› › Structure analysis

Structure of transcription factor UAF in complex with TBP and 35S rRNA promoter DNA

Electron Microscopy
2.8Å resolution
PDB entry 7z0o coloured by chain, front view.
PDB entry 7z0o coloured by chain, side view.
PDB entry 7z0o coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Assembly composition:
hetero decamer (preferred)
Entry contents: 7 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero decamer
Accessible surface area: 67445.35 Å2
Buried surface area: 51235.11 Å2
Dissociation area: 1,669.11 Å2
Dissociation energy (ΔGdiss): 8.07 kcal/mol
Dissociation entropy (TΔSdiss): 13.67 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-122360

Macromolecules

Histone H3
Chains: A, C
Length: 136 amino acids
Theoretical weight: 15.39 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P61830 (Residues: 1-136; Coverage: 100%)
Gene names: HHT1, HHT2, N2749, SIN2, YBR010W, YBR0201, YNL031C
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
Histone H3 in PDB entry 7z0o, assembly 1, front view.
Histone H3 in PDB entry 7z0o, assembly 1, side view.
Histone H3 in PDB entry 7z0o, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P61830  
1136102030405060708090100110120130
 
50100MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTIQKKDIKLARRLRGERS
UniProt
P61830
Chains
Domains
Secondary structure
Flexibility predictions
Interaction interfaces
Sequence conservation
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Histone H4
Chain: B
Length: 103 amino acids
Theoretical weight: 11.4 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P02309 (Residues: 1-103; Coverage: 100%)
Gene names: HHF1, HHF2, N2752, YBR009C, YBR0122, YNL030W
Pfam: Centromere kinetochore component CENP-T histone fold
InterPro:
Histone H4 in PDB entry 7z0o, assembly 1, front view.
Histone H4 in PDB entry 7z0o, assembly 1, side view.
Histone H4 in PDB entry 7z0o, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P02309  
1103102030405060708090100
 
50100MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG
UniProt
P02309
Chains
Domains
Secondary structure
Flexibility predictions
Interaction interfaces
Sequence conservation
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RNA polymerase I-specific transcription initiation factor RRN5
Chain: D
Length: 364 amino acids
Theoretical weight: 41.87 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q02983 (Residues: 1-363; Coverage: 100%)
Gene names: L3165, L9606.3, RRN5, YLR141W
InterPro: RNA polymerase I-specific transcription initiation factor Rrn5
RNA polymerase I-specific transcription initiation factor RRN5 in PDB entry 7z0o, assembly 1, front view.
RNA polymerase I-specific transcription initiation factor RRN5 in PDB entry 7z0o, assembly 1, side view.
RNA polymerase I-specific transcription initiation factor RRN5 in PDB entry 7z0o, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q02983  
136450100150200250300350
 
100200300SMEHQQLRKYVELYNKEVEEFYNGAASGRPAEFHPSKVHVKSIHEKAGTANAGVEISSVGVDWDSEEKNTFFWCLSRYSIHRVDEWRSLLPRKSAMEILGYYRLLRRASASARSRKAGDDGAPIAYEMSAEWVALETKLSETVMAITEGAAEVADEEGHCEGLIDYESWKRRWVAIYSHSRIAEIRPLPRHALPLSRSATQTLERCVSRYTRTLLWCTALAGMASRSVSARAAESRGHKSLPTVVTRRQVERALCTEARSRDLHVLPRRIVLTLRKWELDYPREGKLFRTKEMAHLFLQSQLSRRDAPPVHQDENQENQENQENQEQDNTASEGESEAERDEIDEADLFRSALHENQLLKWLSK
UniProt
Q02983
Chains
Domains
Secondary structure
Flexibility predictions
Interaction interfaces
Sequence conservation
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RNA polymerase I-specific transcription initiation factor RRN9
Chain: E
Length: 366 amino acids
Theoretical weight: 42.96 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P53437 (Residues: 1-365; Coverage: 100%)
Gene names: RRN9, YM8156.12C, YMR270C
Pfam: RNA polymerase I specific transcription initiation factor
InterPro: Rrn9 domain
RNA polymerase I-specific transcription initiation factor RRN9 in PDB entry 7z0o, assembly 1, front view.
RNA polymerase I-specific transcription initiation factor RRN9 in PDB entry 7z0o, assembly 1, side view.
RNA polymerase I-specific transcription initiation factor RRN9 in PDB entry 7z0o, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P53437  
136650100150200250300350
 
100200300SMSDLDEESQIETQIDAPIEDIIRGSELTTTTADKETLKSANELLDSLEHSHRVDLSLHLYSAYLLKRLLYKANEKKHFYEVNQFVKTQIKDNWTSWPNPNTIIDPSVDKLYEDIPEGIANVSVQPGEISNRALMHASDMMRVELDAQWQKFLSKSALDHDVTLDVDELNIPNEISRNILVKLDSLFEGLHDKIAKENEFDVRQDKHSNNIRANQIDDEPMQANRRIKYTYHDLVSRGCEMNEDMTDIYMKSLELYNDIPEKYKKRKFRLPKQILKKYHQPKKTSSYLKELLSKTREDFIPVEKLLKDKRLTSKDKSKLQRLNREETEDALNKRTFFQVKGYLEDENEISDYELDDCLIELPNGNI
UniProt
P53437
Chains
Domains
Secondary structure
Interaction interfaces
Sequence conservation
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RNA polymerase I-specific transcription initiation factor RRN10
Chain: F
Length: 145 amino acids
Theoretical weight: 16.53 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P38204 (Residues: 1-145; Coverage: 100%)
Gene names: RRN10, YBL025W, YBL0426
Pfam: UAF complex subunit Rrn10
InterPro:
RNA polymerase I-specific transcription initiation factor RRN10 in PDB entry 7z0o, assembly 1, front view.
RNA polymerase I-specific transcription initiation factor RRN10 in PDB entry 7z0o, assembly 1, side view.
RNA polymerase I-specific transcription initiation factor RRN10 in PDB entry 7z0o, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P38204  
114520406080100120140
 
50100MDRNVYEACSNIIKEFGTHVVSADEVLAEKIDNAVPIPFKTREEIDADVEKDRNEGVFEGNIIPDIDLRVVHYYATQLCLNKYPHLINAFDETSLITLGLLIEKWVKDYLTSIQTEQGRQSKVIGKGPCEFISKHIDYRHAPGNI
UniProt
P38204
Chains
Domains
Secondary structure
Interaction interfaces
Sequence conservation
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Upstream activation factor subunit UAF30
Chain: G
Length: 228 amino acids
Theoretical weight: 26.01 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q08747 (Residues: 1-228; Coverage: 100%)
Gene names: UAF30, YOR295W
Pfam:
InterPro:
Upstream activation factor subunit UAF30 in PDB entry 7z0o, assembly 1, front view.
Upstream activation factor subunit UAF30 in PDB entry 7z0o, assembly 1, side view.
Upstream activation factor subunit UAF30 in PDB entry 7z0o, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q08747  
122820406080100120140160180200220
 
100200MAELNDYSTMIDILLSDMDLETVTTKKVRMALKEVYAIDVESQGKAINKLIRKHLDLVKERPRFERSLEDLLKENATLAIELTKEITVSKRSSGEEKNDSETKGTHVEKKKGTVSKSPISTRKVTLSKSLASLLGEHELTRTEVVRRLWAYIKAHNLQNPNNKKEILCDEKLELILGKSTNMFEMHKILASHMTEPKKISDCPPLIQEVRRKEKPIVSDSEQSDTKGI
UniProt
Q08747
Chains
Domains
Secondary structure
Flexibility predictions
Interaction interfaces
Sequence conservation
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TATA-box-binding protein
Chain: H
Length: 242 amino acids
Theoretical weight: 27.24 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P13393 (Residues: 1-240; Coverage: 100%)
Gene names: BTF1, SPT15, TBP1, YER148W
Pfam: Transcription factor TFIID (or TATA-binding protein, TBP)
InterPro:
TATA-box-binding protein in PDB entry 7z0o, assembly 1, front view.
TATA-box-binding protein in PDB entry 7z0o, assembly 1, side view.
TATA-box-binding protein in PDB entry 7z0o, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P13393  
124220406080100120140160180200220240
 
100200GHMADEERLKEFKEANKIVFDPNTRQVWENQNRDGTKPATTFQSEEDIKRAAPESEKDTSATSGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM
UniProt
P13393
Chains
Domains
Secondary structure
Flexibility predictions
Interaction interfaces
Sequence conservation
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DNA chain N
Name: Non-template DNA
Representative chains: N
Length: 151 nucleotides
Theoretical weight: 47.27 KDa
Non-template DNA in PDB entry 7z0o, assembly 1, front view.
Non-template DNA in PDB entry 7z0o, assembly 1, side view.
Non-template DNA in PDB entry 7z0o, assembly 1, top view.
115120406080100120140
 
50100150
Chains
Chain I (auth N)
Interaction interfaces
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DNA chain T
Name: Template DNA
Representative chains: T
Length: 151 nucleotides
Theoretical weight: 45.92 KDa
Template DNA in PDB entry 7z0o, assembly 1, front view.
Template DNA in PDB entry 7z0o, assembly 1, side view.
Template DNA in PDB entry 7z0o, assembly 1, top view.
115120406080100120140
 
50100150
Chains
Chain J (auth T)
Interaction interfaces
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