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- EMDB-36883: Cryo-EM structure of 30S ribosome with cleaved AP-mRNA bound comp... -

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Open data

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Basic information

Entry

Database: EMDB / ID: EMD-36883

Title

Cryo-EM structure of 30S ribosome with cleaved AP-mRNA bound complex-II

Map data

Sample

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

Keywords

30S Ribosome / AP-mRNA / RIBOSOME

Function / homology

Function and homology information

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 ...
Similarity search - Function

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 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
Similarity search - Domain/homology

Biological species

Escherichia coli K-12 (bacteria)

Method

single particle reconstruction / cryo EM / Resolution: 3.4 Å

Authors

Ramachandran R / Afsar M / Shukla A

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-II
Authors: Ramachandran R / Afsar M / Shukla A

History

Deposition	Jul 18, 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

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Structure visualization

Supplemental images	emd_36883.png

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Downloads & links

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EMDB archive

Map data	emd_36883.map.gz	59.9 MB		EMDB map data format
Header (meta data)	emd-36883-v30.xml emd-36883.xml	36.1 KB 36.1 KB	Display Display	EMDB header
Images	emd_36883.png	148.2 KB
Masks	emd_36883_msk_1.map	64 MB		Mask map
Filedesc metadata	emd-36883.cif.gz	8.7 KB
Others	emd_36883_half_map_1.map.gz emd_36883_half_map_2.map.gz	49.5 MB 49.5 MB
Archive directory	http://ftp.pdbj.org/pub/emdb/structures/EMD-36883 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36883	HTTPS FTP

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Validation report

Summary document	emd_36883_validation.pdf.gz	902.7 KB	Display	EMDB validaton report
Full document	emd_36883_full_validation.pdf.gz	902.3 KB	Display
Data in XML	emd_36883_validation.xml.gz	12.3 KB	Display
Data in CIF	emd_36883_validation.cif.gz	14.4 KB	Display
Arichive directory	https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36883 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36883	HTTPS FTP

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Related structure data

Related structure data	8k4eMC 36885 36886 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 (28) #157 - Jan 2013 Transfer-Messenger RNA similarity (28) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (28)

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Map

File

Download / File: emd_36883.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)

Projections & slices

Image control

Size
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Others	InvertY flip

Axes	Z (Sec.)	Y (Row.)	X (Col.)
	1.38 Å/pix. x 256 pix. = 353.28 Å	1.38 Å/pix. x 256 pix. = 353.28 Å	1.38 Å/pix. x 256 pix. = 353.28 Å
Surface
Projections
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Images are generated by Spider.

Voxel size

X=Y=Z: 1.38 Å

Density

Histogram

Histogram (log scale)

Contour Level	By AUTHOR: 0.02
Minimum - Maximum	-0.22267926 - 0.38924566
Average (Standard dev.)	0.000054623106 (±0.014101231)

Symmetry

Space group: 1

Details

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Supplemental data

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Mask #1

File

emd_36883_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: #1

File

emd_36883_half_map_1.map

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

File

emd_36883_half_map_2.map

Projections & Slices

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 30S Ribosome with cleaved AP-mRNA

Entire	Name: 30S Ribosome with cleaved AP-mRNA
Components	Complex: 30S Ribosome with cleaved AP-mRNA RNA: 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 Protein or peptide: 30S ribosomal protein S21 RNA: 16S rRNA Protein or peptide: 30S ribosomal protein S14

Entire

Name: 30S Ribosome with cleaved AP-mRNA

Components

Complex: 30S Ribosome with cleaved AP-mRNA
- RNA: 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
- Protein or peptide: 30S ribosomal protein S21
- RNA: 16S rRNA
- Protein or peptide: 30S ribosomal protein S14

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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)

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Macromolecule #1: AP-mRNA

Macromolecule	Name: AP-mRNA / type: rna / ID: 1 / Details: N = rSpacer AP-site mimetic / Number of copies: 1
Source (natural)	Organism: Escherichia coli K-12 (bacteria)
Molecular weight	Theoretical: 22.963521 KDa
Sequence	String: ACUGGGAUCG CUGAAUUAGA GAUCGGCGUC CUUUCAUUUC UAUAUACUAA GGAGGUUAAA AUGUCU(N)UAA GU

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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 ...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

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Macromolecule #2: 30S ribosomal protein S2

Macromolecule	Name: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 2 / 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 ...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

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Macromolecule #3: 30S ribosomal protein S3

Macromolecule	Name: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 3 / 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 ...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

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Macromolecule #4: 30S ribosomal protein S4

Macromolecule	Name: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 4 / 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 ...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

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Macromolecule #5: 30S ribosomal protein S5

Macromolecule	Name: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 5 / 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

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Macromolecule #6: 30S ribosomal protein S6, fully modified isoform

Macromolecule	Name: 30S ribosomal protein S6, fully modified isoform / type: protein_or_peptide / ID: 6 / 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

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Macromolecule #7: 30S ribosomal protein S7

Macromolecule	Name: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 7 / 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

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Macromolecule #8: 30S ribosomal protein S8

Macromolecule	Name: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 8 / 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

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Macromolecule #9: 30S ribosomal protein S9

Macromolecule	Name: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 9 / 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

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Macromolecule #10: 30S ribosomal protein S10

Macromolecule	Name: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 10 / 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

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Macromolecule #11: 30S ribosomal protein S11

Macromolecule	Name: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 11 / 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

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Macromolecule #12: 30S ribosomal protein S12

Macromolecule	Name: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 12 / 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

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Macromolecule #13: 30S ribosomal protein S13

Macromolecule	Name: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 13 / 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

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Macromolecule #14: 30S ribosomal protein S15

Macromolecule	Name: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 14 / 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

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Macromolecule #15: 30S ribosomal protein S16

Macromolecule	Name: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 15 / 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

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Macromolecule #16: 30S ribosomal protein S17

Macromolecule	Name: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 16 / 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

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Macromolecule #17: 30S ribosomal protein S18

Macromolecule	Name: 30S ribosomal protein S18 / type: protein_or_peptide / ID: 17 / 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

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Macromolecule #18: 30S ribosomal protein S19

Macromolecule	Name: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 18 / 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

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Macromolecule #19: 30S ribosomal protein S20

Macromolecule	Name: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 19 / 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

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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

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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

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Experimental details

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Structure determination

Method	cryo EM
Processing	single particle reconstruction
Aggregation state	particle

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Sample preparation

Buffer	pH: 7.5
Grid	Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS
Vitrification	Cryogen name: ETHANE

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Electron microscopy

Microscope	FEI TITAN KRIOS
Image recording	Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 41.53 e/Å²
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
Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup model	Type of model: PDB ENTRY PDB model - PDB ID: 7nat
Final reconstruction	Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42320
Initial angle assignment	Type: ANGULAR RECONSTITUTION
Final angle assignment	Type: ANGULAR RECONSTITUTION

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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-8k4e: Cryo-EM structure of 30S ribosome with cleaved AP-mRNA bound complex-II

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-Mask #1

-Half map: #1

-Half map: #2

-Sample components

+Entire : 30S Ribosome with cleaved AP-mRNA

+Supramolecule #1: 30S Ribosome with cleaved AP-mRNA

+Macromolecule #1: AP-mRNA

+Macromolecule #21: 16S rRNA

+Macromolecule #2: 30S ribosomal protein S2

+Macromolecule #3: 30S ribosomal protein S3

+Macromolecule #4: 30S ribosomal protein S4

+Macromolecule #5: 30S ribosomal protein S5

+Macromolecule #6: 30S ribosomal protein S6, fully modified isoform

+Macromolecule #7: 30S ribosomal protein S7

+Macromolecule #8: 30S ribosomal protein S8

+Macromolecule #9: 30S ribosomal protein S9

+Macromolecule #10: 30S ribosomal protein S10

+Macromolecule #11: 30S ribosomal protein S11

+Macromolecule #12: 30S ribosomal protein S12

+Macromolecule #13: 30S ribosomal protein S13

+Macromolecule #14: 30S ribosomal protein S15

+Macromolecule #15: 30S ribosomal protein S16

+Macromolecule #16: 30S ribosomal protein S17

+Macromolecule #17: 30S ribosomal protein S18

+Macromolecule #18: 30S ribosomal protein S19

+Macromolecule #19: 30S ribosomal protein S20

+Macromolecule #20: 30S ribosomal protein S21

+Macromolecule #22: 30S ribosomal protein S14

-Experimental details

-Structure determination

-Sample preparation

-Electron microscopy

-Image processing

-Atomic model buiding 1

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

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Movie

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Downloads & links

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EMDB archive

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Related structure data

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Links

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Map

Image control

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Supplemental data

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Mask #1

-
Half map: #1

-
Half map: #2

-
Sample components

+
Entire : 30S Ribosome with cleaved AP-mRNA

+
Supramolecule #1: 30S Ribosome with cleaved AP-mRNA

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Macromolecule #1: AP-mRNA

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Macromolecule #21: 16S rRNA

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Macromolecule #2: 30S ribosomal protein S2

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Macromolecule #3: 30S ribosomal protein S3

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Macromolecule #4: 30S ribosomal protein S4

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Macromolecule #5: 30S ribosomal protein S5

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Macromolecule #6: 30S ribosomal protein S6, fully modified isoform

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Macromolecule #7: 30S ribosomal protein S7

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Macromolecule #8: 30S ribosomal protein S8

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Macromolecule #9: 30S ribosomal protein S9

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Macromolecule #10: 30S ribosomal protein S10

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Macromolecule #11: 30S ribosomal protein S11

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Macromolecule #12: 30S ribosomal protein S12

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Macromolecule #13: 30S ribosomal protein S13

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Macromolecule #14: 30S ribosomal protein S15

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Macromolecule #15: 30S ribosomal protein S16

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Macromolecule #16: 30S ribosomal protein S17

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Macromolecule #17: 30S ribosomal protein S18

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Macromolecule #18: 30S ribosomal protein S19

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Macromolecule #19: 30S ribosomal protein S20

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Macromolecule #20: 30S ribosomal protein S21

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Macromolecule #22: 30S ribosomal protein S14

-
Experimental details

-
Structure determination

-
Sample preparation

-
Electron microscopy

-
Image processing

-
Atomic model buiding 1

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