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- EMDB-0482: Role of Era in Assembly and Homeostasis of the Ribosomal Small Subunit -

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Basic information

Entry
Database: EMDB / ID: EMD-0482
TitleRole of Era in Assembly and Homeostasis of the Ribosomal Small Subunit
Map data30S assembly intermediate (class P) generated by depleting Era protein in E.coli
Sample
  • Complex: 30S assembly intermediate (class P)
    • Protein or peptide: x 15 types
    • RNA: x 1 types
  • Ligand: x 1 types
KeywordsRibosome assembly / 30S subunit / YjeQ protein / Era protein / cryo-electron microscopy / RIBOSOME
Function / homology
Function and homology information


ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / four-way junction DNA binding / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA endonuclease activity / transcription antitermination / DNA-templated transcription termination ...ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / four-way junction DNA binding / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / 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 / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S14, bacterial/plastid / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 ...Ribosomal protein S14, bacterial/plastid / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / 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 S18 / Ribosomal protein S18 / Ribosomal protein S2 signature 2. / 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 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 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 protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / S15/NS1, RNA-binding / Ribosomal protein S5 domain 2-type fold, subgroup
Similarity search - Domain/homology
Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS14 / 30S ribosomal protein S17 / 30S ribosomal protein S3 / Small ribosomal subunit protein uS5 / 30S ribosomal protein S10 / 30S ribosomal protein S18 / Small ribosomal subunit protein uS8 / 30S ribosomal protein S19 / 30S ribosomal protein S4 ...Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS14 / 30S ribosomal protein S17 / 30S ribosomal protein S3 / Small ribosomal subunit protein uS5 / 30S ribosomal protein S10 / 30S ribosomal protein S18 / Small ribosomal subunit protein uS8 / 30S ribosomal protein S19 / 30S ribosomal protein S4 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein bS16 / 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 uS15 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS15 / 30S ribosomal protein S16 / 30S ribosomal protein S20 / Small ribosomal subunit protein uS2 / 30S ribosomal protein S12
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli H736 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsOrtega J / Davis JH / Hao Y / Jahagirdar D / Thurlow B / Basu K / Jain N / Gomez-Blanco J / Britton RA / Vargas J ...Ortega J / Davis JH / Hao Y / Jahagirdar D / Thurlow B / Basu K / Jain N / Gomez-Blanco J / Britton RA / Vargas J / Guarne A / Woodson SA / Williamson JR
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-153044 Canada
CitationJournal: Nucleic Acids Res / Year: 2019
Title: Role of Era in assembly and homeostasis of the ribosomal small subunit.
Authors: Aida Razi / Joseph H Davis / Yumeng Hao / Dushyant Jahagirdar / Brett Thurlow / Kaustuv Basu / Nikhil Jain / Josue Gomez-Blanco / Robert A Britton / Javier Vargas / Alba Guarné / Sarah A ...Authors: Aida Razi / Joseph H Davis / Yumeng Hao / Dushyant Jahagirdar / Brett Thurlow / Kaustuv Basu / Nikhil Jain / Josue Gomez-Blanco / Robert A Britton / Javier Vargas / Alba Guarné / Sarah A Woodson / James R Williamson / Joaquin Ortega /
Abstract: Assembly factors provide speed and directionality to the maturation process of the 30S subunit in bacteria. To gain a more precise understanding of how these proteins mediate 30S maturation, it is ...Assembly factors provide speed and directionality to the maturation process of the 30S subunit in bacteria. To gain a more precise understanding of how these proteins mediate 30S maturation, it is important to expand on studies of 30S assembly intermediates purified from bacterial strains lacking particular maturation factors. To reveal the role of the essential protein Era in the assembly of the 30S ribosomal subunit, we analyzed assembly intermediates that accumulated in Era-depleted Escherichia coli cells using quantitative mass spectrometry, high resolution cryo-electron microscopy and in-cell footprinting. Our combined approach allowed for visualization of the small subunit as it assembled and revealed that with the exception of key helices in the platform domain, all other 16S rRNA domains fold even in the absence of Era. Notably, the maturing particles did not stall while waiting for the platform domain to mature and instead re-routed their folding pathway to enable concerted maturation of other structural motifs spanning multiple rRNA domains. We also found that binding of Era to the mature 30S subunit destabilized helix 44 and the decoding center preventing binding of YjeQ, another assembly factor. This work establishes Era's role in ribosome assembly and suggests new roles in maintaining ribosome homeostasis.
History
DepositionJan 20, 2019-
Header (metadata) releaseMay 22, 2019-
Map releaseJun 26, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.18
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 5.18
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6nqb
  • Surface level: 5.18
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0482.png

Downloads & links

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Map

FileDownload / File: emd_0482.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation30S assembly intermediate (class P) generated by depleting Era protein in E.coli
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.07 Å/pix.
x 304 pix.
= 326.192 Å		1.07 Å/pix.
x 304 pix.
= 326.192 Å		1.07 Å/pix.
x 304 pix.
= 326.192 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.073 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.18 / Movie #1: 5.18
Minimum - Maximum-13.176378 - 32.912869999999998
Average (Standard dev.)0.000000000002664 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions304304304
Spacing304304304
CellA=B=C: 326.192 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0731.0731.073
M x/y/z304304304
origin x/y/z0.0000.0000.000
length x/y/z326.192326.192326.192
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ304304304
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS304304304
D min/max/mean-13.17632.9130.000

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Supplemental data

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Sample components

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Entire : 30S assembly intermediate (class P)

EntireName: 30S assembly intermediate (class P)
Components
  • Complex: 30S assembly intermediate (class P)
    • Protein or peptide: 30S ribosomal protein S3
    • Protein or peptide: 30S ribosomal protein S10
    • Protein or peptide: 30S ribosomal protein S14
    • Protein or peptide: 30S ribosomal protein S19
    • RNA: 16S RIBOSOMAL RNA
    • 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 S8
    • Protein or peptide: 30S ribosomal protein S12
    • Protein or peptide: 30S ribosomal protein S15
    • Protein or peptide: 30S RIBOSOMAL PROTEIN bS16
    • Protein or peptide: 30S ribosomal protein S17
    • Protein or peptide: 30S ribosomal protein S18
    • Protein or peptide: 30S ribosomal protein S20
    • Protein or peptide: 30S ribosomal protein S2
  • Ligand: MAGNESIUM ION

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Supramolecule #1: 30S assembly intermediate (class P)

SupramoleculeName: 30S assembly intermediate (class P) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Details: 30S assembly intermediate (class P) purified from Era-depleted E.coli cells
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K-12
Molecular weightTheoretical: 900 KDa

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Macromolecule #1: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 23.078785 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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: 30S ribosomal protein S3

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Macromolecule #2: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.196988 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RIRIRLKAFD HRLIDQATAE IVETAKRTGA QVRGPIPLPT RKERFTVLIS PHVNKDARDQ YEIRTHLRLV DIVEPTEKTV DALMRLDLA AGVDVQISL

UniProtKB: 30S ribosomal protein S10

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Macromolecule #3: 30S ribosomal protein S14

MacromoleculeName: 30S ribosomal protein S14 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.360276 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKQSMKAREV KRVALADKYF AKRAELKAII SDVNASDERW NAVLKLQTLP RDSSPSRQRN RCRQTGRPHG FLRKFGLSRI KVREAAMRG EIPGLKKASW

UniProtKB: Small ribosomal subunit protein uS14

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Macromolecule #4: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli H736 (bacteria)
Molecular weightTheoretical: 8.441836 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPFIDLHLLK KVEKAVESGD KKPLRTWSRR STIFPNMIGL TIAVHNGRQH VPVFVTDEMV GHKLGEFAPT RTYR

UniProtKB: 30S ribosomal protein S19

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Macromolecule #6: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 23.383002 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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: 30S ribosomal protein S4

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Macromolecule #7: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.675102 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ELQEKLIAVN RVSKTVKGGR IFSFTALTVV GDGNGRVGFG YGKAREVPAA IQKAMEKARR NMINVALNNG TLQHPVKGVH TGSRVFMQP ASEGTGIIAG GAMRAVLEVA GVHNVLAKAY GSTNPINVVR ATIDGLENMN SPEMVAAKRG

UniProtKB: Small ribosomal subunit protein uS5

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Macromolecule #8: 30S ribosomal protein S6

MacromoleculeName: 30S ribosomal protein S6 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 10.972643 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MRHYEIVFMV HPDQSEQVPG MIERYTAAIT GAEGKIHRLE DWGRRQLAYP INKLHKAHYV LMNVEAPQEV IDELETTFRF NDAVIRSMV MRTK

UniProtKB: Small ribosomal subunit protein bS6

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Macromolecule #9: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 14.015361 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SMQDPIADML TRIRNGQAAN KAAVTMPSSK LKVAIANVLK EEGFIEDFKV EGDTKPELEL TLKYFQGKAV VESIQRVSRP GLRIYKRKD ELPKVMAGLG IAVVSTSKGV MTDRAARQAG LGGEIICYVA

UniProtKB: Small ribosomal subunit protein uS8

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Macromolecule #10: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.636961 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ATVNQLVRKP RARKVAKSNV PALEACPQKR GVCTRVYTTT PKKPNSALRK VCRVRLTNGF EVTSYIGGEG HNLQEHSVIL IRGGRVKDL PGVRYHTVRG ALDCSGVKDR KQARSKYGVK RPKA

UniProtKB: 30S ribosomal protein S12

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Macromolecule #11: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.944415 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
LSTEATAKIV SEFGRDANDT GSTEVQVALL TAQINHLQGH FAEHKKDHHS RRGLLRMVSQ RRKLLDYLKR KDVARYTRLI ERLGLR

UniProtKB: Small ribosomal subunit protein uS15

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Macromolecule #12: 30S RIBOSOMAL PROTEIN bS16

MacromoleculeName: 30S RIBOSOMAL PROTEIN bS16 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.936237 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MVTIRLARHG AKKRPFYQVV VADSRNARNG RFIERVGFFN PIASEKEEGT RLDLDRIAHW VGQGATISDR VAALIKEVN

UniProtKB: 30S ribosomal protein S16

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Macromolecule #13: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.164815 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KIRTLQGRVV SDKMEKSIVV AIERFVKHPI YGKFIKRTTK LHVHDENNEC GIGDVVEIRE CRPLSKTKSW TLVRVVEKA

UniProtKB: 30S ribosomal protein S17

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Macromolecule #14: 30S ribosomal protein S18

MacromoleculeName: 30S ribosomal protein S18 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 6.109118 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
YKDIATLKNY ITESGKIVPS RITGTRAKYQ RQLARAIKRA RYLSLLPYTD RH

UniProtKB: 30S ribosomal protein S18

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Macromolecule #15: 30S ribosomal protein S20

MacromoleculeName: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.50619 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
NIKSAKKRAI QSEKARKHNA SRRSMMRTFI KKVYAAIEAG DKAAAQKAFN EMQPIVDRQA AKGLIHKNKA ARHKANLTAQ INKLA

UniProtKB: 30S ribosomal protein S20

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Macromolecule #16: 30S ribosomal protein S2

MacromoleculeName: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.12275 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LKAGVHFGHQ TRYWNPKMKP FIFGARNKVH IINLEKTVPM FNEALAELNK IASRKGKILF VGTKRAASEA VKDAALSCDQ FFVNHRWLG GMLTNWKTVR QSIKRLKDLE TQSQDGTFDK LTKKEALMRT RELEKLENSL GGIKDMGGLP DALFVIDADH E HIAIKEAN ...String:
LKAGVHFGHQ TRYWNPKMKP FIFGARNKVH IINLEKTVPM FNEALAELNK IASRKGKILF VGTKRAASEA VKDAALSCDQ FFVNHRWLG GMLTNWKTVR QSIKRLKDLE TQSQDGTFDK LTKKEALMRT RELEKLENSL GGIKDMGGLP DALFVIDADH E HIAIKEAN NLGIPVFAIV DTNSDPDGVD FVIPGNDDAI RAVTLYLGAV AATVREGRS

UniProtKB: Small ribosomal subunit protein uS2

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Macromolecule #5: 16S RIBOSOMAL RNA

MacromoleculeName: 16S RIBOSOMAL RNA / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 499.690031 KDa
SequenceString: 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

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Macromolecule #17: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 17 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Details: 5 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298.15 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.75 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 847135
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2avy
PDB Unreleased entry

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1.0.) / Number images used: 423567
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1.0.)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1.0.)
Final 3D classificationSoftware - Name: RELION (ver. 2.1.0.)

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