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- EMDB-16048: Mature 30S ribosomal subunit from Staphylococcus aureus -

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Open data

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Basic information

Entry

Database: EMDB / ID: EMD-16048

Title

Mature 30S ribosomal subunit from Staphylococcus aureus

Map data

Sample

Complex: Mature 30S ribosomal subunit
- RNA: x 1 types
- Protein or peptide: x 19 types

Keywords

Staphylococcus aureus / Ribosome / TRANSLATION

Function / homology

Function and homology information

ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation ...
Similarity search - Function

Ribosomal protein S14, type Z / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 ...Ribosomal protein S14, type Z / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / 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 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S2 signature 2. / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / 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 S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S7 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S13, conserved site / Ribosomal protein S4/S9 N-terminal domain / 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 S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / 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 / Ribosomal protein S11 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S11 / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e
Similarity search - Domain/homology

Biological species

Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)

Method

single particle reconstruction / cryo EM / Resolution: 3.7 Å

Authors

Garaeva N / Fatkhullin B / Jenner L / Soufari H / Yusupov M / Usachev K

Funding support

Russian Federation, 1 items

Citation

Journal: Structure / Year: 2023
Title: Ribosome maturation factor P (RimP) from Staphylococcus aureus
Authors: Garaeva N / Usachev K

History

Deposition	Oct 30, 2022	-
Header (metadata) release	Sep 20, 2023	-
Map release	Sep 20, 2023	-
Update	Nov 8, 2023	-
Current status	Nov 8, 2023	Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images	emd_16048.png

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Downloads & links

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EMDB archive

Map data	emd_16048.map.gz	204 MB		EMDB map data format
Header (meta data)	emd-16048-v30.xml emd-16048.xml	36.1 KB 36.1 KB	Display Display	EMDB header
FSC (resolution estimation)	emd_16048_fsc.xml	12.7 KB	Display	FSC data file
Images	emd_16048.png	76.1 KB
Filedesc metadata	emd-16048.cif.gz	8.3 KB
Others	emd_16048_half_map_1.map.gz emd_16048_half_map_2.map.gz	200.3 MB 200.3 MB
Archive directory	http://ftp.pdbj.org/pub/emdb/structures/EMD-16048 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16048	HTTPS FTP

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Validation report

Summary document	emd_16048_validation.pdf.gz	869.8 KB	Display	EMDB validaton report
Full document	emd_16048_full_validation.pdf.gz	869.4 KB	Display
Data in XML	emd_16048_validation.xml.gz	21.7 KB	Display
Data in CIF	emd_16048_validation.cif.gz	28.2 KB	Display
Arichive directory	https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16048 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16048	HTTPS FTP

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Related structure data

Related structure data	8bh6MC 16045C 16046C 16049C 8bdvC 8bh7C 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	#121 - Jan 2010 70S Ribosomes similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #10 - Oct 2000 Ribosome similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1)

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Map

File

Download / File: emd_16048.map.gz / Format: CCP4 / Size: 216 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.)
	1.2 Å/pix. x 384 pix. = 460.8 Å	1.2 Å/pix. x 384 pix. = 460.8 Å	1.2 Å/pix. x 384 pix. = 460.8 Å
Surface
Projections
Slices (1/3)
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Images are generated by Spider.

Voxel size

X=Y=Z: 1.2 Å

Density

Histogram

Histogram (log scale)

Contour Level	By AUTHOR: 0.423
Minimum - Maximum	-1.0080175 - 3.4388244
Average (Standard dev.)	-0.0014843387 (±0.108483136)

Symmetry

Space group: 1

Details

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Supplemental data

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Half map: #2

File

emd_16048_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: #1

File

emd_16048_half_map_2.map

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 : Mature 30S ribosomal subunit

Entire	Name: Mature 30S ribosomal subunit
Components	Complex: Mature 30S ribosomal subunit RNA: 16S ribosomal RNA Protein or peptide: 30S ribosomal protein S2 Protein or peptide: 30S ribosomal protein S3 Protein or peptide: 30S ribosomal protein S4 Protein or peptide: 30S ribosomal protein S5 Protein or peptide: 30S ribosomal protein S6 Protein or peptide: 30S ribosomal protein S7 Protein or peptide: 30S ribosomal protein S8 Protein or peptide: 30S ribosomal protein S9 Protein or peptide: 30S ribosomal protein S10 Protein or peptide: 30S ribosomal protein S11 Protein or peptide: 30S ribosomal protein S12 Protein or peptide: 30S ribosomal protein S13 Protein or peptide: 30S ribosomal protein S14 type Z 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

Entire

Name: Mature 30S ribosomal subunit

Components

Complex: Mature 30S ribosomal subunit
- RNA: 16S ribosomal RNA
- Protein or peptide: 30S ribosomal protein S2
- Protein or peptide: 30S ribosomal protein S3
- Protein or peptide: 30S ribosomal protein S4
- Protein or peptide: 30S ribosomal protein S5
- Protein or peptide: 30S ribosomal protein S6
- Protein or peptide: 30S ribosomal protein S7
- Protein or peptide: 30S ribosomal protein S8
- Protein or peptide: 30S ribosomal protein S9
- Protein or peptide: 30S ribosomal protein S10
- Protein or peptide: 30S ribosomal protein S11
- Protein or peptide: 30S ribosomal protein S12
- Protein or peptide: 30S ribosomal protein S13
- Protein or peptide: 30S ribosomal protein S14 type Z
- 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

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Supramolecule #1: Mature 30S ribosomal subunit

Supramolecule	Name: Mature 30S ribosomal subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)	Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)

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Macromolecule #1: 16S ribosomal RNA

Macromolecule	Name: 16S ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)	Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weight	Theoretical: 500.464406 KDa
Sequence	String: GGAGAGUUUG AUCCUGGCUC AGGAUGAACG CUGGCGGCGU GCCUAAUACA UGCAAGUCGA GCGAACGGAC GAGAAGCUUG CUUCUCUGA UGUUAGCGGC GGACGGGUGA GUAACACGUG GAUAACCUAC CUAUAAGACU GGGAUAACUU CGGGAAACCG U AGCUAAUA ...String: GGAGAGUUUG AUCCUGGCUC AGGAUGAACG CUGGCGGCGU GCCUAAUACA UGCAAGUCGA GCGAACGGAC GAGAAGCUUG CUUCUCUGA UGUUAGCGGC GGACGGGUGA GUAACACGUG GAUAACCUAC CUAUAAGACU GGGAUAACUU CGGGAAACCG U AGCUAAUA CCGGAUAAUA UUUUGAACCG CAUGGUUCAA AAGUGAAAGA CGGUCUUGCU GUCACUUAUA GAUGGAUCCG CG CUGCAUU AGCUAGUUGG UAAGGUAACG GCUUACCAAG GCAACGAUGC AUAGCCGACC UGAGAGGGUG AUCGGCCACA CUG GAACUG AGACACGGUC CAGACUCCUA CGGGAGGCAG CAGUAGGGAA UCUUCCGCAA UGGGCGAAAG CCUGACGGAG CAAC GCCGC GUGAGUGAUG AAGGUCUUCG GAUCGUAAAA CUCUGUUAUU AGGGAAGAAC AUAUGUGUAA GUAACUGUGC ACAUC UUGA CGGUACCUAA UCAGAAAGCC ACGGCUAACU ACGUGCCAGC AGCCGCGGUA AUACGUAGGU GGCAAGCGUU AUCCGG AAU UAUUGGGCGU AAAGCGCGCG UAGGCGGUUU UUUAAGUCUG AUGUGAAAGC CCACGGCUCA ACCGUGGAGG GUCAUUG GA AACUGGAAAA CUUGAGUGCA GAAGAGGAAA GUGGAAUUCC AUGUGUAGCG GUGAAAUGCG CAGAGAUAUG GAGGAACA C CAGUGGCGAA GGCGACUUUC UGGUCUGUAA CUGACGCUGA UGUGCGAAAG CGUGGGGAUC AAACAGGAUU AGAUACCCU GGUAGUCCAC GCCGUAAACG AUGAGUGCUA AGUGUUAGGG GGUUUCCCGC CCCUUAGUGC UGCAGCUAAC GCAUUAAGCA CUCCGCCUG GGGAGUACGA CCGCAAGGUU GAAACUCAAA GGAAUUGACG GGGACCCGCA CAAGCGGUGG AGCAUGUGGU U UAAUUCGA AGCAACGCGA AGAACCUUAC CAAAUCUUGA CAUCCUUUGA CAACUCUAGA GAUAGAGCCU UCCCCUUCGG GG GACAAAG UGACAGGUGG UGCAUGGUUG UCGUCAGCUC GUGUCGUGAG AUGUUGGGUU AAGUCCCGCA ACGAGCGCAA CCC UUAAGC UUAGUUGCCA UCAUUAAGUU GGGCACUCUA AGUUGACUGC CGGUGACAAA CCGGAGGAAG GUGGGGAUGA CGUC AAAUC AUCAUGCCCC UUAUGAUUUG GGCUACACAC GUGCUACAAU GGACAAUACA AAGGGCAGCG AAACCGCGAG GUCAA GCAA AUCCCAUAAA GUUGUUCUCA GUUCGGAUUG UAGUCUGCAA CUCGACUACA UGAAGCUGGA AUCGCUAGUA AUCGUA GAU CAGCAUGCUA CGGUGAAUAC GUUCCCGGGU CUUGUACACA CCGCCCGUCA CACCACGAGA GUUUGUAACA CCCGAAG CC GGUGGAGUAA CCUUUUAGGA GCUAGCCGUC GAAGGUGGGA CAAAUGAUUG GGGUGAAGUC GUAACAAGGU AGCCGUAU C GGAAGGUGCG GCUGGAUCAC CUCCUU GENBANK: GENBANK: CP000253.1

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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: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325
Molecular weight	Theoretical: 29.136369 KDa
Sequence	String: MAVISMKQLL EAGVHFGHQT RRWNPKMKKY IFTERNGIYI IDLQKTVKKV DEAYNFLKQV SEDGGQVLFV GTKKQAQESV KSEAERAGQ FYINQRWLGG LLTNYKTISK RIKRISEIEK MEEDGLFEVL PKKEVVELKK EYDRLIKFLG GIRDMKSMPQ A LFVVDPRK ...String: MAVISMKQLL EAGVHFGHQT RRWNPKMKKY IFTERNGIYI IDLQKTVKKV DEAYNFLKQV SEDGGQVLFV GTKKQAQESV KSEAERAGQ FYINQRWLGG LLTNYKTISK RIKRISEIEK MEEDGLFEVL PKKEVVELKK EYDRLIKFLG GIRDMKSMPQ A LFVVDPRK ERNAIAEARK LNIPIVGIVD TNCDPDEIDY VIPANDDAIR AVKLLTAKMA DAILEGQQGV SNEEVAAEQN ID LDEKEKS EETEATEE 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: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325
Molecular weight	Theoretical: 24.143867 KDa
Sequence	String: MGQKINPIGL RVGIIRDWEA KWYAEKDFAS LLHEDLKIRK FIDNELKEAS VSHVEIERAA NRINIAIHTG KPGMVIGKGG SEIEKLRNK LNALTDKKVH INVIEIKKVD LDARLVAENI ARQLENRASF RRVQKQAITR AMKLGAKGIK TQVSGRLGGA D IARAEQYS ...String: MGQKINPIGL RVGIIRDWEA KWYAEKDFAS LLHEDLKIRK FIDNELKEAS VSHVEIERAA NRINIAIHTG KPGMVIGKGG SEIEKLRNK LNALTDKKVH INVIEIKKVD LDARLVAENI ARQLENRASF RRVQKQAITR AMKLGAKGIK TQVSGRLGGA D IARAEQYS EGTVPLHTLR ADIDYAHAEA DTTYGKLGVK VWIYRGEVLP TKNTSGGGK 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: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325
Molecular weight	Theoretical: 23.051416 KDa
Sequence	String: MARFRGSNWK KSRRLGISLS GTGKELEKRP YAPGQHGPNQ RKKLSEYGLQ LREKQKLRYL YGMTERQFRN TFDIAGKKFG VHGENFMIL LASRLDAVVY SLGLARTRRQ ARQLVNHGHI LVDGKRVDIP SYSVKPGQTI SVREKSQKLN IIVESVEINN F VPEYLNFD ...String: MARFRGSNWK KSRRLGISLS GTGKELEKRP YAPGQHGPNQ RKKLSEYGLQ LREKQKLRYL YGMTERQFRN TFDIAGKKFG VHGENFMIL LASRLDAVVY SLGLARTRRQ ARQLVNHGHI LVDGKRVDIP SYSVKPGQTI SVREKSQKLN IIVESVEINN F VPEYLNFD ADSLTGTFVR LPERSELPAE INEQLIVEYY SR 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: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325
Molecular weight	Theoretical: 17.770512 KDa
Sequence	String: MARREEETKE FEERVVTINR VAKVVKGGRR FRFTALVVVG DKNGRVGFGT GKAQEVPEAI KKAVEAAKKD LVVVPRVEGT TPHTITGRY GSGSVFMKPA APGTGVIAGG PVRAVLELAG ITDILSKSLG SNTPINMVRA TIDGLQNLKN AEDVAKLRGK T VEELYN UniProtKB: Small ribosomal subunit protein uS5

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Macromolecule #6: 30S ribosomal protein S6

Macromolecule	Name: 30S ribosomal protein S6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325
Molecular weight	Theoretical: 11.613146 KDa
Sequence	String: MRTYEVMYIV RPNIEEDAKK ALVERFNGIL ATEGAEVLEA KDWGKRRLAY EINDFKDGFY NIVRVKSDNN KATDEFQRLA KISDDIIRY MVIREDEDK 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: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325
Molecular weight	Theoretical: 17.826555 KDa
Sequence	String: MPRKGSVPKR DVLPDPIHNS KLVTKLINKI MLDGKRGTAQ RILYSAFDLV EQRSGRDALE VFEEAINNIM PVLEVKARRV GGSNYQVPV EVRPERRTTL GLRWLVNYAR LRGEKTMEDR LANEILDAAN NTGGAVKKRE DTHKMAEANK AFAHYRW 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: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325
Molecular weight	Theoretical: 14.854315 KDa
Sequence	String: MTMTDPIADM LTRVRNANMV RHEKLELPAS NIKKEIAEIL KSEGFIKNVE YVEDDKQGVL RLFLKYGQND ERVITGLKRI SKPGLRVYA KASEMPKVLN GLGIALVSTS EGVITDKEAR KRNVGGEIIA YVW 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: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325
Molecular weight	Theoretical: 14.856987 KDa
Sequence	String: MTLAQVEYRG TGRRKNSVAR VRLVPGEGNI TVNNRDVREY LPFESLILDL NQPFDVTETK GNYDVLVNVH GGGFTGQAQA IRHGIARAL LEADPEYRGS LKRAGLLTRD PRMKERKKPG LKAARRSPQF SKR 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: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weight	Theoretical: 11.60052 KDa
Sequence	String: MAKQKIRIRL KAYDHRVIDQ SAEKIVETAK RSGADVSGPI PLPTEKSVYT IIRAVHMYKD SREQFEQRTH KRLIDIVNPT PKTVDALMG LNLPSGVDIE IKL 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: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325
Molecular weight	Theoretical: 13.907978 KDa
Sequence	String: MARKQVSRKR RVKKNIENGV AHIRSTFNNT IVTITDEFGN ALSWSSAGAL GFKGSKKSTP FAAQMASETA SKSAMEHGLK TVEVTVKGP GPGRESAIRA LQSAGLEVTA IRDVTPVPHN GCRPPKRRRV 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: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weight	Theoretical: 15.376897 KDa
Sequence	String: MPTINQLVRK PRQSKIKKSD SPALNKGFNS KKKKFTDLNS PQKRGVCTRV GTMTPRKPNS ALRKYARVRL SNNIEINAYI PGIGHNLQE HSVVLVRGGR VRDLPGVRYH IVRGALDTSG VDGRRQGRSL YGTKKPKN 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: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325
Molecular weight	Theoretical: 13.747919 KDa
Sequence	String: MARIAGVDIP REKRVVISLT YIYGIGTSTA QKILEEANVS ADTRVKDLTD DELGRIREVV DGYKVEGDLR RETNLNIKRL MEISSYRGI RHRRGLPVRG QKTKNNARTR KGPVKTVANK KK UniProtKB: Small ribosomal subunit protein uS13

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Macromolecule #14: 30S ribosomal protein S14 type Z

Macromolecule	Name: 30S ribosomal protein S14 type Z / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325
Molecular weight	Theoretical: 7.317769 KDa
Sequence	String: MAKTSMVAKQ QKKQKYAVRE YTRCERCGRP HSVYRKFKLC RICFRELAYK GQIPGVRKAS W UniProtKB: Small ribosomal subunit protein uS14B

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Macromolecule #15: 30S ribosomal protein S15

Macromolecule	Name: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325
Molecular weight	Theoretical: 10.63433 KDa
Sequence	String: MAISQERKNE IIKEYRVHET DTGSPEVQIA VLTAEINAVN EHLRTHKKDH HSRRGLLKMV GRRRHLLNYL RSKDIQRYRE LIKSLGIRR UniProtKB: Small ribosomal subunit protein uS15

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Macromolecule #16: 30S ribosomal protein S16

Macromolecule	Name: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325
Molecular weight	Theoretical: 10.253886 KDa
Sequence	String: MAVKIRLTRL GSKRNPFYRI VVADARSPRD GRIIEQIGTY NPTSANAPEI KVDEALALKW LNDGAKPTDT VHNILSKEGI MKKFDEQKK AK UniProtKB: Small ribosomal subunit protein bS16

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Macromolecule #17: 30S ribosomal protein S17

Macromolecule	Name: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325
Molecular weight	Theoretical: 10.196888 KDa
Sequence	String: MSERNDRKVY VGKVVSDKMD KTITVLVETY KTHKLYGKRV KYSKKYKTHD ENNSAKLGDI VKIQETRPLS ATKRFRLVEI VEESVII UniProtKB: Small ribosomal subunit protein uS17

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Macromolecule #18: 30S ribosomal protein S18

Macromolecule	Name: 30S ribosomal protein S18 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325
Molecular weight	Theoretical: 9.332018 KDa
Sequence	String: MAGGPRRGGR RRKKVCYFTA NGITHIDYKD TELLKRFISE RGKILPRRVT GTSAKYQRML TTAIKRSRHM ALLPYVKEEQ UniProtKB: Small ribosomal subunit protein bS18

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Macromolecule #19: 30S ribosomal protein S19

Macromolecule	Name: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325
Molecular weight	Theoretical: 10.639309 KDa
Sequence	String: MARSIKKGPF VDEHLMKKVE AQEGSEKKQV IKTWSRRSTI FPNFIGHTFA VYDGRKHVPV YVTEDMVGHK LGEFAPTRTF KGHVADDKK TRR UniProtKB: Small ribosomal subunit protein uS19

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Macromolecule #20: 30S ribosomal protein S20

Macromolecule	Name: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325
Molecular weight	Theoretical: 9.039472 KDa
Sequence	String: MANIKSAIKR VKTTEKAEAR NISQKSAMRT AVKNAKTAVS NNADNKNELV SLAVKLVDKA AQSNLIHSNK ADRIKSQLMT ANK UniProtKB: Small ribosomal subunit protein bS20

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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
Component:

Concentration	Formula	Name
10.0 mM/L	MgOAc	magnesium acetate
30.0 mM/L	NH₄Cl	Ammonium chloride
10.0 mM/L	HEPES	HEPES
1.0 mM/L	DTT	Dithiothreitol

Grid

Model: C-flat-2/2 / Material: COPPER / Pretreatment - Type: PLASMA CLEANING

Vitrification

Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK II

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Electron microscopy

Microscope	TFS GLACIOS
Image recording	Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 3.7 e/Å²
Electron beam	Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron optics	Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm
Sample stage	Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Startup model	Type of model: NONE
Final reconstruction	Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 326920
Initial angle assignment	Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignment	Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classification	Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Refinement	Protocol: RIGID BODY FIT
Output model	PDB-8bh6: Mature 30S ribosomal subunit from Staphylococcus aureus

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+Entire : Mature 30S ribosomal subunit

+Supramolecule #1: Mature 30S ribosomal subunit

+Macromolecule #1: 16S ribosomal RNA

+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

+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 S14 type Z

+Macromolecule #15: 30S ribosomal protein S15

+Macromolecule #16: 30S ribosomal protein S16

+Macromolecule #17: 30S ribosomal protein S17

+Macromolecule #18: 30S ribosomal protein S18

+Macromolecule #19: 30S ribosomal protein S19

+Macromolecule #20: 30S ribosomal protein S20

-Experimental details

-Structure determination

-Sample preparation

-Electron microscopy

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-Atomic model buiding 1

+About Yorodumi

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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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Related structure data

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Links

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Image control

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Supplemental data

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Half map: #2

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Half map: #1

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Sample components

+
Entire : Mature 30S ribosomal subunit

+
Supramolecule #1: Mature 30S ribosomal subunit

+
Macromolecule #1: 16S ribosomal RNA

+
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

+
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 S14 type Z

+
Macromolecule #15: 30S ribosomal protein S15

+
Macromolecule #16: 30S ribosomal protein S16

+
Macromolecule #17: 30S ribosomal protein S17

+
Macromolecule #18: 30S ribosomal protein S18

+
Macromolecule #19: 30S ribosomal protein S19

+
Macromolecule #20: 30S ribosomal protein S20

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Experimental details

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Structure determination

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Sample preparation

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Electron microscopy

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Atomic model buiding 1

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