5XON image
Deposition Date 2017-05-29
Release Date 2017-08-16
Last Version Date 2024-03-27
Entry Detail
PDB ID:
5XON
Keywords:
TRANSCRIPTION/RNA
Title:
RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS
Biological Source:
Source Organism:
Komagataella phaffii (strain GS115 / ATCC 20864) (Taxon ID: 644223)
synthetic construct (Taxon ID: 32630)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.83 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
5XON 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, PF04561, PF04565, PF04566, PF04567, PF00562, 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:PF03876, PF00575
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):PAS_chr1-4_0359
Chain IDs:I
Chain Length:115
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4QY79 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, found in RNA polymerase complexes I, II, and III
Gene (Uniprot):PAS_chr1-1_0166
Chain IDs:L
Chain Length:72
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4QWA8 Pfam ID:PF03604
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (48-MER)
Chain IDs:O (auth: N)
Chain Length:48
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Molecule:RNA (30-MER)
Chain IDs:M (auth: P)
Chain Length:30
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (48-MER)
Chain IDs:N (auth: T)
Chain Length:48
Number of Molecules:1
Biological Source:synthetic construct
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription elongation factor TFIIS
Gene (Uniprot):PAS_chr2-2_0135
Chain IDs:P (auth: U)
Chain Length:190
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R2R6 Pfam ID:PF07500, PF01096
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor SPT4
Gene (Uniprot):PAS_chr2-1_0350
Chain IDs:Q (auth: V)
Chain Length:108
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R0E6 Pfam ID:PF06093
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein that forms a complex with Spt4p
Gene (Uniprot):PAS_chr3_1136
Chain IDs:R (auth: W)
Chain Length:612
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R370 Pfam ID:PF00467, PF03439
Ligand Molecules
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
5XON