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- EMDB-75144: 30S ribosomal subunit from E. coli missing the gene encoding for ... -

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Open data

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Basic information

Entry

Database: EMDB / ID: EMD-75144

Title

30S ribosomal subunit from E. coli missing the gene encoding for the 16S rRNA 2'-O-methyltransferase RsmI

Map data

Full map

Sample

Complex: small ribosomal subunit from a delta rsmI E. coli strain
- RNA: x 1 types
- Protein or peptide: x 20 types
Ligand: x 2 types

Keywords

Ribosome / methylation / 30S subunit / helix 44 / RsmI

Function / homology

Function and homology information

transcription antitermination factor activity, RNA binding / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / regulation of mRNA stability / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / regulation of DNA-templated transcription elongation ...
Similarity search - Function

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

Biological species

Escherichia coli BW25113 (bacteria)

Method

single particle reconstruction / cryo EM / Resolution: 2.91 Å

Authors

Barmada MI / Nandi S / Conn GL

Funding support

United States, 3 items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01 AI088025	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	F31 AI186518	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	T32 GM135060	United States

Citation

Journal: To Be Published
Title: Mechanism of 30S subunit recognition and modification by the conserved bacterial ribosomal RNA methyltransferase RsmI
Authors: Barmada MI / McGinity EN / Nandi S / Dey D / Zelinskaya N / Harris GM / Comstock LR / Dunham CM / Conn GL

History

Deposition	Jan 18, 2026	-
Header (metadata) release	Mar 18, 2026	-
Map release	Mar 18, 2026	-
Update	Mar 18, 2026	-
Current status	Mar 18, 2026	Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images	emd_75144.png

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Downloads & links

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EMDB archive

Map data	emd_75144.map.gz	172.1 MB		EMDB map data format
Header (meta data)	emd-75144-v30.xml emd-75144.xml	40.9 KB 40.9 KB	Display Display	EMDB header
FSC (resolution estimation)	emd_75144_fsc.xml	14.8 KB	Display	FSC data file
Images	emd_75144.png	92.6 KB
Masks	emd_75144_msk_1.map	343 MB		Mask map
Filedesc metadata	emd-75144.cif.gz	9.6 KB
Others	emd_75144_half_map_1.map.gz emd_75144_half_map_2.map.gz	317.8 MB 317.9 MB
Archive directory	http://ftp.pdbj.org/pub/emdb/structures/EMD-75144 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-75144	HTTPS FTP

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Related structure data

Related structure data	10fzMC M: atomic model generated by this map C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

EMDB pages	EMDB (EBI/PDBe) / EMDataResource
Related items in Molecule of the Month	#253 - Jan 2021 Expressome similarity (27) #157 - Jan 2013 Transfer-Messenger RNA similarity (27) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (27)

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Map

File

Download / File: emd_75144.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)

Annotation

Full map

Projections & slices

Image control

Size
Brightness
Contrast
Others	InvertY flip

Axes	Z (Sec.)	Y (Row.)	X (Col.)
	0.83 Å/pix. x 448 pix. = 369.6 Å	0.83 Å/pix. x 448 pix. = 369.6 Å	0.83 Å/pix. x 448 pix. = 369.6 Å
Surface
Projections
Slices (1/3)
Slices (1/2)
Slices (2/3)

Images are generated by Spider.

Voxel size

X=Y=Z: 0.825 Å

Density

Histogram

Histogram (log scale)

Contour Level	By AUTHOR: 0.108
Minimum - Maximum	-0.25876325 - 0.6994859
Average (Standard dev.)	0.0008955014 (±0.02712201)

Symmetry

Space group: 1

Details

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Supplemental data

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Mask #1

File

emd_75144_msk_1.map

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

File

emd_75144_half_map_1.map

Annotation

Half map A

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

File

emd_75144_half_map_2.map

Annotation

Half map B

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : small ribosomal subunit from a delta rsmI E. coli strain

Entire	Name: small ribosomal subunit from a delta rsmI E. coli strain
Components	Complex: small ribosomal subunit from a delta rsmI E. coli strain RNA: 16S rRNA Protein or peptide: Small ribosomal subunit protein uS4 Protein or peptide: Small ribosomal subunit protein uS5 Protein or peptide: Small ribosomal subunit protein bS6, fully modified isoform Protein or peptide: Small ribosomal subunit protein uS8 Protein or peptide: Small ribosomal subunit protein uS11 Protein or peptide: Small ribosomal subunit protein uS12 Protein or peptide: Small ribosomal subunit protein uS15 Protein or peptide: Small ribosomal subunit protein bS16 Protein or peptide: Small ribosomal subunit protein uS17 Protein or peptide: Small ribosomal subunit protein bS18 Protein or peptide: Small ribosomal subunit protein bS20 Protein or peptide: Small ribosomal subunit protein uS2 Protein or peptide: Small ribosomal subunit protein bS21 Protein or peptide: Small ribosomal subunit protein uS3 Protein or peptide: Small ribosomal subunit protein uS7 Protein or peptide: Small ribosomal subunit protein uS9 Protein or peptide: Small ribosomal subunit protein uS10 Protein or peptide: Small ribosomal subunit protein uS13 Protein or peptide: Small ribosomal subunit protein uS14 Protein or peptide: Small ribosomal subunit protein uS19 Ligand: MAGNESIUM ION Ligand: water

Entire

Name: small ribosomal subunit from a delta rsmI E. coli strain

Components

Complex: small ribosomal subunit from a delta rsmI E. coli strain
- RNA: 16S rRNA
- Protein or peptide: Small ribosomal subunit protein uS4
- Protein or peptide: Small ribosomal subunit protein uS5
- Protein or peptide: Small ribosomal subunit protein bS6, fully modified isoform
- Protein or peptide: Small ribosomal subunit protein uS8
- Protein or peptide: Small ribosomal subunit protein uS11
- Protein or peptide: Small ribosomal subunit protein uS12
- Protein or peptide: Small ribosomal subunit protein uS15
- Protein or peptide: Small ribosomal subunit protein bS16
- Protein or peptide: Small ribosomal subunit protein uS17
- Protein or peptide: Small ribosomal subunit protein bS18
- Protein or peptide: Small ribosomal subunit protein bS20
- Protein or peptide: Small ribosomal subunit protein uS2
- Protein or peptide: Small ribosomal subunit protein bS21
- Protein or peptide: Small ribosomal subunit protein uS3
- Protein or peptide: Small ribosomal subunit protein uS7
- Protein or peptide: Small ribosomal subunit protein uS9
- Protein or peptide: Small ribosomal subunit protein uS10
- Protein or peptide: Small ribosomal subunit protein uS13
- Protein or peptide: Small ribosomal subunit protein uS14
- Protein or peptide: Small ribosomal subunit protein uS19
Ligand: MAGNESIUM ION
Ligand: water

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Supramolecule #1: small ribosomal subunit from a delta rsmI E. coli strain

Supramolecule	Name: small ribosomal subunit from a delta rsmI E. coli strain type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#21 Details: E. coli 30S subunit lacking Cm1402 modification. This map was generated as part of an EM sample containing the complex of the 16S 2'-O-methyltransferase RsmI and the delta rsmI 30S (PDB ...Details: E. coli 30S subunit lacking Cm1402 modification. This map was generated as part of an EM sample containing the complex of the 16S 2'-O-methyltransferase RsmI and the delta rsmI 30S (PDB 9PZG/EMDB 72071). Particles with no enzyme occupancy were isolated to generate the map of the unbound delta rsmI 30S subunit.
Source (natural)	Organism: Escherichia coli BW25113 (bacteria) / Strain: delta rsmI
Molecular weight	Theoretical: 850 KDa

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Macromolecule #1: 16S rRNA

Macromolecule	Name: 16S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)	Organism: Escherichia coli BW25113 (bacteria)
Molecular weight	Theoretical: 499.690031 KDa
Sequence	String: AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAAGA AGCUUGCUU CUUUGCUGAC GAGUGGCGGA CGGGUGAGUA AUGUCUGGGA AACUGCCUGA UGGAGGGGGA UAACUACUGG A AACGGUAG ...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 A GENBANK: GENBANK: CP047127.1

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Macromolecule #2: Small ribosomal subunit protein uS4

Macromolecule	Name: Small ribosomal subunit protein uS4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (bacteria)
Molecular weight	Theoretical: 23.383002 KDa
Sequence	String: 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

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Macromolecule #3: Small ribosomal subunit protein uS5

Macromolecule	Name: Small ribosomal subunit protein uS5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (bacteria)
Molecular weight	Theoretical: 17.498203 KDa
Sequence	String: AHIEKQAGEL QEKLIAVNRV SKTVKGGRIF SFTALTVVGD GNGRVGFGYG KAREVPAAIQ KAMEKARRNM INVALNNGTL QHPVKGVHT GSRVFMQPAS EGTGIIAGGA MRAVLEVAGV HNVLAKAYGS TNPINVVRAT IDGLENMNSP EMVAAKRGKS V EEILGK UniProtKB: Small ribosomal subunit protein uS5

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Macromolecule #4: Small ribosomal subunit protein bS6, fully modified isoform

Macromolecule	Name: Small ribosomal subunit protein bS6, fully modified isoform type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (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

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Macromolecule #5: Small ribosomal subunit protein uS8

Macromolecule	Name: Small ribosomal subunit protein uS8 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (bacteria)
Molecular weight	Theoretical: 14.015361 KDa
Sequence	String: SMQDPIADML TRIRNGQAAN KAAVTMPSSK LKVAIANVLK EEGFIEDFKV EGDTKPELEL TLKYFQGKAV VESIQRVSRP GLRIYKRKD ELPKVMAGLG IAVVSTSKGV MTDRAARQAG LGGEIICYVA UniProtKB: Small ribosomal subunit protein uS8

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Macromolecule #6: Small ribosomal subunit protein uS11

Macromolecule	Name: Small ribosomal subunit protein uS11 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (bacteria)
Molecular weight	Theoretical: 13.739778 KDa
Sequence	String: AKAPIRARKR VRKQVSDGVA HIHASFNNTI VTITDRQGNA LGWATAGGSG FRGSRKSTPF AAQVAAERCA DAVKEYGIKN LEVMVKGPG PGRESTIRAL NAAGFRITNI TDVTPIPHNG CRPPKKRRV UniProtKB: Small ribosomal subunit protein uS11

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Macromolecule #7: Small ribosomal subunit protein uS12

Macromolecule	Name: Small ribosomal subunit protein uS12 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (bacteria)
Molecular weight	Theoretical: 13.636961 KDa
Sequence	String: ATVNQLVRKP RARKVAKSNV PALEACPQKR GVCTRVYTTT PKKPNSALRK VCRVRLTNGF EVTSYIGGEG HNLQEHSVIL IRGGRVKDL PGVRYHTVRG ALDCSGVKDR KQARSKYGVK RPKA UniProtKB: Small ribosomal subunit protein uS12

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Macromolecule #8: Small ribosomal subunit protein uS15

Macromolecule	Name: Small ribosomal subunit protein uS15 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (bacteria)
Molecular weight	Theoretical: 10.319882 KDa
Sequence	String: MSLSTEATAK IVSEFGRDAN DTGSTEVQVA LLTAQINHLQ GHFAEHKKDH HSRRGLLRMV SQRRKLLDYL KRKDVARYTR LIERLGLRR UniProtKB: Small ribosomal subunit protein uS15

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Macromolecule #9: Small ribosomal subunit protein bS16

Macromolecule	Name: Small ribosomal subunit protein bS16 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (bacteria)
Molecular weight	Theoretical: 9.207572 KDa
Sequence	String: MVTIRLARHG AKKRPFYQVV VADSRNARNG RFIERVGFFN PIASEKEEGT RLDLDRIAHW VGQGATISDR VAALIKEVNK AA UniProtKB: Small ribosomal subunit protein bS16

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Macromolecule #10: Small ribosomal subunit protein uS17

Macromolecule	Name: Small ribosomal subunit protein uS17 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (bacteria)
Molecular weight	Theoretical: 9.593296 KDa
Sequence	String: TDKIRTLQGR VVSDKMEKSI VVAIERFVKH PIYGKFIKRT TKLHVHDENN ECGIGDVVEI RECRPLSKTK SWTLVRVVEK AVL UniProtKB: Small ribosomal subunit protein uS17

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Macromolecule #11: Small ribosomal subunit protein bS18

Macromolecule	Name: Small ribosomal subunit protein bS18 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (bacteria)
Molecular weight	Theoretical: 8.874276 KDa
Sequence	String: ARYFRRRKFC RFTAEGVQEI DYKDIATLKN YITESGKIVP SRITGTRAKY QRQLARAIKR ARYLSLLPYT DRHQ UniProtKB: Small ribosomal subunit protein bS18

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Macromolecule #12: Small ribosomal subunit protein bS20

Macromolecule	Name: Small ribosomal subunit protein bS20 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (bacteria)
Molecular weight	Theoretical: 9.577268 KDa
Sequence	String: ANIKSAKKRA IQSEKARKHN ASRRSMMRTF IKKVYAAIEA GDKAAAQKAF NEMQPIVDRQ AAKGLIHKNK AARHKANLTA QINKLA UniProtKB: Small ribosomal subunit protein bS20

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Macromolecule #13: Small ribosomal subunit protein uS2

Macromolecule	Name: Small ribosomal subunit protein uS2 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (bacteria)
Molecular weight	Theoretical: 26.650475 KDa
Sequence	String: ATVSMRDMLK AGVHFGHQTR YWNPKMKPFI FGARNKVHII NLEKTVPMFN EALAELNKIA SRKGKILFVG TKRAASEAVK DAALSCDQF FVNHRWLGGM LTNWKTVRQS IKRLKDLETQ SQDGTFDKLT KKEALMRTRE LEKLENSLGG IKDMGGLPDA L FVIDADHE ...String: ATVSMRDMLK AGVHFGHQTR YWNPKMKPFI FGARNKVHII NLEKTVPMFN EALAELNKIA SRKGKILFVG TKRAASEAVK DAALSCDQF FVNHRWLGGM LTNWKTVRQS IKRLKDLETQ SQDGTFDKLT KKEALMRTRE LEKLENSLGG IKDMGGLPDA L FVIDADHE HIAIKEANNL GIPVFAIVDT NSDPDGVDFV IPGNDDAIRA VTLYLGAVAA TVREGRSQDL ASQAEESFVE AE UniProtKB: Small ribosomal subunit protein uS2

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Macromolecule #14: Small ribosomal subunit protein bS21

Macromolecule	Name: Small ribosomal subunit protein bS21 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (bacteria)
Molecular weight	Theoretical: 8.524039 KDa
Sequence	String: MPVIKVRENE PFDVALRRFK RSCEKAGVLA EVRRREFYEK PTTERKRAKA SAVKRHAKKL ARENARRTRL Y UniProtKB: Small ribosomal subunit protein bS21

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Macromolecule #15: Small ribosomal subunit protein uS3

Macromolecule	Name: Small ribosomal subunit protein uS3 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (bacteria)
Molecular weight	Theoretical: 25.900117 KDa
Sequence	String: 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 VWIFKGEILG GMAAVEQPEK PAAQPKKQQR KGRK UniProtKB: Small ribosomal subunit protein uS3

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Macromolecule #16: Small ribosomal subunit protein uS7

Macromolecule	Name: Small ribosomal subunit protein uS7 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (bacteria)
Molecular weight	Theoretical: 19.923959 KDa
Sequence	String: PRRRVIGQRK ILPDPKFGSE LLAKFVNILM VDGKKSTAES IVYSALETLA QRSGKSELEA FEVALENVRP TVEVKSRRVG GSTYQVPVE VRPVRRNALA MRWIVEAARK RGDKSMALRL ANELSDAAEN KGTAVKKRED VHRMAEANKA FAHYRWLSLR S FSHQAGAS SKQPALGYLN UniProtKB: Small ribosomal subunit protein uS7

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Macromolecule #17: Small ribosomal subunit protein uS9

Macromolecule	Name: Small ribosomal subunit protein uS9 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (bacteria)
Molecular weight	Theoretical: 14.755074 KDa
Sequence	String: AENQYYGTGR RKSSAARVFI KPGNGKIVIN QRSLEQYFGR ETARMVVRQP LELVDMVEKL DLYITVKGGG ISGQAGAIRH GITRALMEY DESLRSELRK AGFVTRDARQ VERKKVGLRK ARRRPQFSKR UniProtKB: Small ribosomal subunit protein uS9

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Macromolecule #18: Small ribosomal subunit protein uS10

Macromolecule	Name: Small ribosomal subunit protein uS10 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (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

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Macromolecule #19: Small ribosomal subunit protein uS13

Macromolecule	Name: Small ribosomal subunit protein uS13 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (bacteria)
Molecular weight	Theoretical: 12.997271 KDa
Sequence	String: ARIAGINIPD HKHAVIALTS IYGVGKTRSK AILAAAGIAE DVKISELSEG QIDTLRDEVA KFVVEGDLRR EISMSIKRLM DLGCYRGLR HRRGLPVRGQ RTKTNARTRK GPRKPIKK UniProtKB: Small ribosomal subunit protein uS13

+
Macromolecule #20: Small ribosomal subunit protein uS14

Macromolecule	Name: Small ribosomal subunit protein uS14 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (bacteria)
Molecular weight	Theoretical: 11.475364 KDa
Sequence	String: AKQSMKAREV KRVALADKYF AKRAELKAII SDVNASDEDR WNAVLKLQTL PRDSSPSRQR NRCRQTGRPH GFLRKFGLSR IKVREAAMR GEIPGLKKAS W UniProtKB: Small ribosomal subunit protein uS14

+
Macromolecule #21: Small ribosomal subunit protein uS19

Macromolecule	Name: Small ribosomal subunit protein uS19 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BW25113 (bacteria)
Molecular weight	Theoretical: 10.32416 KDa
Sequence	String: PRSLKKGPFI DLHLLKKVEK AVESGDKKPL RTWSRRSTIF PNMIGLTIAV HNGRQHVPVF VTDEMVGHKL GEFAPTRTYR GHAADKKAK KK UniProtKB: Small ribosomal subunit protein uS19

+
Macromolecule #22: MAGNESIUM ION

Macromolecule	Name: MAGNESIUM ION / type: ligand / ID: 22 / Number of copies: 77 / Formula: MG
Molecular weight	Theoretical: 24.305 Da

+
Macromolecule #23: water

Macromolecule	Name: water / type: ligand / ID: 23 / Number of copies: 32 / Formula: HOH
Molecular weight	Theoretical: 18.015 Da
Chemical component information	ChemComp-HOH: WATER

-
Experimental details

-
Structure determination

Method	cryo EM
Processing	single particle reconstruction
Aggregation state	particle

-
Sample preparation

Buffer	pH: 7.6 Details: 10 mM HEPES, 10 mM MgCl2, 100 mM NH4Cl, 6 mM Beta-mercaptoethanol
Grid	Model: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
Vitrification	Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details	Recombinant RsmI (1.2 uM), delta-rsmI 30S (0.4 uM), and the SAM analog NM6 (24 uM) were incubated for 30 minutes at 37C to prepare the complex.

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Electron microscopy

Microscope	TFS KRIOS
Image recording	Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8164 / Average exposure time: 1.8 sec. / Average electron dose: 49.27 e/Å²
Electron beam	Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics	Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 105000
Sample stage	Cooling holder cryogen: NITROGEN
Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selection	Number selected: 3781314
CTF correction	Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup model	Type of model: INSILICO MODEL / In silico model: Ab initio model generated by CryoSPARC
Final reconstruction	Resolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 58273
Initial angle assignment	Type: MAXIMUM LIKELIHOOD
Final angle assignment	Type: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model	PDB ID: 7oe1 Chain - Source name: PDB / Chain - Initial model type: experimental model
Software	Name: UCSF ChimeraX
Refinement	Space: REAL / Protocol: FLEXIBLE FIT
Output model	PDB-10fz: 30S ribosomal subunit from E. coli missing the gene encoding for the 16S rRNA 2'-O-methyltransferase RsmI

+
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+Entire : small ribosomal subunit from a delta rsmI E. coli strain

+Supramolecule #1: small ribosomal subunit from a delta rsmI E. coli strain

+Macromolecule #1: 16S rRNA

+Macromolecule #2: Small ribosomal subunit protein uS4

+Macromolecule #3: Small ribosomal subunit protein uS5

+Macromolecule #4: Small ribosomal subunit protein bS6, fully modified isoform

+Macromolecule #5: Small ribosomal subunit protein uS8

+Macromolecule #6: Small ribosomal subunit protein uS11

+Macromolecule #7: Small ribosomal subunit protein uS12

+Macromolecule #8: Small ribosomal subunit protein uS15

+Macromolecule #9: Small ribosomal subunit protein bS16

+Macromolecule #10: Small ribosomal subunit protein uS17

+Macromolecule #11: Small ribosomal subunit protein bS18

+Macromolecule #12: Small ribosomal subunit protein bS20

+Macromolecule #13: Small ribosomal subunit protein uS2

+Macromolecule #14: Small ribosomal subunit protein bS21

+Macromolecule #15: Small ribosomal subunit protein uS3

+Macromolecule #16: Small ribosomal subunit protein uS7

+Macromolecule #17: Small ribosomal subunit protein uS9

+Macromolecule #18: Small ribosomal subunit protein uS10

+Macromolecule #19: Small ribosomal subunit protein uS13

+Macromolecule #20: Small ribosomal subunit protein uS14

+Macromolecule #21: Small ribosomal subunit protein uS19

+Macromolecule #22: MAGNESIUM ION

+Macromolecule #23: water

-Experimental details

-Structure determination

-Sample preparation

-Electron microscopy

+Image processing

-Atomic model buiding 1

+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

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Movie

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Viewer log

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This page

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Open data

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Related structure data

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Links

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Map

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Supplemental data

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Mask #1

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Half map: Half map A

-
Half map: Half map B

-
Sample components

+
Entire : small ribosomal subunit from a delta rsmI E. coli strain

+
Supramolecule #1: small ribosomal subunit from a delta rsmI E. coli strain

+
Macromolecule #1: 16S rRNA

+
Macromolecule #2: Small ribosomal subunit protein uS4

+
Macromolecule #3: Small ribosomal subunit protein uS5

+
Macromolecule #4: Small ribosomal subunit protein bS6, fully modified isoform

+
Macromolecule #5: Small ribosomal subunit protein uS8

+
Macromolecule #6: Small ribosomal subunit protein uS11

+
Macromolecule #7: Small ribosomal subunit protein uS12

+
Macromolecule #8: Small ribosomal subunit protein uS15

+
Macromolecule #9: Small ribosomal subunit protein bS16

+
Macromolecule #10: Small ribosomal subunit protein uS17

+
Macromolecule #11: Small ribosomal subunit protein bS18

+
Macromolecule #12: Small ribosomal subunit protein bS20

+
Macromolecule #13: Small ribosomal subunit protein uS2

+
Macromolecule #14: Small ribosomal subunit protein bS21

+
Macromolecule #15: Small ribosomal subunit protein uS3

+
Macromolecule #16: Small ribosomal subunit protein uS7

+
Macromolecule #17: Small ribosomal subunit protein uS9

+
Macromolecule #18: Small ribosomal subunit protein uS10

+
Macromolecule #19: Small ribosomal subunit protein uS13

+
Macromolecule #20: Small ribosomal subunit protein uS14

+
Macromolecule #21: Small ribosomal subunit protein uS19

+
Macromolecule #22: MAGNESIUM ION

+
Macromolecule #23: water

-
Experimental details

-
Structure determination

-
Sample preparation

-
Electron microscopy

+
Image processing

-
Atomic model buiding 1

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About Yorodumi

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