zsb	Download File View File

Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C

Wang, H., Cramer, P.

(2023) Nat Struct Mol Biol 30: 226-232

Released	2022-11-16
Method	ELECTRON MICROSCOPY 6.6 Å
Organisms	Saccharomyces cerevisiae Xenopus laevis synthetic construct
Macromolecule	Unique protein chains: 32 Unique nucleic acid chains: 2
Unique Ligands	MG, SF4, ZN

1 to 19 of 19 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

2K2U | pdb_00002k2u

NMR Structure of the complex between Tfb1 subunit of TFIIH and the activation domain of VP16

2L2I | pdb_00002l2i

NMR Structure of the complex between the Tfb1 subunit of TFIIH and the activation domain of EKLF

2LOX | pdb_00002lox

NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad2

2M14 | pdb_00002m14

NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad4

2MKR | pdb_00002mkr

Structural Characterization of a Complex Between the Acidic Transactivation Domain of EBNA2 and the Tfb1/p62 subunit of TFIIH.

2N0Y | pdb_00002n0y

NMR structure of the complex between the C-terminal domain of the Rift Valley fever virus protein NSs and the PH domain of the Tfb1 subunit of TFIIH

2N23 | pdb_00002n23

NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the N-terminal activation domain of EKLF (TAD1)

5OQJ | pdb_00005oqj

STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH

5OQM | pdb_00005oqm

STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR

5URN | pdb_00005urn

NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the transactivation domain 1 of p65

6GYM | pdb_00006gym

Structure of a yeast closed complex with distorted DNA (CCdist)

7O4I | pdb_00007o4i

Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble

7O4J | pdb_00007o4j

Yeast RNA polymerase II transcription pre-initiation complex (consensus)

7O4K | pdb_00007o4k

Yeast TFIIH in the contracted state within the pre-initiation complex

7O4L | pdb_00007o4l

Yeast TFIIH in the expanded state within the pre-initiation complex

7O73 | pdb_00007o73

Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA

7ZS9 | pdb_00007zs9

Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A)

7ZSA | pdb_00007zsa

Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B)

7ZSB | pdb_00007zsb

Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

2K2U | pdb_00002k2u

2L2I | pdb_00002l2i

2LOX | pdb_00002lox

2M14 | pdb_00002m14

2MKR | pdb_00002mkr

2N0Y | pdb_00002n0y

2N23 | pdb_00002n23

5OQJ | pdb_00005oqj

5OQM | pdb_00005oqm

5URN | pdb_00005urn

6GYM | pdb_00006gym

7O4I | pdb_00007o4i

7O4J | pdb_00007o4j

7O4K | pdb_00007o4k

7O4L | pdb_00007o4l

7O73 | pdb_00007o73

7ZS9 | pdb_00007zs9

7ZSA | pdb_00007zsa

7ZSB | pdb_00007zsb