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Sigm28-transcription initiation complex with specific promoter at the state 1

Electron Microscopy
3.86Å resolution
PDB entry 6pmi coloured by chain, front view.
PDB entry 6pmi coloured by chain, side view.
PDB entry 6pmi coloured by chain, top view.
Source organisms:
Assembly composition:
hetero nonamer (preferred)
Entry contents: 5 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DNA-directed RNA polymerase holoenzyme complex, SigmaF variant and RNA and DNA
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Multimeric state: hetero nonamer
Accessible surface area: 182503.49 Å2
Buried surface area: 44302.88 Å2
Dissociation area: 1,398.67 Å2
Dissociation energy (ΔGdiss): 2.92 kcal/mol
Dissociation entropy (TΔSdiss): 12.2 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-199498

Macromolecules

DNA-directed RNA polymerase subunit alpha
Chains: A, B
Length: 329 amino acids
Theoretical weight: 36.56 KDa
Source organism: Escherichia coli O157:H7
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A7Z4 (Residues: 1-329; Coverage: 100%)
Gene names: JW3257, b3295, pez, phs, rpoA, sez
Pfam:
InterPro:
DNA-directed RNA polymerase subunit alpha in PDB entry 6pmi, assembly 1, front view.
DNA-directed RNA polymerase subunit alpha in PDB entry 6pmi, assembly 1, side view.
DNA-directed RNA polymerase subunit alpha in PDB entry 6pmi, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P0A7Z4  
132950100150200250300
 
100200300MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIADE
UniProt
P0A7Z4
Chains
Domains
Secondary structure
Flexibility predictions
Interaction interfaces
Sequence conservation
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DNA-directed RNA polymerase subunit beta
Chain: C
Length: 1342 amino acids
Theoretical weight: 150.82 KDa
Source organism: Escherichia coli S88
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A8V2 (Residues: 1-1342; Coverage: 100%)
Gene names: JW3950, b3987, groN, nitB, rif, ron, rpoB, stl, stv, tabD
Pfam:
InterPro:
DNA-directed RNA polymerase subunit beta in PDB entry 6pmi, assembly 1, front view.
DNA-directed RNA polymerase subunit beta in PDB entry 6pmi, assembly 1, side view.
DNA-directed RNA polymerase subunit beta in PDB entry 6pmi, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P0A8V2  
113421002003004005006007008009001,0001,1001,2001,300
 
5001000MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE
UniProt
P0A8V2
Chains
Domains
Secondary structure
Flexibility predictions
Interaction interfaces
Sequence conservation
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DNA-directed RNA polymerase subunit beta'
Chain: D
Length: 1407 amino acids
Theoretical weight: 155.37 KDa
Source organism: Escherichia coli O157:H7
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A8T7 (Residues: 1-1407; Coverage: 100%)
Gene names: JW3951, b3988, rpoC, tabB
Pfam:
InterPro:
DNA-directed RNA polymerase subunit beta' in PDB entry 6pmi, assembly 1, front view.
DNA-directed RNA polymerase subunit beta' in PDB entry 6pmi, assembly 1, side view.
DNA-directed RNA polymerase subunit beta' in PDB entry 6pmi, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P0A8T7  
114071002003004005006007008009001,0001,1001,2001,3001,400
 
5001000
UniProt
P0A8T7
Chains
Domains
Secondary structure
Flexibility predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
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DNA-directed RNA polymerase subunit omega
Chain: E
Length: 91 amino acids
Theoretical weight: 10.25 KDa
Source organism: Escherichia coli S88
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A800 (Residues: 1-91; Coverage: 100%)
Gene names: JW3624, b3649, rpoZ
Pfam: RNA polymerase Rpb6
InterPro:
DNA-directed RNA polymerase subunit omega in PDB entry 6pmi, assembly 1, front view.
DNA-directed RNA polymerase subunit omega in PDB entry 6pmi, assembly 1, side view.
DNA-directed RNA polymerase subunit omega in PDB entry 6pmi, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P0A800  
191102030405060708090
 
20406080MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAELQAVTAIAEGRR
UniProt
P0A800
Chains
Domains
Secondary structure
Flexibility predictions
Interaction interfaces
Sequence conservation
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RNA polymerase sigma factor FliA
Chain: F
Length: 247 amino acids
Theoretical weight: 28.63 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AEM6 (Residues: 1-239; Coverage: 100%)
Gene names: JW1907, b1922, flaD, fliA, rpoF
Pfam:
InterPro:
RNA polymerase sigma factor FliA in PDB entry 6pmi, assembly 1, front view.
RNA polymerase sigma factor FliA in PDB entry 6pmi, assembly 1, side view.
RNA polymerase sigma factor FliA in PDB entry 6pmi, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P0AEM6  
124720406080100120140160180200220240
 
100200MNSLYTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWVPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGKLLEHHHHHH
UniProt
P0AEM6
Chains
Domains
Secondary structure
Flexibility predictions
Interaction interfaces
Sequence conservation
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DNA chain 1
Name: SYNTHETIC NONTEMPLATE STRAND DNA (54-MER)
Representative chains: 1
Length: 54 nucleotides
Theoretical weight: 16.56 KDa
SYNTHETIC NONTEMPLATE STRAND DNA (54-MER) in PDB entry 6pmi, assembly 1, front view.
SYNTHETIC NONTEMPLATE STRAND DNA (54-MER) in PDB entry 6pmi, assembly 1, side view.
SYNTHETIC NONTEMPLATE STRAND DNA (54-MER) in PDB entry 6pmi, assembly 1, top view.
1545101520253035404550
 
2040AGCAATAAAGTTTCCTTCCTCCTTGCCGATAACGAGATCAACTTGTTTGCGGCG
Chains
Chain G (auth 1)
Interaction interfaces
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DNA chain 2
Name: SYNTHETIC TEMPLATE STRAND DNA (54-MER)
Representative chains: 2
Length: 54 nucleotides
Theoretical weight: 16.76 KDa
SYNTHETIC TEMPLATE STRAND DNA (54-MER) in PDB entry 6pmi, assembly 1, front view.
SYNTHETIC TEMPLATE STRAND DNA (54-MER) in PDB entry 6pmi, assembly 1, side view.
SYNTHETIC TEMPLATE STRAND DNA (54-MER) in PDB entry 6pmi, assembly 1, top view.
1545101520253035404550
 
2040CGCCGCAAACAAGTTGTAGAGCTTATCGGCAAGGAGGAAGGAAACTTTATTGCT
Chains
Chain H (auth 2)
Interaction interfaces
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RNA chain 3
Name: Nascent RNA
Representative chains: 3
Length: 3 nucleotides
Theoretical weight: 1.08 KDa
Nascent RNA in PDB entry 6pmi, assembly 1, front view.
Nascent RNA in PDB entry 6pmi, assembly 1, side view.
Nascent RNA in PDB entry 6pmi, assembly 1, top view.
131.01.21.41.61.82.02.22.42.62.83.0
 
1234*AC
Chains
Chain I (auth 3)
Ligand binding sites
Interaction interfaces
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