5XOG image
Deposition Date 2017-05-28
Release Date 2017-08-16
Last Version Date 2024-03-27
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 (Taxon ID: 4922)
Komagataella phaffii (Taxon ID: 981350)
synthetic construct (Taxon ID: 32630)
Komagataella phaffii (strain GS115 / ATCC 20864) (Taxon ID: 644223)
Host Organism:
Escherichia coli
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit
Gene (Uniprot):PAS_chr3_0568
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta
Gene (Uniprot):PAS_chr2-1_0125
Chain IDs:B
Chain Length:1227
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4QZQ7 Pfam ID:PF04563, PF00562, PF04561, PF04565, PF04566, PF04567, PF04560
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II third largest subunit B44, part of central core
Gene (Uniprot):PAS_chr4_0344
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit B32
Gene (Uniprot):PAS_chr2-2_0104
Chain IDs:D
Chain Length:186
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R2U9 Pfam ID:PF03874
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
Gene (Uniprot):PAS_chr3_0157
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
Gene (Uniprot):PAS_chr2-2_0434
Chain IDs:F
Chain Length:155
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R1V1 Pfam ID:PF01192
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit
Gene (Uniprot):PAS_chr4_0906
Chain IDs:G
Chain Length:171
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R9A1 Pfam ID:PF00575, PF03876
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III
Gene (Uniprot):PAS_chr2-2_0309
Chain IDs:H
Chain Length:145
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R273 Pfam ID:PF03870
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit
Gene (Uniprot):RPB9
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
Gene (Uniprot):PAS_chr2-1_0223
Chain IDs:J
Chain Length:72
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R009 Pfam ID:PF01194
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit B12.5
Gene (Uniprot):PAS_chr3_0244
Chain IDs:K
Chain Length:118
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R3Z5 Pfam ID:PF13656
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase subunit ABC10-alpha
Gene (Uniprot):RPC10
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor 1 homolog
Gene (Uniprot):ELF1
Mutagens: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
Molecule:DNA (30-MER)
Chain IDs:O (auth: N)
Chain Length:30
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Molecule: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
Molecule:DNA (39-MER)
Chain IDs:N (auth: T)
Chain Length:39
Number of Molecules:1
Biological Source:synthetic construct
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Spt4/5 complex component
Gene (Uniprot):SPT5
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
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