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1ngm

Crystal structure of a yeast Brf1-TBP-DNA ternary complex

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Transcription initiation factor TFIID

Saccharomyces cerevisiae

UniProt P13393

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 2 DNA 2 5'-D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T)-3' × 1 5'-D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G)-3' × 1 Transcription factor IIIB BRF1 subunit × 1 （P29056） Consistent with all polymers
2 Protein–DNA Heteromer Protein 2 DNA 2 5'-D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T)-3' × 1 5'-D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G)-3' × 1 Transcription factor IIIB BRF1 subunit × 1 （P29056） Consistent with all polymers
3 Protein–DNA Heteromer Protein 2 DNA 2 5'-D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T)-3' × 1 5'-D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G)-3' × 1 Transcription factor IIIB BRF1 subunit × 1 （P29056） Consistent with all polymers
4 Protein–DNA Heteromer Protein 2 DNA 2 5'-D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T)-3' × 1 5'-D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G)-3' × 1 Transcription factor IIIB BRF1 subunit × 1 （P29056） Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1tbp

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1ngm 1ngm 1ngm 1ngm 1nh2 1rm1 1tba 1ytb 1ytb 1ytf 4b0a 4v1n

52 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name TBP_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–180； UniProt 60–239 Author chain E； PDBConstruct 1–180； UniProt 60–239 Author chain I； PDBConstruct 1–180； UniProt 60–239 Author chain M； PDBConstruct 1–180； UniProt 60–239

Transcription factor IIIB BRF1 subunit

Saccharomyces cerevisiae

UniProt P29056

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 2 DNA 2 5'-D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T)-3' × 1 5'-D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G)-3' × 1 Transcription initiation factor TFIID × 1 （P13393） Consistent with all polymers
2 Protein–DNA Heteromer Protein 2 DNA 2 5'-D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T)-3' × 1 5'-D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G)-3' × 1 Transcription initiation factor TFIID × 1 （P13393） Consistent with all polymers
3 Protein–DNA Heteromer Protein 2 DNA 2 5'-D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T)-3' × 1 5'-D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G)-3' × 1 Transcription initiation factor TFIID × 1 （P13393） Consistent with all polymers
4 Protein–DNA Heteromer Protein 2 DNA 2 5'-D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T)-3' × 1 5'-D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G)-3' × 1 Transcription initiation factor TFIID × 1 （P13393） Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1ngm 1ngm 1ngm 1ngm 6cnb 6cnc 6cnd 6cnf 6eu0 6f40 6f41 6f42

15 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name TF3B_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain B； PDBConstruct 3–72； UniProt 437–506 Author chain F； PDBConstruct 3–72； UniProt 437–506 Author chain J； PDBConstruct 3–72； UniProt 437–506 Author chain N； PDBConstruct 3–72； UniProt 437–506

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ngm
Deposition date deposition_date2002-12-17
Structure title titleCrystal structure of a yeast Brf1-TBP-DNA ternary complex
Keywords keywordsTRANSCRIPTION, TFIIIB, TBP, BRF, BRF1, TAF, PROTEIN-DNA COMPLEX, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1ngm__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1ngm__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1ngm__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）24.39 Å
Rg (electron density)23.77 Å
Total Rg24.52 Å
Atom count2775
Residues290
Excluded volume47552 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1ngm__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1ngm__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1ngm__assembly_3__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1ngm__assembly_4__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

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6. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

Domain ID domain_idd1ngma1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.129 — TBP-like
Superfamily Superfamily superfamilyd.129.1 — TATA-box binding protein-like
Family Family familyd.129.1.1 — TATA-box binding protein (TBP), C-terminal domain
Domain ID domain_idd1ngma2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.129 — TBP-like
Superfamily Superfamily superfamilyd.129.1 — TATA-box binding protein-like
Family Family familyd.129.1.1 — TATA-box binding protein (TBP), C-terminal domain
Domain ID domain_idd1ngmb1
Class classj — Peptides
Fold Fold foldj.104 — TBP-binding domain of the transcription factor IIIb Brf1 subunit
Superfamily Superfamily superfamilyj.104.1 — TBP-binding domain of the transcription factor IIIb Brf1 subunit
Family Family familyj.104.1.1 — TBP-binding domain of the transcription factor IIIb Brf1 subunit
Domain ID domain_idd1ngmb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1ngme1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.129 — TBP-like
Superfamily Superfamily superfamilyd.129.1 — TATA-box binding protein-like
Family Family familyd.129.1.1 — TATA-box binding protein (TBP), C-terminal domain
Domain ID domain_idd1ngme2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.129 — TBP-like
Superfamily Superfamily superfamilyd.129.1 — TATA-box binding protein-like
Family Family familyd.129.1.1 — TATA-box binding protein (TBP), C-terminal domain
Domain ID domain_idd1ngmf1
Class classj — Peptides
Fold Fold foldj.104 — TBP-binding domain of the transcription factor IIIb Brf1 subunit
Superfamily Superfamily superfamilyj.104.1 — TBP-binding domain of the transcription factor IIIb Brf1 subunit
Family Family familyj.104.1.1 — TBP-binding domain of the transcription factor IIIb Brf1 subunit
Domain ID domain_idd1ngmf2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1ngmi1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.129 — TBP-like
Superfamily Superfamily superfamilyd.129.1 — TATA-box binding protein-like
Family Family familyd.129.1.1 — TATA-box binding protein (TBP), C-terminal domain
Domain ID domain_idd1ngmi2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.129 — TBP-like
Superfamily Superfamily superfamilyd.129.1 — TATA-box binding protein-like
Family Family familyd.129.1.1 — TATA-box binding protein (TBP), C-terminal domain
Domain ID domain_idd1ngmj_
Class classj — Peptides
Fold Fold foldj.104 — TBP-binding domain of the transcription factor IIIb Brf1 subunit
Superfamily Superfamily superfamilyj.104.1 — TBP-binding domain of the transcription factor IIIb Brf1 subunit
Family Family familyj.104.1.1 — TBP-binding domain of the transcription factor IIIb Brf1 subunit
Domain ID domain_idd1ngmm1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.129 — TBP-like
Superfamily Superfamily superfamilyd.129.1 — TATA-box binding protein-like
Family Family familyd.129.1.1 — TATA-box binding protein (TBP), C-terminal domain
Domain ID domain_idd1ngmm2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.129 — TBP-like
Superfamily Superfamily superfamilyd.129.1 — TATA-box binding protein-like
Family Family familyd.129.1.1 — TATA-box binding protein (TBP), C-terminal domain
Domain ID domain_idd1ngmn_
Class classj — Peptides
Fold Fold foldj.104 — TBP-binding domain of the transcription factor IIIb Brf1 subunit
Superfamily Superfamily superfamilyj.104.1 — TBP-binding domain of the transcription factor IIIb Brf1 subunit
Family Family familyj.104.1.1 — TBP-binding domain of the transcription factor IIIb Brf1 subunit

CATH v4.4 (12 domains)

Domain ID domain_id1ngmA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily10 — TATA-Binding Protein
Domain ID domain_id1ngmA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily10 — TATA-Binding Protein
Domain ID domain_id1ngmB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily650 — Single helix bin
Domain ID domain_id1ngmE01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily10 — TATA-Binding Protein
Domain ID domain_id1ngmE02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily10 — TATA-Binding Protein
Domain ID domain_id1ngmF00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily650 — Single helix bin
Domain ID domain_id1ngmI01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily10 — TATA-Binding Protein
Domain ID domain_id1ngmI02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily10 — TATA-Binding Protein
Domain ID domain_id1ngmJ00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily650 — Single helix bin
Domain ID domain_id1ngmM01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily10 — TATA-Binding Protein
Domain ID domain_id1ngmM02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily10 — TATA-Binding Protein
Domain ID domain_id1ngmN00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily650 — Single helix bin
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7. Citations (1)