ISDA

Deposition Date 2016-12-07

Release Date 2017-03-29

Last Version Date 2024-11-20

Entry Detail

PDB ID:

5U5Q

Keywords:

TRANSFERASE

Title:

12 Subunit RNA Polymerase II at Room Temperature collected using SFX

Biological Source:

Source Organism:

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Taxon ID: 559292)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.80 Å

R-Value Free:

0.27

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

C 2 2 21

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB1
Gene (Uniprot):RPO21
Chain IDs:A
Chain Length:1733
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P04050 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998, PF04992, PF04990, PF05001 EC:2.7.7.6

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB2
Gene (Uniprot):RPB2
Chain IDs:B
Chain Length:1224
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P08518 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB3
Gene (Uniprot):RPB3
Chain IDs:C
Chain Length:318
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P16370 Pfam ID:PF01193, PF01000

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB4
Gene (Uniprot):RPB4
Chain IDs:D
Chain Length:221
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P20433 Pfam ID:PF03874

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC1
Gene (Uniprot):RPB5
Chain IDs:E
Chain Length:215
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P20434 Pfam ID:PF03871, PF01191

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC2
Gene (Uniprot):RPO26
Chain IDs:F
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P20435 Pfam ID:PF01192

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB7
Gene (Uniprot):RPB7
Chain IDs:G
Chain Length:171
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P34087 Pfam ID:PF03876, PF00575

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC3
Gene (Uniprot):RPB8
Chain IDs:H
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P20436 Pfam ID:PF03870

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB9
Gene (Uniprot):RPB9
Chain IDs:I
Chain Length:122
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P27999 Pfam ID:PF02150, PF01096

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC5
Gene (Uniprot):RPB10
Chain IDs:J
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P22139 Pfam ID:PF01194

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB11
Gene (Uniprot):RPB11
Chain IDs:K
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P38902 Pfam ID:PF13656

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC4
Gene (Uniprot):RPC10
Chain IDs:L
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P40422 Pfam ID:PF03604

Ligand Molecules

Primary Citation

Double-flow focused liquid injector for efficient serial femtosecond crystallography.

Oberthuer, D, Knoska, J, Wiedorn, M.O, Beyerlein, K.R, Bushnell, D.A, Kovaleva, E.G, Heymann, M, Gumprecht, L, Kirian, R.A, Barty, A, Mariani, V, Tolstikova, A, Adriano, L, Awel, S, Barthelmess, M, Dorner, K, Xavier, P.L, Yefanov, O, James, D.R, Nelson, G, Wang, D, Calvey, G, Chen, Y, Schmidt, A, Szczepek, M, Frielingsdorf, S, Lenz, O, Snell, E, Robinson, P.J, Sarler, B, Belsak, G, Macek, M, Wilde, F, Aquila, A, Boutet, S, Liang, M, Hunter, M.S, Scheerer, P, Lipscomb, J.D, Weierstall, U, Kornberg, R.D, Spence, J.C, Pollack, L, Chapman, H.N, Bajt, S.Show

Sci Rep 7 44628 44628 (2017)

PMID: 28300169 DOI: 10.1038/srep44628

Abstact

Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Moreover, the double-flow focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improved operation and characteristics of these devices [corrected].

Legend

Protein

Chemical

Disease

Primary Citation of related structures