ISDA: 7EGB

Deposition Date 2021-03-24

Release Date 2021-05-05

Last Version Date 2024-11-20

Entry Detail

PDB ID:

7EGB

Keywords:

TRANSCRIPTION

Title:

TFIID-based holo PIC on SCP promoter

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:

3.30 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:CDK-activating kinase assembly factor MAT1
Gene (Uniprot):MNAT1
Chain IDs:A (auth: 0)
Chain Length:309
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P51948 Pfam ID:PF06391, PF17121

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:General transcription factor IIH subunit 1
Gene (Uniprot):GTF2H1
Chain IDs:B (auth: 1)
Chain Length:548
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P32780 Pfam ID:PF03909, PF08567

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:General transcription factor IIH subunit 2
Gene (Uniprot):GTF2H2
Chain IDs:C (auth: 2)
Chain Length:395
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q13888 Pfam ID:PF07975, PF04056

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:General transcription factor IIH subunit 3
Gene (Uniprot):GTF2H3
Chain IDs:D (auth: 3)
Chain Length:308
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q13889 Pfam ID:PF03850

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:General transcription factor IIH subunit 4
Gene (Uniprot):GTF2H4
Chain IDs:E (auth: 4)
Chain Length:462
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q92759 Pfam ID:PF03849, PF18307

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:General transcription factor IIH subunit 5
Gene (Uniprot):GTF2H5
Chain IDs:F (auth: 5)
Chain Length:71
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q6ZYL4 Pfam ID:PF06331

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:General transcription and DNA repair factor IIH helicase subunit XPB
Gene (Uniprot):ERCC3
Chain IDs:G (auth: 6)
Chain Length:782
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P19447 Pfam ID:PF13625, PF04851, PF16203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:General transcription and DNA repair factor IIH helicase subunit XPD
Gene (Uniprot):ERCC2
Chain IDs:H (auth: 7)
Chain Length:760
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P18074 Pfam ID:PF06733, PF06777, PF13307 EC:3.6.4.12

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cyclin-dependent kinase 7
Gene (Uniprot):CDK7
Chain IDs:I (auth: 8)
Chain Length:346
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P50613 Pfam ID:PF00069 EC:2.7.11.22

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cyclin-H
Gene (Uniprot):CCNH
Chain IDs:J (auth: 9)
Chain Length:323
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P51946 Pfam ID:PF00134, PF16899

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor TFIID subunit 1
Gene (Uniprot):TAF1
Chain IDs:K (auth: A)
Chain Length:1872
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P21675 Pfam ID:PF09247, PF12157, PF15288, PF00439 EC:2.3.1.48

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor TFIID subunit 2
Gene (Uniprot):TAF2
Chain IDs:L (auth: B)
Chain Length:1199
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q6P1X5

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor TFIID subunit 4
Gene (Uniprot):TAF4
Chain IDs:M (auth: D), FA (auth: d)
Chain Length:1085
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:O00268 Pfam ID:PF07531, PF05236

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor TFIID subunit 5
Gene (Uniprot):TAF5
Chain IDs:N (auth: E), GA (auth: e)
Chain Length:800
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:Q15542 Pfam ID:PF04494, PF00400

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor TFIID subunit 6
Gene (Uniprot):TAF6
Chain IDs:O (auth: F), HA (auth: f)
Chain Length:677
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P49848 Pfam ID:PF02969, PF07571

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor TFIID subunit 7
Gene (Uniprot):TAF7
Chain IDs:P (auth: G)
Chain Length:349
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q15545 Pfam ID:PF04658

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor TFIID subunit 8
Gene (Uniprot):TAF8
Chain IDs:Q (auth: H)
Chain Length:310
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q7Z7C8 Pfam ID:PF07524, PF10406

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor TFIID subunit 9
Gene (Uniprot):TAF9
Chain IDs:R (auth: I), IA (auth: i)
Chain Length:264
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:Q16594 Pfam ID:PF02291

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor TFIID subunit 10
Gene (Uniprot):TAF10
Chain IDs:S (auth: J), JA (auth: j)
Chain Length:218
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:Q12962 Pfam ID:PF03540

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor TFIID subunit 12
Gene (Uniprot):TAF12
Chain IDs:T (auth: L), LA (auth: l)
Chain Length:161
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:Q16514 Pfam ID:PF03847

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIA subunit 2
Gene (Uniprot):GTF2A2
Chain IDs:U (auth: O)
Chain Length:109
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P52657 Pfam ID:PF02268, PF02751

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:TATA-box-binding protein
Gene (Uniprot):TBP
Chain IDs:V (auth: P)
Chain Length:339
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P20226 Pfam ID:PF00352

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIA subunit 1
Gene (Uniprot):GTF2A1
Chain IDs:W (auth: Q)
Chain Length:376
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P52655 Pfam ID:PF03153

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIB
Gene (Uniprot):GTF2B
Chain IDs:X (auth: R)
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q00403 Pfam ID:PF08271, PF00382

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:General transcription factor IIF subunit 1
Gene (Uniprot):GTF2F1
Chain IDs:Y (auth: S)
Chain Length:210
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P35269 Pfam ID:PF05793

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:General transcription factor IIF subunit 2
Gene (Uniprot):GTF2F2
Chain IDs:Z (auth: T)
Chain Length:249
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P13984 Pfam ID:PF02270, PF17683

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:General transcription factor IIE subunit 1
Gene (Uniprot):GTF2E1
Chain IDs:AA (auth: U)
Chain Length:439
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P29083 Pfam ID:PF02002, PF08271, PF11521

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIE subunit beta
Gene (Uniprot):GTF2E2
Chain IDs:BA (auth: V)
Chain Length:150
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P29084 Pfam ID:PF02186, PF18121

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (69-MER)
Chain IDs:CA (auth: X)
Chain Length:67
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (69-MER)
Chain IDs:DA (auth: Y)
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor TFIID subunit 3
Gene (Uniprot):TAF3
Chain IDs:EA (auth: c)
Chain Length:929
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q5VWG9 Pfam ID:PF07524, PF00628

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor TFIID subunit 11
Gene (Uniprot):TAF11
Chain IDs:KA (auth: k)
Chain Length:211
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q15544 Pfam ID:PF04719

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor TFIID subunit 13
Gene (Uniprot):TAF13
Chain IDs:MA (auth: m)
Chain Length:124
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q15543 Pfam ID:PF02269

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB1
Gene (Uniprot):POLR2A
Chain IDs:NA (auth: o)
Chain Length:109
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P24928 Pfam ID:PF05001, PF04997, PF00623, PF04983, PF05000, PF04998, PF04992, PF04990

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta
Chain IDs:OA (auth: p)
Chain Length:339
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A4X1TVZ5 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB3
Gene (Uniprot):POLR2C
Chain IDs:PA (auth: q)
Chain Length:376
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:I3LCH3 Pfam ID:PF01193, PF01000

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB4
Chain IDs:QA (auth: r)
Chain Length:142
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A481BYI6 Pfam ID:PF03874

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit E
Gene (Uniprot):POLR2E
Chain IDs:RA (auth: s)
Chain Length:210
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A4X1VTX4 Pfam ID:PF03871, PF01191

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit F
Gene (Uniprot):POLR2F
Chain IDs:SA (auth: t)
Chain Length:249
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A4X1VEK9 Pfam ID:PF01192

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB7
Gene (Uniprot):POLR2G
Chain IDs:TA (auth: u)
Chain Length:439
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A4X1VKG7 Pfam ID:PF03876, PF00575

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC3
Chain IDs:UA (auth: v)
Chain Length:150
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:I3LCB2 Pfam ID:PF03870

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB9
Gene (Uniprot):POLR2I
Chain IDs:VA (auth: w)
Chain Length:125
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:P60899 Pfam ID:PF02150, PF01096

Polymer Type:polypeptide(L)
Molecule:RPB10
Chain IDs:WA (auth: x)
Chain Length:67
Number of Molecules:1
Biological Source:Sus scrofa

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RNA_pol_L_2 domain-containing protein
Chain IDs:XA (auth: y)
Chain Length:117
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:F1RKE4 Pfam ID:PF13656

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RPB12
Gene (Uniprot):POLR2K
Chain IDs:YA (auth: z)
Chain Length:58
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A4X1TRS6 Pfam ID:PF03604

Ligand Molecules

SF4

Primary Citation

Structural insights into preinitiation complex assembly on core promoters.

Chen, X, Qi, Y, Wu, Z, Wang, X, Li, J, Zhao, D, Hou, H, Li, Y, Yu, Z, Liu, W, Wang, M, Ren, Y, Li, Z, Yang, H, Xu, Y.Show

Science 372 ? ? (2021)

PMID: 33795473 DOI: 10.1126/science.aba8490

Abstact

Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)-mediated eukaryotic transcription. We determined the structures of human TFIID-based PIC in three stepwise assembly states and revealed two-track PIC assembly: stepwise promoter deposition to Pol II and extensive modular reorganization on track I (on TATA-TFIID-binding element promoters) versus direct promoter deposition on track II (on TATA-only and TATA-less promoters). The two tracks converge at an ~50-subunit holo PIC in identical conformation, whereby TFIID stabilizes PIC organization and supports loading of cyclin-dependent kinase (CDK)-activating kinase (CAK) onto Pol II and CAK-mediated phosphorylation of the Pol II carboxyl-terminal domain. Unexpectedly, TBP of TFIID similarly bends TATA box and TATA-less promoters in PIC. Our study provides structural visualization of stepwise PIC assembly on highly diversified promoters.

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Primary Citation of related structures

Abstact

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