9VD9 image
Deposition Date 2025-06-07
Release Date 2025-06-25
Last Version Date 2025-06-25
Entry Detail
PDB ID:
9VD9
Keywords:
TRANSCRIPTION
Title:
Cryo-EM structure of the human DSS1-INTAC-PEC complex
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Sus scrofa (Taxon ID: 9823)
Host Organism:
Homo sapiens
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.60 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9VD9 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:26S proteasome complex subunit SEM1
Gene (Uniprot):SEM1
Chain IDs:A (auth: 0)
Chain Length:70
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P60896 Pfam ID:PF05160
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB1
Gene (Uniprot):POLR2A
Chain IDs:L (auth: 1)
Chain Length:1970
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P24928 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998, PF04992, PF04990, PF05001
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta,DNA-directed RNA polymerase II subunit RPB2
Gene (Uniprot):POLR2B
Chain IDs:M (auth: 2)
Chain Length:1300
Number of Molecules:1
Biological Source:Sus scrofa, Homo sapiens
UniProt ID:I3LGP4 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):POLR2C
Chain IDs:N (auth: 3)
Chain Length:275
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P19387 Pfam ID:PF01193, PF01000
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC1
Gene (Uniprot):POLR2E
Chain IDs:O (auth: 4)
Chain Length:210
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P19388 Pfam ID:PF03871, PF01191
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC2
Gene (Uniprot):POLR2F
Chain IDs:P (auth: 5)
Chain Length:127
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61218 Pfam ID:PF01192
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC3
Gene (Uniprot):POLR2H
Chain IDs:Q (auth: 6)
Chain Length:150
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P52434 Pfam ID:PF03870
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB9
Gene (Uniprot):POLR2I
Chain IDs:R (auth: 7)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P36954 Pfam ID:PF02150, PF01096
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC5
Gene (Uniprot):POLR2L
Chain IDs:S (auth: 8)
Chain Length:67
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62875 Pfam ID:PF01194
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB11-a
Gene (Uniprot):POLR2J
Chain IDs:T (auth: 9)
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P52435 Pfam ID:PF13656
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Integrator complex subunit 1
Gene (Uniprot):INTS1
Chain IDs:FA (auth: A)
Chain Length:2190
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8N201 Pfam ID:PF12432, PF22929, PF22927, PF22928
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Integrator complex subunit 2
Gene (Uniprot):INTS2
Chain IDs:E (auth: B)
Chain Length:1204
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H0H0 Pfam ID:PF14750
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Integrator complex subunit 4
Gene (Uniprot):INTS4
Chain IDs:F (auth: D)
Chain Length:963
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96HW7 Pfam ID:PF20168, PF13646
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Integrator complex subunit 5
Gene (Uniprot):INTS5
Chain IDs:GA (auth: E)
Chain Length:1019
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6P9B9 Pfam ID:PF14837, PF14838
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Integrator complex subunit 6
Gene (Uniprot):INTS6
Chain IDs:HA (auth: F)
Chain Length:887
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9UL03 Pfam ID:PF13519, PF15300
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Integrator complex subunit 7
Gene (Uniprot):INTS7
Chain IDs:G
Chain Length:962
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NVH2 Pfam ID:PF22965
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Integrator complex subunit 8
Gene (Uniprot):INTS8
Chain IDs:IA (auth: H)
Chain Length:995
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q75QN2
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Integrator complex subunit 9
Gene (Uniprot):INTS9
Chain IDs:B (auth: I)
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NV88 Pfam ID:PF16661, PF10996, PF21382
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Integrator complex subunit 11
Gene (Uniprot):INTS11
Chain IDs:C (auth: K)
Chain Length:172
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q5TA45 Pfam ID:PF16661, PF10996, PF07521, PF21386
Polymer Type:polypeptide(L)
Molecule:Unknown2
Chain IDs:JA (auth: M)
Chain Length:17
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
Gene (Uniprot):PPP2R1A
Chain IDs:J (auth: P)
Chain Length:589
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P30153 Pfam ID:PF02985
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
Gene (Uniprot):PPP2CA
Chain IDs:K (auth: Q)
Chain Length:309
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P67775 Pfam ID:PF00149 EC:3.1.3.16
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC4
Gene (Uniprot):POLR2K
Chain IDs:U (auth: a)
Chain Length:2190
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P53803 Pfam ID:PF03604
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (48-MER)
Chain IDs:V (auth: b)
Chain Length:1204
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3')
Chain IDs:D (auth: c)
Chain Length:21
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (45-MER)
Chain IDs:W (auth: d)
Chain Length:963
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Negative elongation factor A
Gene (Uniprot):NELFA
Chain IDs:X (auth: e)
Chain Length:1019
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H3P2
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Negative elongation factor B
Gene (Uniprot):NELFB
Chain IDs:Y (auth: f)
Chain Length:887
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8WX92 Pfam ID:PF06209
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Negative elongation factor C/D
Gene (Uniprot):NELFCD
Chain IDs:Z (auth: g)
Chain Length:962
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8IXH7 Pfam ID:PF04858
Polymer Type:polypeptide(L)
Molecule:Negative elongation factor E
Chain IDs:AA (auth: h)
Chain Length:995
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor SPT4
Gene (Uniprot):SUPT4H1
Chain IDs:BA (auth: i)
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P63272 Pfam ID:PF06093
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor SPT5
Gene (Uniprot):SUPT5H
Chain IDs:CA (auth: j)
Chain Length:1087
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O00267 Pfam ID:PF11942, PF03439, PF00467
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB7
Gene (Uniprot):POLR2G
Chain IDs:DA (auth: k)
Chain Length:172
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62487 Pfam ID:PF03876, PF00575
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB4
Gene (Uniprot):POLR2D
Chain IDs:EA (auth: l)
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O15514 Pfam ID:PF03874
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB1
Gene (Uniprot):POLR2A
Chain IDs:H (auth: m)
Chain Length:17
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P24928 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998, PF04992, PF04990, PF05001
Polymer Type:polypeptide(L)
Molecule:THR-SER-PRO-SER-TYR-SER-PRO-THR
Chain IDs:I (auth: n)
Chain Length:8
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:SER-PRO-LYS-TYR-SER-PRO-THR-SER
Chain IDs:LA (auth: o)
Chain Length:8
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:SER-PRO-THR-SER
Chain IDs:KA (auth: p)
Chain Length:589
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
MG
MN
ZN
Primary Citation
The small but versatile DSS1 protein is required for proper Integrator-PP2A function
To Be Published ? ? ? (?)
Primary Citation of related structures
9VD9