EMDB-36854: Cryo-EM structure of 30S ribosome with cleaved AP-mRNA bound complex I

Basic information

Entry

Database: EMDB / ID: EMD-36854

• Title: Cryo-EM structure of 30S ribosome with cleaved AP-mRNA bound complex I

Sample

• Complex: 30S ribosome with cleaved AP-mRNA
  • Protein or peptide: x 20 types
  • RNA: x 2 types

• Keywords: Ribosome / AP-mRNA

Function / homology

Function:

ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA endonuclease activity / transcription antitermination / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm

Domain/homology:

Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S2 signature 2. / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / : / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / K homology domain superfamily, prokaryotic type / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 / K homology domain-like, alpha/beta / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal S11, conserved site

Component:

Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS21

• Biological species: Escherichia coli K-12 (bacteria)
• Method: single particle reconstruction / cryo EM / Resolution: 3.88 Å
• Authors: Afsar M / Shukla A / Ramachandran R

Funding support

India, 3 items

Organization	Grant number	Country
Department of Science & Technology (DST, India)	GAP0292	India
Council of Scientific & Industrial Research (CSIR)	CII7032 & MLP0107	India
Department of Biotechnology (DBT, India)	GAP0384	India

• Citation: Journal: To Be Published; Title: Cryo-EM structure of 30S ribosome with cleaved AP-mRNA bound complex I; Authors: Afsar M / Shukla A / Ramachandran R

History

Deposition	Jul 16, 2023	-
Header (metadata) release	Jul 24, 2024	-
Map release	Jul 24, 2024	-
Update	Jul 24, 2024	-
Current status	Jul 24, 2024	Processing site: PDBj / Status: Released

Map

• File: Download / File: emd_36854.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.38 Å

Density

Contour Level	By AUTHOR: 0.02
Minimum - Maximum	-0.11698935 - 0.2824548
Average (Standard dev.)	0.0000020815105 (±0.010364875)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 256 256 256 Spacing 256 256 256
Cell	A=B=C: 353.28 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_36854_msk_1.map

Half map: #2

• File: emd_36854_half_map_1.map

Half map: #1

• File: emd_36854_half_map_2.map

Sample components

Entire : 30S ribosome with cleaved AP-mRNA

• Entire: Name: 30S ribosome with cleaved AP-mRNA

Components

• Complex: 30S ribosome with cleaved AP-mRNA
  • 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, fully modified isoform
  • 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 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
  • RNA: Cleaved AP-mRNA
  • Protein or peptide: 30S ribosomal protein S21
  • RNA: 16S rRNA
  • Protein or peptide: 30S ribosomal protein S14

Supramolecule #1: 30S ribosome with cleaved AP-mRNA

• Supramolecule: Name: 30S ribosome with cleaved AP-mRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#22
• Source (natural): Organism: Escherichia coli K-12 (bacteria)

Macromolecule #1: 30S ribosomal protein S2

• Macromolecule: Name: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 26.78167 KDa

Sequence

String:

MATVSMRDML KAGVHFGHQT RYWNPKMKPF IFGARNKVHI INLEKTVPMF NEALAELNKI ASRKGKILFV GTKRAASEAV KDAALSCDQ FFVNHRWLGG MLTNWKTVRQ SIKRLKDLET QSQDGTFDKL TKKEALMRTR ELEKLENSLG GIKDMGGLPD A LFVIDADH EHIAIKEANN LGIPVFAIVD TNSDPDGVDF VIPGNDDAIR AVTLYLGAVA ATVREGRSQD LASQAEESFV EA E

UniProtKB: Small ribosomal subunit protein uS2

Macromolecule #2: 30S ribosomal protein S3

• Macromolecule: Name: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 26.031316 KDa

Sequence

String:

MGQKVHPNGI RLGIVKPWNS TWFANTKEFA DNLDSDFKVR QYLTKELAKA SVSRIVIERP AKSIRVTIHT ARPGIVIGKK GEDVEKLRK VVADIAGVPA QINIAEVRKP ELDAKLVADS ITSQLERRVM FRRAMKRAVQ NAMRLGAKGI KVEVSGRLGG A EIARTEWY REGRVPLHTL RADIDYNTSE AHTTYGVIGV KVWIFKGEIL GGMAAVEQPE KPAAQPKKQQ RKGRK

UniProtKB: Small ribosomal subunit protein uS3

Macromolecule #3: 30S ribosomal protein S4

• Macromolecule: Name: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 23.514199 KDa

Sequence

String:

MARYLGPKLK LSRREGTDLF LKSGVRAIDT KCKIEQAPGQ HGARKPRLSD YGVQLREKQK VRRIYGVLER QFRNYYKEAA RLKGNTGEN LLALLEGRLD NVVYRMGFGA TRAEARQLVS HKAIMVNGRV VNIASYQVSP NDVVSIREKA KKQSRVKAAL E LAEQREKP TWLEVDAGKM EGTFKRKPER SDLSADINEH LIVELYSK

UniProtKB: Small ribosomal subunit protein uS4

Macromolecule #4: 30S ribosomal protein S5

• Macromolecule: Name: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 17.629398 KDa

Sequence

String:

MAHIEKQAGE LQEKLIAVNR VSKTVKGGRI FSFTALTVVG DGNGRVGFGY GKAREVPAAI QKAMEKARRN MINVALNNGT LQHPVKGVH TGSRVFMQPA SEGTGIIAGG AMRAVLEVAG VHNVLAKAYG STNPINVVRA TIDGLENMNS PEMVAAKRGK S VEEILGK

UniProtKB: Small ribosomal subunit protein uS5

Macromolecule #5: 30S ribosomal protein S6, fully modified isoform

• Macromolecule: Name: 30S ribosomal protein S6, fully modified isoform / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 15.727512 KDa

Sequence

String:

MRHYEIVFMV HPDQSEQVPG MIERYTAAIT GAEGKIHRLE DWGRRQLAYP INKLHKAHYV LMNVEAPQEV IDELETTFRF NDAVIRSMV MRTKHAVTEA SPMVKAKDER RERRDDFANE TADDAEAGDS EEEEEE

UniProtKB: Small ribosomal subunit protein bS6

Macromolecule #6: 30S ribosomal protein S7

• Macromolecule: Name: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 20.055156 KDa

Sequence

String:

MPRRRVIGQR KILPDPKFGS ELLAKFVNIL MVDGKKSTAE SIVYSALETL AQRSGKSELE AFEVALENVR PTVEVKSRRV GGSTYQVPV EVRPVRRNAL AMRWIVEAAR KRGDKSMALR LANELSDAAE NKGTAVKKRE DVHRMAEANK AFAHYRWLSL R SFSHQAGA SSKQPALGYL N

UniProtKB: Small ribosomal subunit protein uS7

Macromolecule #7: 30S ribosomal protein S8

• Macromolecule: Name: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 14.146557 KDa

Sequence

String:

MSMQDPIADM LTRIRNGQAA NKAAVTMPSS KLKVAIANVL KEEGFIEDFK VEGDTKPELE LTLKYFQGKA VVESIQRVSR PGLRIYKRK DELPKVMAGL GIAVVSTSKG VMTDRAARQA GLGGEIICYV A

UniProtKB: Small ribosomal subunit protein uS8

Macromolecule #8: 30S ribosomal protein S9

• Macromolecule: Name: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 14.88627 KDa

Sequence

String:

MAENQYYGTG RRKSSAARVF IKPGNGKIVI NQRSLEQYFG RETARMVVRQ PLELVDMVEK LDLYITVKGG GISGQAGAIR HGITRALME YDESLRSELR KAGFVTRDAR QVERKKVGLR KARRRPQFSK R

UniProtKB: Small ribosomal subunit protein uS9

Macromolecule #9: 30S ribosomal protein S10

• Macromolecule: Name: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 11.755597 KDa

Sequence

String:

MQNQRIRIRL KAFDHRLIDQ ATAEIVETAK RTGAQVRGPI PLPTRKERFT VLISPHVNKD ARDQYEIRTH LRLVDIVEPT EKTVDALMR LDLAAGVDVQ ISLG

UniProtKB: Small ribosomal subunit protein uS10

Macromolecule #10: 30S ribosomal protein S11

• Macromolecule: Name: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 13.870975 KDa

Sequence

String:

MAKAPIRARK RVRKQVSDGV AHIHASFNNT IVTITDRQGN ALGWATAGGS GFRGSRKSTP FAAQVAAERC ADAVKEYGIK NLEVMVKGP GPGRESTIRA LNAAGFRITN ITDVTPIPHN GCRPPKKRRV

UniProtKB: Small ribosomal subunit protein uS11

Macromolecule #11: 30S ribosomal protein S12

• Macromolecule: Name: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 13.768157 KDa

Sequence

String:

MATVNQLVRK PRARKVAKSN VPALEACPQK RGVCTRVYTT TPKKPNSALR KVCRVRLTNG FEVTSYIGGE GHNLQEHSVI LIRGGRVKD LPGVRYHTVR GALDCSGVKD RKQARSKYGV KRPKA

UniProtKB: Small ribosomal subunit protein uS12

Macromolecule #12: 30S ribosomal protein S13

• Macromolecule: Name: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 13.128467 KDa

Sequence

String:

MARIAGINIP DHKHAVIALT SIYGVGKTRS KAILAAAGIA EDVKISELSE GQIDTLRDEV AKFVVEGDLR REISMSIKRL MDLGCYRGL RHRRGLPVRG QRTKTNARTR KGPRKPIKK

UniProtKB: Small ribosomal subunit protein uS13

Macromolecule #13: 30S ribosomal protein S15

• Macromolecule: Name: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 10.290816 KDa

Sequence

String:

MSLSTEATAK IVSEFGRDAN DTGSTEVQVA LLTAQINHLQ GHFAEHKKDH HSRRGLLRMV SQRRKLLDYL KRKDVARYTQ LIERLGLRR

UniProtKB: Small ribosomal subunit protein uS15

Macromolecule #14: 30S ribosomal protein S16

• Macromolecule: Name: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 9.207572 KDa

Sequence

String:

MVTIRLARHG AKKRPFYQVV VADSRNARNG RFIERVGFFN PIASEKEEGT RLDLDRIAHW VGQGATISDR VAALIKEVNK AA

UniProtKB: Small ribosomal subunit protein bS16

Macromolecule #15: 30S ribosomal protein S17

• Macromolecule: Name: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 9.724491 KDa

Sequence

String:

MTDKIRTLQG RVVSDKMEKS IVVAIERFVK HPIYGKFIKR TTKLHVHDEN NECGIGDVVE IRECRPLSKT KSWTLVRVVE KAVL

UniProtKB: Small ribosomal subunit protein uS17

Macromolecule #16: 30S ribosomal protein S18

• Macromolecule: Name: 30S ribosomal protein S18 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 9.005472 KDa

Sequence

String:

MARYFRRRKF CRFTAEGVQE IDYKDIATLK NYITESGKIV PSRITGTRAK YQRQLARAIK RARYLSLLPY TDRHQ

UniProtKB: Small ribosomal subunit protein bS18

Macromolecule #17: 30S ribosomal protein S19

• Macromolecule: Name: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 10.455355 KDa

Sequence

String:

MPRSLKKGPF IDLHLLKKVE KAVESGDKKP LRTWSRRSTI FPNMIGLTIA VHNGRQHVPV FVTDEMVGHK LGEFAPTRTY RGHAADKKA KKK

UniProtKB: Small ribosomal subunit protein uS19

Macromolecule #18: 30S ribosomal protein S20

• Macromolecule: Name: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 9.708464 KDa

Sequence

String:

MANIKSAKKR AIQSEKARKH NASRRSMMRT FIKKVYAAIE AGDKAAAQKA FNEMQPIVDR QAAKGLIHKN KAARHKANLT AQINKLA

UniProtKB: Small ribosomal subunit protein bS20

Macromolecule #20: 30S ribosomal protein S21

• Macromolecule: Name: 30S ribosomal protein S21 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 8.524039 KDa

Sequence

String:

MPVIKVRENE PFDVALRRFK RSCEKAGVLA EVRRREFYEK PTTERKRAKA SAVKRHAKKL ARENARRTRL Y

UniProtKB: Small ribosomal subunit protein bS21

Macromolecule #22: 30S ribosomal protein S14

• Macromolecule: Name: 30S ribosomal protein S14 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 11.60656 KDa

Sequence

String:

MAKQSMKARE VKRVALADKY FAKRAELKAI ISDVNASDED RWNAVLKLQT LPRDSSPSRQ RNRCRQTGRP HGFLRKFGLS RIKVREAAM RGEIPGLKKA SW

UniProtKB: Small ribosomal subunit protein uS14

Macromolecule #19: Cleaved AP-mRNA

• Macromolecule: Name: Cleaved AP-mRNA / type: rna / ID: 19 / Details: N = rSpacer for AP-site / Number of copies: 1
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 7.694664 KDa

Sequence

String:

GGCAAGGAGG UAAAA(N)UGUU CAAA

Macromolecule #21: 16S rRNA

• Macromolecule: Name: 16S rRNA / type: rna / ID: 21 / Number of copies: 1
• Source (natural): Organism: Escherichia coli K-12 (bacteria)
• Molecular weight: Theoretical: 503.554562 KDa

Sequence

String:

AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAAGA AGCUUGCUU CUUUGCUGAC GAGUGGCGGA CGGGUGAGUA AUGUCUGGGA AACUGCCUGA UGGAGGGGGA UAACUACUGG A AACGGUAG CUAAUACCGC AUAACGUCGC AAGACCAAAG AGGGGGACCU UCGGGCCUCU UGCCAUCGGA UGUGCCCAGA UG GGAUUAG CUAGUAGGUG GGGUAACGGC UCACCUAGGC GACGAUCCCU AGCUGGUCUG AGAGGAUGAC CAGCCACACU GGA ACUGAG ACACGGUCCA GACUCCUACG GGAGGCAGCA GUGGGGAAUA UUGCACAAUG GGCGCAAGCC UGAUGCAGCC AUGC CGCGU GUAUGAAGAA GGCCUUCGGG UUGUAAAGUA CUUUCAGCGG GGAGGAAGGG AGUAAAGUUA AUACCUUUGC UCAUU GACG UUACCCGCAG AAGAAGCACC GGCUAACUCC GUGCCAGCAG CCGCGGUAAU ACGGAGGGUG CAAGCGUUAA UCGGAA UUA CUGGGCGUAA AGCGCACGCA GGCGGUUUGU UAAGUCAGAU GUGAAAUCCC CGGGCUCAAC CUGGGAACUG CAUCUGA UA CUGGCAAGCU UGAGUCUCGU AGAGGGGGGU AGAAUUCCAG GUGUAGCGGU GAAAUGCGUA GAGAUCUGGA GGAAUACC G GUGGCGAAGG CGGCCCCCUG GACGAAGACU GACGCUCAGG UGCGAAAGCG UGGGGAGCAA ACAGGAUUAG AUACCCUGG UAGUCCACGC CGUAAACGAU GUCGACUUGG AGGUUGUGCC CUUGAGGCGU GGCUUCCGGA GCUAACGCGU UAAGUCGACC GCCUGGGGA GUACGGCCGC AAGGUUAAAA CUCAAAUGAA UUGACGGGGG CCCGCACAAG CGGUGGAGCA UGUGGUUUAA U UCGAUGCA ACGCGAAGAA CCUUACCUGG UCUUGACAUC CACGGAAGUU UUCAGAGAUG AGAAUGUGCC UUCGGGAACC GU GAGACAG GUGCUGCAUG GCUGUCGUCA GCUCGUGUUG UGAAAUGUUG GGUUAAGUCC CGCAACGAGC GCAACCCUUA UCC UUUGUU GCCAGCGGUC CGGCCGGGAA CUCAAAGGAG ACUGCCAGUG AUAAACUGGA GGAAGGUGGG GAUGACGUCA AGUC AUCAU GGCCCUUACG ACCAGGGCUA CACACGUGCU ACAAUGGCGC AUACAAAGAG AAGCGACCUC GCGAGAGCAA GCGGA CCUC AUAAAGUGCG UCGUAGUCCG GAUUGGAGUC UGCAACUCGA CUCCAUGAAG UCGGAAUCGC UAGUAAUCGU GGAUCA GAA UGCCACGGUG AAUACGUUCC CGGGCCUUGU ACACACCGCC CGUCACACCA UGGGAGUGGG UUGCAAAAGA AGUAGGU AG CUUAACCUUC GGGAGGGCGC UUACCACUUU GUGAUUCAUG ACUGGGGUGA AGUCGUAACA AGGUAACCGU AGGGGAAC C UGCGGUUGGA UCACCUCCUU ACCUUAAAGA AGC

GENBANK: GENBANK: CP047127.1

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 0.2 mg/mL
• Buffer: pH: 7.5
• Grid: Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Specialist optics: Phase plate: VOLTA PHASE PLATE
• Image recording: Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.42 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

Startup model

Type of model: PDB ENTRY
PDB model - PDB ID:

7nat

• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77582
• Initial angle assignment: Type: ANGULAR RECONSTITUTION
• Final angle assignment: Type: ANGULAR RECONSTITUTION

Atomic model buiding 1

Initial model

PDB ID:

7nat

Chain - Source name: PDB / Chain - Initial model type: experimental model

• Refinement: Protocol: RIGID BODY FIT

Output model

PDB-8k3o:
Cryo-EM structure of 30S ribosome with cleaved AP-mRNA bound complex I