5XOG image
Entry Detail
PDB ID:
5XOG
Keywords:
TRANSCRIPTION
Title:
RNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1
Biological Source:
Source Organism:
Komagataella pastoris, Komagataella phaffii, synthetic construct, Komagataella phaffii (strain GS115 / ATCC 20864)
Host Organism:
Escherichia coli
PDB Version:
Deposition Date:
2017-05-28
Release Date:
2017-08-16
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.00 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 21
5XOG validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase subunit
Chain IDs:A
Chain Length:1743
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R4Y0 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998, PF04992, PF04990, PF05001
Protein Blast
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase subunit beta
Chain IDs:B
Chain Length:1227
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4QZQ7 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560
Protein Blast
Polymer Type:polypeptide(L)
Description:RNA polymerase II third largest subunit B44, part of central core
Chain IDs:C
Chain Length:304
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R7L2 Pfam ID:PF01193, PF01000
Protein Blast
Polymer Type:polypeptide(L)
Description:RNA polymerase II subunit B32
Chain IDs:D
Chain Length:186
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R2U9 Pfam ID:PF03874
Protein Blast
Polymer Type:polypeptide(L)
Description:RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
Chain IDs:E
Chain Length:214
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R3P8 Pfam ID:PF03871, PF01191
Protein Blast
Polymer Type:polypeptide(L)
Description:RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
Chain IDs:F
Chain Length:155
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R1V1 Pfam ID:PF01192
Protein Blast
Polymer Type:polypeptide(L)
Description:RNA polymerase II subunit
Chain IDs:G
Chain Length:171
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R9A1 Pfam ID:PF03876, PF00575
Protein Blast
Polymer Type:polypeptide(L)
Description:RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III
Chain IDs:H
Chain Length:145
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R273 Pfam ID:PF03870
Protein Blast
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase subunit
Chain IDs:I
Chain Length:115
Number of Molecules:1
Biological Source:Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)
UniProt ID:F2QPE6 Pfam ID:PF02150, PF01096
Protein Blast
Polymer Type:polypeptide(L)
Description:RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
Chain IDs:J
Chain Length:72
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R009 Pfam ID:PF01194
Protein Blast
Polymer Type:polypeptide(L)
Description:RNA polymerase II subunit B12.5
Chain IDs:K
Chain Length:118
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R3Z5 Pfam ID:PF13656
Protein Blast
Polymer Type:polypeptide(L)
Description:RNA polymerase subunit ABC10-alpha
Chain IDs:L
Chain Length:72
Number of Molecules:1
Biological Source:Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)
UniProt ID:F2QMI1 Pfam ID:PF03604
Protein Blast
Polymer Type:polypeptide(L)
Description:Transcription elongation factor 1 homolog
Mutations:N53G, L54Q, S55R
Chain IDs:P (auth: M)
Chain Length:85
Number of Molecules:1
Biological Source:Komagataella pastoris
UniProt ID:A0A1B2JER8 Pfam ID:PF05129
Polymer Type:polydeoxyribonucleotide
Description:DNA (30-MER)
Chain IDs:O (auth: N)
Chain Length:30
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Description:RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3')
Chain IDs:M (auth: P)
Chain Length:17
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:DNA (39-MER)
Chain IDs:N (auth: T)
Chain Length:39
Number of Molecules:1
Biological Source:synthetic construct
Protein Blast
Polymer Type:polypeptide(L)
Description:Spt4/5 complex component
Chain IDs:Q (auth: W)
Chain Length:83
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:F2QUC3 Pfam ID:PF00467
Ligand Molecules
APC
MG
ZN
Primary Citation
Structure of the complete elongation complex of RNA polymerase II with basal factors
Science 357 921 924 (2017)
PMID: 28775211 DOI: 10.1126/science.aan8552

Abstact

In the early stage of transcription, eukaryotic RNA polymerase II (Pol II) exchanges initiation factors with elongation factors to form an elongation complex for processive transcription. Here we report the structure of the Pol II elongation complex bound with the basal elongation factors Spt4/5, Elf1, and TFIIS. Spt4/5 (the Spt4/Spt5 complex) and Elf1 modify a wide area of the Pol II surface. Elf1 bridges the Pol II central cleft, completing a "DNA entry tunnel" for downstream DNA. Spt4 and the Spt5 NGN and KOW1 domains encircle the upstream DNA, constituting a "DNA exit tunnel." The Spt5 KOW4 and KOW5 domains augment the "RNA exit tunnel," directing the exiting nascent RNA. Thus, the elongation complex establishes a completely different transcription and regulation platform from that of the initiation complexes.

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Primary Citation of related structures
5XOG