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- EMDB-7014: Structure of 30S ribosomal subunit and RNA polymerase complex in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-7014
TitleStructure of 30S ribosomal subunit and RNA polymerase complex in non-rotated state
Map dataStructure of 30S ribosomal subunit and RNA polymerase complex in non-rotated state
Sample
  • Complex: 30S ribosomal subunit and RNA polymerase complex
    • Complex: 30S ribosomal subunitProkaryotic small ribosomal subunit
      • RNA: x 1 types
      • Protein or peptide: x 21 types
    • Complex: RNA polymerase
      • Protein or peptide: x 4 types
Keywords30S subunit RNA polymerase complex / RIBOSOME
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / small ribosomal subunit / tRNA binding / protein dimerization activity / ribosome / rRNA binding / structural constituent of ribosome ...DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / small ribosomal subunit / tRNA binding / protein dimerization activity / ribosome / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit ...DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / RNA polymerase Rpb6 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / RNA polymerase Rpb1, clamp domain superfamily / Ribosomal protein S9, bacterial/plastid / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / Ribosomal protein S4, bacterial-type / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / Ribosomal protein S6, plastid/chloroplast / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / Ribosomal protein S2, bacteria/mitochondria/plastid / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S2 signature 2. / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1.
Similarity search - Domain/homology
Small ribosomal subunit protein bS21 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 ...Small ribosomal subunit protein bS21 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / DNA-directed RNA polymerase subunit omega / Small ribosomal subunit protein bS16 / DNA-directed RNA polymerase subunit beta / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS5 / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta'
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsDemo G / Rasouly A
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106105 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107465 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107329 United States
CitationJournal: Elife / Year: 2017
Title: Structure of RNA polymerase bound to ribosomal 30S subunit.
Authors: Gabriel Demo / Aviram Rasouly / Nikita Vasilyev / Vladimir Svetlov / Anna B Loveland / Ruben Diaz-Avalos / Nikolaus Grigorieff / Evgeny Nudler / Andrei A Korostelev /
Abstract: In bacteria, mRNA transcription and translation are coupled to coordinate optimal gene expression and maintain genome stability. Coupling is thought to involve direct interactions between RNA ...In bacteria, mRNA transcription and translation are coupled to coordinate optimal gene expression and maintain genome stability. Coupling is thought to involve direct interactions between RNA polymerase (RNAP) and the translational machinery. We present cryo-EM structures of RNAP core bound to the small ribosomal 30S subunit. The complex is stable under cell-like ionic conditions, consistent with functional interaction between RNAP and the 30S subunit. The RNA exit tunnel of RNAP aligns with the Shine-Dalgarno-binding site of the 30S subunit. Ribosomal protein S1 forms a wall of the tunnel between RNAP and the 30S subunit, consistent with its role in directing mRNAs onto the ribosome. The nucleic-acid-binding cleft of RNAP samples distinct conformations, suggesting different functional states during transcription-translation coupling. The architecture of the 30S•RNAP complex provides a structural basis for co-localization of the transcriptional and translational machineries, and inform future mechanistic studies of coupled transcription and translation.
History
DepositionSep 5, 2017-
Header (metadata) releaseOct 18, 2017-
Map releaseOct 18, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6awb
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6awb
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_7014.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of 30S ribosomal subunit and RNA polymerase complex in non-rotated state
Voxel sizeX=Y=Z: 1.6428 Å
Density
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-3.4754603 - 10.059796
Average (Standard dev.)-0.0134722935 (±0.6573377)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 459.98398 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.64281.64281.6428
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z459.984459.984459.984
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-3.47510.060-0.013

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Supplemental data

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Sample components

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Entire : 30S ribosomal subunit and RNA polymerase complex

EntireName: 30S ribosomal subunit and RNA polymerase complex
Components
  • Complex: 30S ribosomal subunit and RNA polymerase complex
    • Complex: 30S ribosomal subunitProkaryotic small ribosomal subunit
      • RNA: 16S rRNA
      • Protein or peptide: 30S ribosomal protein S1
      • Protein or peptide: 30S ribosomal protein S2
      • Protein or peptide: 30S ribosomal protein S3
      • Protein or peptide: 30S ribosomal protein S4
      • Protein or peptide: 30S ribosomal protein S5
      • Protein or peptide: 30S ribosomal protein S6
      • Protein or peptide: 30S ribosomal protein S7
      • Protein or peptide: 30S ribosomal protein S8
      • Protein or peptide: 30S ribosomal protein S9
      • Protein or peptide: 30S ribosomal protein S10
      • Protein or peptide: 30S ribosomal protein S11
      • Protein or peptide: 30S ribosomal protein S12
      • Protein or peptide: 30S ribosomal protein S13
      • Protein or peptide: 30S ribosomal protein S14
      • Protein or peptide: 30S ribosomal protein S15
      • Protein or peptide: 30S ribosomal protein S16
      • Protein or peptide: 30S ribosomal protein S17
      • Protein or peptide: 30S ribosomal protein S18
      • Protein or peptide: 30S ribosomal protein S19
      • Protein or peptide: 30S ribosomal protein S20
      • Protein or peptide: 30S ribosomal protein S21
    • Complex: RNA polymerase
      • Protein or peptide: DNA-directed RNA polymerase subunit alphaPolymerase
      • Protein or peptide: DNA-directed RNA polymerase subunit betaPolymerase
      • Protein or peptide: DNA-directed RNA polymerase subunit beta'Polymerase
      • Protein or peptide: DNA-directed RNA polymerase subunit omegaPolymerase

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Supramolecule #1: 30S ribosomal subunit and RNA polymerase complex

SupramoleculeName: 30S ribosomal subunit and RNA polymerase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 1.3 MDa

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Supramolecule #2: 30S ribosomal subunit

SupramoleculeName: 30S ribosomal subunit / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #6-#26
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: RNA polymerase

SupramoleculeName: RNA polymerase / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#5
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: 16S rRNA

MacromoleculeName: 16S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 498.725406 KDa
SequenceString: AAUUGAAGAG UUUGAUCAUG GCUCAGAUUG AACGCUGGCG GCAGGCCUAA CACAUGCAAG UCGAACGGUA ACAGGAAGAA GCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA A ACGGUAGC ...String:
AAUUGAAGAG UUUGAUCAUG GCUCAGAUUG AACGCUGGCG GCAGGCCUAA CACAUGCAAG UCGAACGGUA ACAGGAAGAA GCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA A ACGGUAGC UAAUACCGCA UAACGUCGCA AGACCAAAGA GGGGGACCUU CGGGCCUCUU GCCAUCGGAU GUGCCCAGAU GG GAUUAGC UAGUAGGUGG GGUAACGGCU CACCUAGGCG ACGAUCCCUA GCUGGUCUGA GAGGAUGACC AGCCACACUG GAA CUGAGA CACGGUCCAG ACUCCUACGG GAGGCAGCAG UGGGGAAUAU UGCACAAUGG GCGCAAGCCU GAUGCAGCCA UGCC GCGUG UAUGAAGAAG GCCUUCGGGU UGUAAAGUAC UUUCAGCGGG GAGGAAGGGA GUAAAGUUAA UACCUUUGCU CAUUG ACGU UACCCGCAGA AGAAGCACCG GCUAACUCCG UGCCAGCAGC CGCGGUAAUA CGGAGGGUGC AAGCGUUAAU CGGAAU UAC UGGGCGUAAA GCGCACGCAG GCGGUUUGUU AAGUCAGAUG UGAAAUCCCC GGGCUCAACC UGGGAACUGC AUCUGAU AC UGGCAAGCUU GAGUCUCGUA GAGGGGGGUA GAAUUCCAGG UGUAGCGGUG AAAUGCGUAG AGAUCUGGAG GAAUACCG G UGGCGAAGGC GGCCCCCUGG ACGAAGACUG ACGCUCAGGU GCGAAAGCGU GGGGAGCAAA CAGGAUUAGA UACCCUGGU AGUCCACGCC GUAAACGAUG UCGACUUGGA GGUUGUGCCC UUGAGGCGUG GCUUCCGGAG CUAACGCGUU AAGUCGACCG CCUGGGGAG UACGGCCGCA AGGUUAAAAC UCAAAUGAAU UGACGGGGGC CCGCACAAGC GGUGGAGCAU GUGGUUUAAU U CGAUGCAA CGCGAAGAAC CUUACCUGGU CUUGACAUCC ACGGAAGUUU UCAGAGAUGA GAAUGUGCCU UCGGGAACCG UG AGACAGG UGCUGCAUGG CUGUCGUCAG CUCGUGUUGU GAAAUGUUGG GUUAAGUCCC GCAACGAGCG CAACCCUUAU CCU UUGUUG CCAGCGGUCC GGCCGGGAAC UCAAAGGAGA CUGCCAGUGA UAAACUGGAG GAAGGUGGGG AUGACGUCAA GUCA UCAUG GCCCUUACGA CCAGGGCUAC ACACGUGCUA CAAUGGCGCA UACAAAGAGA AGCGACCUCG CGAGAGCAAG CGGAC CUCA UAAAGUGCGU CGUAGUCCGG AUUGGAGUCU GCAACUCGAC UCCAUGAAGU CGGAAUCGCU AGUAAUCGUG GAUCAG AAU GCCACGGUGA AUACGUUCCC GGGCCUUGUA CACACCGCCC GUCACACCAU GGGAGUGGGU UGCAAAAGAA GUAGGUA GC UUAACCUUCG GGAGGGCGCU UACCACUUUG UGAUUCAUGA CUGGGGUGAA GUCGUAACAA GGUAACCGUA GGGGAACC U GCGGUUGGAU CACCUCCU

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Macromolecule #2: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 25.33983 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TEFLKPRLVD IEQVSSTHAK VTLEPLERGF GHTLGNALRR ILLSSMPGCA VTEVEIDGVL HEYSTKEGVQ EDILEILLNL KGLAVRVQG KDEVILTLNK SGIGPVTAAD ITHDGDVEIV KPQHVICHLT DENASISMRI KVQRGRGYVP ASTRIHSEED E RPIGRLLV ...String:
TEFLKPRLVD IEQVSSTHAK VTLEPLERGF GHTLGNALRR ILLSSMPGCA VTEVEIDGVL HEYSTKEGVQ EDILEILLNL KGLAVRVQG KDEVILTLNK SGIGPVTAAD ITHDGDVEIV KPQHVICHLT DENASISMRI KVQRGRGYVP ASTRIHSEED E RPIGRLLV DACYSPVERI AYNVEAARVE QRTDLDKLVI EMETNGTIDP EEAIRRAATI LAEQLEAFVD L

UniProtKB: DNA-directed RNA polymerase subunit alpha

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Macromolecule #3: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 150.560562 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VYSYTEKKRI RKDFGKRPQV LDVPYLLSIQ LDSFQKFIEQ DPEGQYGLEA AFRSVFPIQS YSGNSELQYV SYRLGEPVFD VQECQIRGV TYSAPLRVKL RLVIYEREAP EGTVKDIKEQ EVYMGEIPLM TDNGTFVING TERVIVSQLH RSPGVFFDSD K GKTHSSGK ...String:
VYSYTEKKRI RKDFGKRPQV LDVPYLLSIQ LDSFQKFIEQ DPEGQYGLEA AFRSVFPIQS YSGNSELQYV SYRLGEPVFD VQECQIRGV TYSAPLRVKL RLVIYEREAP EGTVKDIKEQ EVYMGEIPLM TDNGTFVING TERVIVSQLH RSPGVFFDSD K GKTHSSGK VLYNARIIPY RGSWLDFEFD PKDNLFVRID RRRKLPATII LRALNYTTEQ ILDLFFEKVI FEIRDNKLQM EL VPERLRG ETASFDIEAN GKVYVEKGRR ITARHIRQLE KDDVKLIEVP VEYIAGKVVA KDYIDESTGE LICAANMELS LDL LAKLSQ SGHKRIETLF TNDLDHGPYI SETLRVDPTN DRLSALVEIY RMMRPGEPPT REAAESLFEN LFFSEDRYDL SAVG RMKFN RSLLREEIEG SGILSKDDII DVMKKLIDIR NGKGEVDDID HLGNRRIRSV GEMAENQFRV GLVRVERAVK ERLSL GDLD TLMPQDMINA KPISAAVKEF FGSSQLSQFM DQNNPLSEIT HKRRISALGP GGLTRERAGF EVRDVHPTHY GRVCPI ETP EGPNIGLINS LSVYAQTNEY GFLETPYRKV TDGVVTDEIH YLSAIEEGNY VIAQANSNLD EEGHFVEDLV TCRSKGE SS LFSRDQVDYM DVSTQQVVSV GASLIPFLEH DDANRALMGA NMQRQAVPTL RADKPLVGTG MERAVAVDSG VTAVAKRG G VVQYVDASRI VIKVNEDEMY PGEAGIDIYN LTKYTRSNQN TCINQMPCVS LGEPVERGDV LADGPSTDLG ELALGQNMR VAFMPWNGYN FEDSILVSER VVQEDRFTTI HIQELACVSR DTKLGPEEIT ADIPNVGEAA LSKLDESGIV YIGAEVTGGD ILVGKVTPK GETQLTPEEK LLRAIFGEKA SDVKDSSLRV PNGVSGTVID VQVFTRDGVE KDKRALEIEE MQLKQAKKDL S EELQILEA GLFSRIRAVL VAGGVEAEKL DKLPRDRWLE LGLTDEEKQN QLEQLAEQYD ELKHEFEKKL EAKRRKITQG DD LAPGVLK IVKVYLAVKR RIQPGDKMAG RHGNKGVISK INPIEDMPYD ENGTPVDIVL NPLGVPSRMN IGQILETHLG MAA KGIGDK INAMLKQQQE VAKLREFIQR AYDLGADVRQ KVDLSTFSDE EVMRLAENLR KGMPIATPVF DGAKEAEIKE LLKL GDLPT SGQIRLYDGR TGEQFERPVT VGYMYMLKLN HLVDDKMHAR STGSYSLVTQ QPLGGKAQFG GQRFGEMEVW ALEAY GAAY TLQEMLTVKS DDVNGRTKMY KNIVDGNHQM EPGMPESFNV LLKEIRSLGI NIELED

UniProtKB: DNA-directed RNA polymerase subunit beta

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Macromolecule #4: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 151.537594 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LKAQTKTEEF DAIKIALASP DMIRSWSFGE VKKPETINYR TFKPERDGLF CARIFGPVKD YECLCGKYKR LKHRGVICEK CGVEVTQTK VRRERMGHIE LASPTAHIWF LKSLPSRIGL LLDMPLRDIE RVLYFESYVV IEGGMTNLER QQILTEEQYL D ALEEFGDE ...String:
LKAQTKTEEF DAIKIALASP DMIRSWSFGE VKKPETINYR TFKPERDGLF CARIFGPVKD YECLCGKYKR LKHRGVICEK CGVEVTQTK VRRERMGHIE LASPTAHIWF LKSLPSRIGL LLDMPLRDIE RVLYFESYVV IEGGMTNLER QQILTEEQYL D ALEEFGDE FDAKMGAEAI QALLKSMDLE QECEQLREEL NETNSETKRK KLTKRIKLLE AFVQSGNKPE WMILTVLPVL PP DLRPLVP LDGGRFATSD LNDLYRRVIN RNNRLKRLLD LAAPDIIVRN EKRMLQEAVD ALLDNGRRGR AITGSNKRPL KSL ADMIKG KQGRFRQNLL GKRVDYSGRS VITVGPYLRL HQCGLPKKMA LELFKPFIYG KLELRGLATT IKAAKKMVER EEAV VWDIL DEVIREHPVL LNRAPTLHRL GIQAFEPVLI EGKAIQLHPL VCAAYNADFD GDQMAVHVPL TLEAQLEARA LMMST NNIL SPANGEPIIV PSQDVVLGLY YMTRDCVNAK GEGMVLTGPK EAERLYRSGL ASLHARVKVR ITEYEKDANG ELVAKT SLK DTTVGRAILW MIVPKGLPYS IVNQALGKKA ISKMLNTCYR ILGLKPTVIF ADQIMYTGFA YAARSGASVG IDDMVIP EK KHEIISEAEA EVAEIQEQFQ SGLVTAGERY NKVIDIWAAA NDRVSKAMMD NLQTETVINR DGQEEKQVSF NSIYMMAD S GARGSAAQIR QLAGMRGLMA KPDGSIIETP ITANFREGLN VLQYFISTHG ARKGLADTAL KTANSGYLTR RLVDVAQDL VVTEDDCGTH EGIMMTPVIE GGDVKEPLRD RVLGRVTAED VLKPGTADIL VPRNTLLHEQ WCDLLEENSV DAVKVRSVVS CDTDFGVCA HCYGRDLARG HIINKGEAIG VIAAQSIGEP GTQLTMRTFH IGGAASRAAA ESSIQVKNKG SIKLSNVKSV V NSSGKLVI TSRNTELKLI DEFGRTKESY KVPYGAVLAK GDGEQVAGGE TVANWDPHTM PVITEVSGFV RFTDMIDGQT IT RQTDELT GLSSLVVLDS AERTAGGKDL RPALKIVDAQ GNDVLIPGTD MPAQYFLPGK AIVQLEDGVQ ISSGDTLARI PQE SGGTKD ITGGLPRVAD LFEARRPKEP AILAEISGIV SFGKETKGKR RLVITPVDGS DPYEEMIPKW RQLNVFEGER VERG DVISD GPEAPHDILR LRGVHAVTRY IVNEVQDVYR LQGVKINDKH IEVIVRQMLR KATIVNAGSS DFLEGEQVEY SRVKI ANRE LEANGKVGAT YSRDLLGITK ASLATESFIS AASFQETTRV LTEAAVAGKR DELRGLKENV IVGRLIPAGT GYAYHQ DRM RRRAAG

UniProtKB: DNA-directed RNA polymerase subunit beta'

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Macromolecule #5: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.649695 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARVTVQDAVE KIGNRFDLVL VAARRARQMQ VGGKDPLVPE ENDKTTVIAL REIEEGLINN QILDVRERQE QQEQEA

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #6: 30S ribosomal protein S1

MacromoleculeName: 30S ribosomal protein S1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.310244 KDa
SequenceString: ESFAQLFE(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
ESFAQLFE(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)

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Macromolecule #7: 30S ribosomal protein S2

MacromoleculeName: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.253943 KDa
SequenceString: MLKAGVHFGH QTRYWNPKMK PFIFGARNKV HIINLEKTVP MFNEALAELN KIASRKGKIL FVGTKRAASE AVKDAALSCD QFFVNHRWL GGMLTNWKTV RQSIKRLKDL ETQSQDGTFD KLTKKEALMR TRELEKLENS LGGIKDMGGL PDALFVIDAD H EHIAIKEA ...String:
MLKAGVHFGH QTRYWNPKMK PFIFGARNKV HIINLEKTVP MFNEALAELN KIASRKGKIL FVGTKRAASE AVKDAALSCD QFFVNHRWL GGMLTNWKTV RQSIKRLKDL ETQSQDGTFD KLTKKEALMR TRELEKLENS LGGIKDMGGL PDALFVIDAD H EHIAIKEA NNLGIPVFAI VDTNSDPDGV DFVIPGNDDA IRAVTLYLGA VAATVREGRS

UniProtKB: Small ribosomal subunit protein uS2

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Macromolecule #8: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 23.078785 KDa
SequenceString: GQKVHPNGIR LGIVKPWNST WFANTKEFAD NLDSDFKVRQ YLTKELAKAS VSRIVIERPA KSIRVTIHTA RPGIVIGKKG EDVEKLRKV VADIAGVPAQ INIAEVRKPE LDAKLVADSI TSQLERRVMF RRAMKRAVQN AMRLGAKGIK VEVSGRLGGA E IARTEWYR ...String:
GQKVHPNGIR LGIVKPWNST WFANTKEFAD NLDSDFKVRQ YLTKELAKAS VSRIVIERPA KSIRVTIHTA RPGIVIGKKG EDVEKLRKV VADIAGVPAQ INIAEVRKPE LDAKLVADSI TSQLERRVMF RRAMKRAVQN AMRLGAKGIK VEVSGRLGGA E IARTEWYR EGRVPLHTLR ADIDYNTSEA HTTYGVIGVK VWIFKGEI

UniProtKB: Small ribosomal subunit protein uS3

+
Macromolecule #9: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 23.383002 KDa
SequenceString: ARYLGPKLKL SRREGTDLFL KSGVRAIDTK CKIEQAPGQH GARKPRLSDY GVQLREKQKV RRIYGVLERQ FRNYYKEAAR LKGNTGENL LALLEGRLDN VVYRMGFGAT RAEARQLVSH KAIMVNGRVV NIASYQVSPN DVVSIREKAK KQSRVKAALE L AEQREKPT ...String:
ARYLGPKLKL SRREGTDLFL KSGVRAIDTK CKIEQAPGQH GARKPRLSDY GVQLREKQKV RRIYGVLERQ FRNYYKEAAR LKGNTGENL LALLEGRLDN VVYRMGFGAT RAEARQLVSH KAIMVNGRVV NIASYQVSPN DVVSIREKAK KQSRVKAALE L AEQREKPT WLEVDAGKME GTFKRKPERS DLSADINEHL IVELYSK

UniProtKB: Small ribosomal subunit protein uS4

+
Macromolecule #10: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 16.532088 KDa
SequenceString:
ELQEKLIAVN RVSKTVKGGR IFSFTALTVV GDGNGRVGFG YGKAREVPAA IQKAMEKARR NMINVALNNG TLQHPVKGVH TGSRVFMQP ASEGTGIIAG GAMRAVLEVA GVHNVLAKAY GSTNPINVVR ATIDGLENMN SPEMVAAKRG KSVEEILG

UniProtKB: Small ribosomal subunit protein uS5

+
Macromolecule #11: 30S ribosomal protein S6

MacromoleculeName: 30S ribosomal protein S6 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.669371 KDa
SequenceString:
MRHYEIVFMV HPDQSEQVPG MIERYTAAIT GAEGKIHRLE DWGRRQLAYP INKLHKAHYV LMNVEAPQEV IDELETTFRF NDAVIRSMV MRTKHAVTEA S

UniProtKB: Small ribosomal subunit protein bS6

+
Macromolecule #12: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 16.861523 KDa
SequenceString:
PRRRVIGQRK ILPDPKFGSE LLAKFVNILM VDGKKSTAES IVYSALETLA QRSGKSELEA FEVALENVRP TVEVKSRRVG GSTYQVPVE VRPVRRNALA MRWIVEAARK RGDKSMALRL ANELSDAAEN KGTAVKKRED VHRMAEANKA FA

UniProtKB: Small ribosomal subunit protein uS7

+
Macromolecule #13: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 14.015361 KDa
SequenceString:
SMQDPIADML TRIRNGQAAN KAAVTMPSSK LKVAIANVLK EEGFIEDFKV EGDTKPELEL TLKYFQGKAV VESIQRVSRP GLRIYKRKD ELPKVMAGLG IAVVSTSKGV MTDRAARQAG LGGEIICYVA

UniProtKB: Small ribosomal subunit protein uS8

+
Macromolecule #14: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 14.554882 KDa
SequenceString:
NQYYGTGRRK SSAARVFIKP GNGKIVINQR SLEQYFGRET ARMVVRQPLE LVDMVEKLDL YITVKGGGIS GQAGAIRHGI TRALMEYDE SLRSELRKAG FVTRDARQVE RKKVGLRKAR RRPQFSKR

UniProtKB: Small ribosomal subunit protein uS9

+
Macromolecule #15: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.196988 KDa
SequenceString:
RIRIRLKAFD HRLIDQATAE IVETAKRTGA QVRGPIPLPT RKERFTVLIS PHVNKDARDQ YEIRTHLRLV DIVEPTEKTV DALMRLDLA AGVDVQISL

UniProtKB: Small ribosomal subunit protein uS10

+
Macromolecule #16: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 12.388068 KDa
SequenceString:
RKQVSDGVAH IHASFNNTIV TITDRQGNAL GWATAGGSGF RGSRKSTPFA AQVAAERCAD AVKEYGIKNL EVMVKGPGPG RESTIRALN AAGFRITNIT DVTPIPHNGC RPPKKRR

UniProtKB: Small ribosomal subunit protein uS11

+
Macromolecule #17: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.636961 KDa
SequenceString:
ATVNQLVRKP RARKVAKSNV PALEACPQKR GVCTRVYTTT PKKPNSALRK VCRVRLTNGF EVTSYIGGEG HNLQEHSVIL IRGGRVKDL PGVRYHTVRG ALDCSGVKDR KQARSKYGVK RPKA

UniProtKB: Small ribosomal subunit protein uS12

+
Macromolecule #18: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 12.625753 KDa
SequenceString:
ARIAGINIPD HKHAVIALTS IYGVGKTRSK AILAAAGIAE DVKISELSEG QIDTLRDEVA KFVVEGDLRR EISMSIKRLM DLGCYRGLR HRRGLPVRGQ RTKTNARTRK GPRKP

UniProtKB: Small ribosomal subunit protein uS13

+
Macromolecule #19: 30S ribosomal protein S14

MacromoleculeName: 30S ribosomal protein S14 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.475364 KDa
SequenceString:
AKQSMKAREV KRVALADKYF AKRAELKAII SDVNASDEDR WNAVLKLQTL PRDSSPSRQR NRCRQTGRPH GFLRKFGLSR IKVREAAMR GEIPGLKKAS W

UniProtKB: Small ribosomal subunit protein uS14

+
Macromolecule #20: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 10.159621 KDa
SequenceString:
SLSTEATAKI VSEFGRDAND TGSTEVQVAL LTAQINHLQG HFAEHKKDHH SRRGLLRMVS QRRKLLDYLK RKDVARYTQL IERLGLRR

UniProtKB: Small ribosomal subunit protein uS15

+
Macromolecule #21: 30S ribosomal protein S16

MacromoleculeName: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.207572 KDa
SequenceString:
MVTIRLARHG AKKRPFYQVV VADSRNARNG RFIERVGFFN PIASEKEEGT RLDLDRIAHW VGQGATISDR VAALIKEVNK AA

UniProtKB: Small ribosomal subunit protein bS16

+
Macromolecule #22: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.263946 KDa
SequenceString:
KIRTLQGRVV SDKMEKSIVV AIERFVKHPI YGKFIKRTTK LHVHDENNEC GIGDVVEIRE CRPLSKTKSW TLVRVVEKAV

UniProtKB: Small ribosomal subunit protein uS17

+
Macromolecule #23: 30S ribosomal protein S18

MacromoleculeName: 30S ribosomal protein S18 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 7.606768 KDa
SequenceString:
FCRFTAEGVQ EIDYKDIATL KNYITESGKI VPSRITGTRA KYQRQLARAI KRARYLSLLP YTDRH

UniProtKB: Small ribosomal subunit protein bS18

+
Macromolecule #24: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.057626 KDa
SequenceString:
RSLKKGPFID LHLLKKVEKA VESGDKKPLR TWSRRSTIFP NMIGLTIAVH NGRQHVPVFV TDEMVGHKLG EFAPTRTYR

UniProtKB: Small ribosomal subunit protein uS19

+
Macromolecule #25: 30S ribosomal protein S20

MacromoleculeName: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.50619 KDa
SequenceString:
NIKSAKKRAI QSEKARKHNA SRRSMMRTFI KKVYAAIEAG DKAAAQKAFN EMQPIVDRQA AKGLIHKNKA ARHKANLTAQ INKLA

UniProtKB: Small ribosomal subunit protein bS20

+
Macromolecule #26: 30S ribosomal protein S21

MacromoleculeName: 30S ribosomal protein S21 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 7.763073 KDa
SequenceString:
IKVRENEPFD VALRRFKRSC EKAGVLAEVR RREFYEKPTT ERKRAKASAV KRHAKKLARE NARRT

UniProtKB: Small ribosomal subunit protein bS21

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
Details: 20 mM Tris-HCl, pH 7.0, 100 mM NH4Cl, 10 mM MgCl2, 0.5 mM EDTA, 6 mM BME
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV
Details: 2.5 uL of 50 nM 30S and 150 nM RNAP was applied to the grid. After a 30 second incubation, the grid was blotted for 5 seconds at blotting power 8..
Details50 nM 30S, 150 nM RNAP

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 25000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 2527 / Average electron dose: 40.0 e/Å2
Details: The average electron dose 40.0 (e-/A2) represents the total dose for one collected movie.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 184530
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

Details: 30S-RNAP reference was build using PDB entries 5U9F and 3LU0.
Initial angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 5.0 degrees
Software - Name: FREALIGN (ver. 9.11)
Final 3D classificationNumber classes: 8 / Software - Name: FREALIGN (ver. 9.11)
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 5.0 degrees
Software - Name: FREALIGN (ver. 9.11)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11) / Number images used: 15012

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 500 / Target criteria: Correlation coefficient
Output model

PDB-6awb:
Structure of 30S ribosomal subunit and RNA polymerase complex in non-rotated state

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