EMDB-0243: Improved model derived from cryo-EM map of Staphylococcus aureus ...

Basic information

• Entry: Database: EMDB / ID: EMD-0243
• Title: Improved model derived from cryo-EM map of Staphylococcus aureus large ribosomal subunit
• Map data: resolution 2.65 A

Sample

• Complex: Staphylococcus aureus large ribosomal subunit
  • RNA: x 2 types
  • Protein or peptide: x 27 types
• Ligand: x 1 types

Function / homology

Function:

ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / cytoplasm

Domain/homology:

Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L5, conserved site / : / Ribosomal protein L5, N-terminal / Ribosomal protein L5 signature. / Ribosomal protein L15, conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein L2, conserved site / Ribosomal protein L2 signature. / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L5 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / ribosomal L5P family C-terminus / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L6 / Ribosomal protein L2, domain 3 / Ribosomal protein L14P, conserved site

Component:

Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL25 / 50S ribosomal protein L32 / 50S ribosomal protein L5 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / 50S ribosomal protein L33 1 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / 50S ribosomal protein L21 / 50S ribosomal protein L27 / 50S ribosomal protein L35 / 50S ribosomal protein L20 / 50S ribosomal protein L28 / 50S ribosomal protein L19 / 50S ribosomal protein L14 / 50S ribosomal protein L24 / 50S ribosomal protein L6 / 50S ribosomal protein L30 / 50S ribosomal protein L15 / 50S ribosomal protein L17 / 50S ribosomal protein L13 / 50S ribosomal protein L29 / Large ribosomal subunit protein uL3 / 50S ribosomal protein L4 / 50S ribosomal protein L23 / 50S ribosomal protein L2 / 50S ribosomal protein L22 / 50S ribosomal protein L16 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL18

• Biological species: Staphylococcus aureus (bacteria)
• Method: single particle reconstruction / cryo EM / Resolution: 2.65 Å
• Authors: Eyal Z / Cimicata G / Matzov D / Fox T / de Val N / Zimmerman E / Bashan A / Yonath A
• Citation: Journal: Proc Natl Acad Sci U S A / Year: 2015; Title: Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus.; Authors: Zohar Eyal / Donna Matzov / Miri Krupkin / Itai Wekselman / Susanne Paukner / Ella Zimmerman / Haim Rozenberg / Anat Bashan / Ada Yonath / ; Abstract: The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from Staphylococcus aureus, a versatile Gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, BC-3205. These crystal structures shed light on specific structural motifs of the S. aureus ribosome and the binding modes of the aforementioned antibiotics. Moreover, by analyzing the ribosome structure and comparing it with those of nonpathogenic bacterial models, we identified some unique internal and peripheral structural motifs that may be potential candidates for improving known antibiotics and for use in the design of selective antibiotic drugs against S. aureus.

History

Deposition	Sep 12, 2018	-
Header (metadata) release	Nov 14, 2018	-
Map release	Nov 14, 2018	-
Update	Nov 25, 2020	-
Current status	Nov 25, 2020	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_0243.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: resolution 2.65 A
• Voxel size: X=Y=Z: 0.858 Å

Density

Contour Level	By AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum	-0.39862263 - 0.69084954
Average (Standard dev.)	0.00029412095 (±0.025747413)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 328 328 328 Spacing 328 328 328
Cell	A=B=C: 281.42398 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	0.858	0.858	0.858
M x/y/z	328	328	328
origin x/y/z	0.000	0.000	0.000
length x/y/z	281.424	281.424	281.424
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	328	328	328
D min/max/mean	-0.399	0.691	0.000

Supplemental data

Additional map: resolution 2.87 A

• File: emd_0243_additional.map
• Annotation: resolution 2.87 A

Half map: #2

• File: emd_0243_half_map_1.map

Half map: #1

• File: emd_0243_half_map_2.map

Sample components

Entire : Staphylococcus aureus large ribosomal subunit

• Entire: Name: Staphylococcus aureus large ribosomal subunit

Components

• Complex: Staphylococcus aureus large ribosomal subunit
  • RNA: 23S ribosomal RNA
  • RNA: 5S ribosomal RNA
  • Protein or peptide: 50S ribosomal protein L2
  • Protein or peptide: 50S ribosomal protein L3
  • Protein or peptide: 50S ribosomal protein L4
  • Protein or peptide: 50S ribosomal protein L5
  • Protein or peptide: 50S ribosomal protein L6
  • Protein or peptide: 50S ribosomal protein L13
  • Protein or peptide: 50S ribosomal protein L14
  • Protein or peptide: 50S ribosomal protein L15
  • Protein or peptide: 50S ribosomal protein L16
  • Protein or peptide: 50S ribosomal protein L17
  • Protein or peptide: 50S ribosomal protein L18
  • Protein or peptide: 50S ribosomal protein L19
  • Protein or peptide: 50S ribosomal protein L20
  • Protein or peptide: 50S ribosomal protein L21
  • Protein or peptide: 50S ribosomal protein L22
  • Protein or peptide: 50S ribosomal protein L23
  • Protein or peptide: 50S ribosomal protein L24
  • Protein or peptide: 50S ribosomal protein L25
  • Protein or peptide: 50S ribosomal protein L27
  • Protein or peptide: 50S ribosomal protein L28
  • Protein or peptide: 50S ribosomal protein L29
  • Protein or peptide: 50S ribosomal protein L30
  • Protein or peptide: 50S ribosomal protein L32
  • Protein or peptide: 50S ribosomal protein L33
  • Protein or peptide: 50S ribosomal protein L34
  • Protein or peptide: 50S ribosomal protein L35
  • Protein or peptide: 50S ribosomal protein L36
• Ligand: MAGNESIUM ION

Supramolecule #1: Staphylococcus aureus large ribosomal subunit

• Supramolecule: Name: Staphylococcus aureus large ribosomal subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#29
• Source (natural): Organism: Staphylococcus aureus (bacteria)

Macromolecule #1: 23S ribosomal RNA

• Macromolecule: Name: 23S ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 946.738688 KDa

Sequence

String:

GAUUAAGUUA UUAAGGGCGC ACGGUGGAUG CCUUGGCACU AGAAGCCGAU GAAGGACGUU ACUAACGACG AUAUGCUUUG GGGAGCUGU AAGUAAGCUU UGAUCCAGAG AUUUCCGAAU GGGGAAACCC AGCAUGAGUU AUGUCAUGUU AUCGAUAUGU G AAUACAUA GCAUAUCAGA AGGCACACCC GGAGAACUGA AACAUCUUAG UACCCGGAGG AAGAGAAAGA AAAUUCGAUU CC CUUAGUA GCGGCGAGCG AAACGGGAAG AGCCCAAACC AACAAGCUUG CUUGUUGGGG UUGUAGGACA CUCUAUACGG AGU UACAAA GGACGACAUU AGACGAAUCA UCUGGAAAGA UGAAUCAAAG AAGGUAAUAA UCCUGUAGUC GAAAAUGUUG UCUC UCUUG AGUGGAUCCU GAGUACGACG GAGCACGUGA AAUUCCGUCG GAAUCUGGGA GGACCAUCUC CUAAGGCUAA AUACU CUCU AGUGACCGAU AGUGAACCAG UACCGUGAGG GAAAGGUGAA AAGCACCCCG GAAGGGGAGU GAAAUAGAAC CUGAAA CCG UGUGCUUACA AGUAGUCAGA GCCCGUUAAU GGGUGAUGGC GUGCCUUUUG UAGAAUGAAC CGGCGAGUUA CGAUUUG AU GCAAGGUUAA GCAGUAAAUG UGGAGCCGUA GCGAAAGCGA GUCUGAAUAG GGCGUUUAGU AUUUGGUCGU AGACCCGA A ACCAGGUGAU CUACCCUUGG UCAGGUUGAA GUUCAGGUAA CACUGAAUGG AGGACCGAAC CGACUUACGU (5MU)GAAA AGUG AGCGGAUGAA CUGAGGGUAG CGGAGAAAUU CCAAUCGAAC CUGGAGAUAG CUGGUUCUCU CCGAAAUAGC UUUAGG GCU AGCCUCAAGU GAUGAUUAUU GGAGGUAGAG CACUGUUUGG ACGAGGGGCC CCUCUCGGGU UACCGAAUUC AGACAAA CU CCGAAUGCCA AUUAAUUUAA CUUGGGAGUC AGAACAUGGG UGAUAAGGUC CGUGUUCGAA AGGGAAACAG CCCAGACC A CCAGCUAAGG UCCCAAAAUA UAUGUUAAGU GGAAAAGGAU GUGGCGUUGC CCAGACAACU AGGAUGUUGG CUUAGAAGC AGCCAUCAUU UAAAGAGUGC GUAAUAGCUC ACUAGUCGAG UGACACUGCG CCGAAAAUGU ACCGGGGCUA AACAUAUUAC CGAAGCUGU GGAUUGUCCU UUGGACAAUG GUAGGAGAGC GUUCUAAGGG CGUUGAAGCA UGAUCGUAAG GACAUGUGGA G CGCUUAGA AGUGAGAAUG CCGGUGUGAG UAGCGAAAGA CGGGUGAGAA UCCCGUCCAC CGAUUGACUA AGGUUUCCAG AG GAAGGCU CGUCCGCUCU GGGUUAGUCG GGUCCUAAGC UGAGGCCGAC AGGCGUAGGC GAUGGAUAAC AGGUUGAUAU UCC UGUACC ACCUAUAAUC GUUUUAAUCG AUGGGGGGAC GCAGUAGGAU AGGCGAAGCG UGCGAUUGGA UUGCACGUCU AAGC AGUAA GGCUGAGUAU UAGGCAAAUC CGGUACUCGU UAAGGCUGAG CUGUGAUGGG GAGAAGACAU UGUGUCUUCG AGUCG UUGA UUUCACACUG CCGAGAAAAG CCUCUAGAUA GAAAAUAGGU GCCCGUACCG CAAACCGACA CAGGUAGUCA AGAUGA GAA UUCUAAGGUG AGCGAGCGAA CUCUCGUUAA GGAACUCGGC AAAAUGACCC CGUAACUUCG GGAGAAGGGG UGCUCUU UA GGGUUAACGC CCAGAAGAGC CGCAGUGAAU AGGCCCAAGC GACUGUUUAU CAAAAACACA GGUCUCUGCU AAACCGUA A GGUGAUGUAU AGGGGCUGAC GCCUGCCCGG UGCUGGAAGG UUAAGAGGAG UGGUUAGCUU CUGCGAAGCU ACGAAUCGA AGCCCCAGUA AACGGCGGCC GUAACUAUAA CGGUCCUAAG GUAGCGAAA(5MU) UCCUUGUCGG GUAAGUUCCG ACCCGC ACG AAAGGCGUAA CGAUUUGGGC ACUGUCUCAA CGAGAGACUC GGUGAAAUCA UAGUACCUGU GAAGAUGCAG GUUACCC GC GACAGGACGG AAAGACCCCG UGGAGCUUUA CUGUAGCCUG AUAUUGAAAU UCGGCACAGC UUGUACAGGA UAGGUAGG A GCCUUUGAAA CGUGAGCGCU AGCUUACGUG GAGGCGCUGG UGGGAUACUA CCCUAGCUGU GUUGGCUUUC UAACCCGCA CCACUUAUCG UGGUGGGAGA CAGUGUCAGG CGGGCAGUUU GACUGGGGCG GUCGCCUCCU AAAAGGUAAC GGAGGCGCUC AAAGGUUCC CUCAGAAUGG UUGGAAAUCA UUCAUAGAGU GUAAAGGCAU AAGGGAGCUU GACUGCGAGA CCUACAAGUC G AGCAGGGU CGAAAGACGG ACUUAGUGAU CCGGUGGUUC CGCAUGGAAG GGCCAUCGCU CAACGGAUAA AAGCUACCCC GG GGAUAAC AGGCUUAUCU CCCCCAAGAG UUCACAUCGA CGGGGAGGUU UGGCACCUCG (2MA)UGUCGGCUC AUCGCAUCC UGGGGCUGUA GUCGGUCCCA AGGGUUGGGC UGUUCGCCCA UUAAAGCGGU ACGCGAGCUG GGUUCAGAAC GUCGUGAGAC AGUUCGGUC CCUAUCCGUC GUGGGCGUAG GAAAUUUGAG AGGAGCUGUC CUUAGUACGA GAGGACCGGG AUGGACAUAC C UCUGGUGU ACCAGUUGUC GUGCCAACGG CAUAGCUGGG UAGCUAUGUG UGGACGGGAU AAGUGCUGAA AGCAUCUAAG CA UGAAGCC CCCCUCAAGA UGAGAUUUCC CAACUUCGGU UAUAAGAUCC CUCAAAGAUG AUGAGGUUAA UAGGUUCGAG GUG GAAGCA UGGUGACAUG UGGAGCUGAC GAAUACUAAU CGAUCGAAGA CUUAAUCAA

Macromolecule #2: 5S ribosomal RNA

• Macromolecule: Name: 5S ribosomal RNA / type: rna / ID: 2 / Number of copies: 1
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 36.974945 KDa

Sequence

String:

UCUGGUGACU AUAGCAAGGA GGUCACACCU GUUCCCAUGC CGAACACAGA AGUUAAGCUC CUUAGCGUCG AUGGUAGUCG AACUUACGU UCCGCUAGAG UAGAACGUUG CCAGGC

Macromolecule #3: 50S ribosomal protein L2

• Macromolecule: Name: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 29.827607 KDa

Sequence

String:

AIKKYKPITN GRRNMTSLDF AEITKTTPEK SLLKPLPKKA GRNNQGKLTV RHHGGGHKRQ YRVIDFKRNK DGINAKVDSI QYDPNRSAN IALVVYADGE KRYIIAPKGL EVGQIVESGA EADIKVGNAL PLQNIPVGTV VHNIELKPGK GGQIARSAGA S AQVLGKEG KYVLIRLRSG EVRMILSTCR ATIGQVGNLQ HELVNVGKAG RSRWKGIRPT VRGSVMNPND HPHGGGEGRA PI GRPSPMS PWGKPTLGKK TRRGKKSSDK LIVRGRK

Macromolecule #4: 50S ribosomal protein L3

• Macromolecule: Name: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 23.199545 KDa

Sequence

String:

TKGILGRKIG MTQVFGENGE LIPVTVVEAK ENVVLQKKTV EVDGYNAIQV GFEDKKAYKK DAKSNKYANK PAEGHAKKAD AAPKRFIRE FRNVDVDAYE VGQEVSVDTF VAGDVIDVTG VSKGKGFQGA IKRHGQSRGP MSHGSHFHRA PGSVGMASDA S RVFKGQKM PGRMGGNTVT VQNLEVVQVD TENKVILVKG NVPGPKKGLV EIRTSIK

Macromolecule #5: 50S ribosomal protein L4

• Macromolecule: Name: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 22.364504 KDa

Sequence

String:

ANYDVLKLDG TKSGSIELSD AVFGIEPNNS VLFEAINLQR ASLRQGTHAV KNRSAVSGGG RKPWKQKGTG RARQGTIRAP QWRGGGIVF GPTPRSYAYK MPKKMRRLAL RSALSFKAQE NGLTVVDAFN FEAPKTKEFK NVLSTLEQPK KVLVVTENED V NVELSARN IPGVQVTTAQ GLNVLDITNA DSLVITEAAA KKVEEVLG

Macromolecule #6: 50S ribosomal protein L5

• Macromolecule: Name: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 17.651479 KDa

Sequence

String:

KFNYSSVMEV PKIDKIVVNM GVGDAVQNSK VLDNAVEELE LITGQKPLVT KAKKSIATFR LREGMPIGAK VTLRGERMYE FLDKLISVS LPRVRDFQGV SKKAFDGRGN YTLGVKEQLI FPEIDYDKVS KVRGMDIVIV TTANTDEEAR ELLANFGMP

Macromolecule #7: 50S ribosomal protein L6

• Macromolecule: Name: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 19.501154 KDa

Sequence

String:

SRVGKKIIDI PSDVTVTFDG NHVTVKGPKG ELSRTLNERM TFKQEENTIE VVRPSDSKED RTNHGTTRAL LNNMVQGVSQ GYVKVLELV GVGYRAQMQG KDLILNVGYS HPVEIKAEEN ITFSVEKNTV VKVEGISKEQ VGALASNIRS VRPPEPYKGK G IRYQGEYV RRKEGKT

Macromolecule #8: 50S ribosomal protein L13

• Macromolecule: Name: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 16.359427 KDa

Sequence

String:

MRQTFMANES NIERKWYVID AEGQTLGRLS SEVASILRGK NKVTYTPHVD TGDYVIVINA SKIEFTGNKE TDKVYYRHSN HPGGIKSIT AGELRRTNPE RLIENSIKGM LPSTRLGEKQ GKKLFVYGGA EHPHAAQQPE NYELRG

Macromolecule #9: 50S ribosomal protein L14

• Macromolecule: Name: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 13.157342 KDa

Sequence

String:

MIQQETRLKV ADNSGAREVL TIKVLGGSGR KTANIGDVIV CTVKNATPGG VVKKGDVVKA VIVRTKSGVR RNDGSYIKFD ENACVIIRD DKGPRGTRIF GPVARELREG NFMKIVSLAP EVL

Macromolecule #10: 50S ribosomal protein L15

• Macromolecule: Name: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 15.62889 KDa

Sequence

String:

MKLHELKPAE GSRKERNRVG RGVATGNGKT SGRGHKGQKA RSGGGVRPGF EGGQLPLFRR LPKRGFTNIN RKEYAIVNLD QLNKFEDGT EVTPALLVES GVVKNEKSGI KILGNGSLDK KLTVKAHKFS ASAAEAIDAK GGAHEVI

Macromolecule #11: 50S ribosomal protein L16

• Macromolecule: Name: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 15.599435 KDa

Sequence

String:

MLLPKRVKYR RQHRPKTTGR SKGGNYVTFG EFGLQATTTS WITSRQIESA RIAMTRYMKR GGKVWIKIFP HTPYTKKPLE VRMGAGKGA VEGWIAVVKP GRILFEVAGV SEEVAREALR LASHKLPVKT KFVKREEL

Macromolecule #12: 50S ribosomal protein L17

• Macromolecule: Name: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 13.583523 KDa

Sequence

String:

YRKLGRTSDQ RKAMLRDLAT SLIISERIET TEARAKEVRS VVEKLITLGK KGDLASRRNA AKTLRNVEIL NEDETTQTAL QKLFGEIAE RYTERQGGYT RILKQGPRRG DGAESVIIEL V

Macromolecule #13: 50S ribosomal protein L18

• Macromolecule: Name: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 13.124093 KDa

Sequence

String:

MISKIDKNKV RLKRHARVRT NLSGTAEKPR LNVYRSNKHI YAQIIDDNKG VTLAQASSKD SDIATTATKV ELATKVGEAI AKKAADKGI KEIVFDRGGY LYHGRVKALA EAARESGLEF

Macromolecule #14: 50S ribosomal protein L19

• Macromolecule: Name: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 13.392771 KDa

Sequence

String:

MTNHKLIEAV TKSQLRTDLP SFRPGDTLRV HVRIIEGTRE RIQVFEGVVI KRRGGGVSET FTVRKISSGV GVERTFPLHT PKIEKIEVK RRGKVRRAKL YYLRSLRGKA ARIQEIR

Macromolecule #15: 50S ribosomal protein L20

• Macromolecule: Name: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 13.459919 KDa

Sequence

String:

PRVKGGTVTR ARRKKTIKLA KGYFGSKHTL YKVAKQQVMK SGQYAFRDRR QRKRDFRKLW ITRINAAARQ HEMSYSRLMN GLKKAGIDI NRKMLSEIAI SDEKAFAQLV TKAKDAL

Macromolecule #16: 50S ribosomal protein L21

• Macromolecule: Name: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 11.354081 KDa

Sequence

String:

MFAIIETGGK QIKVEEGQEI FVEKLDVNEG DTFTFDKVLF VGGDSVKVGA PTVEGATVTA TVNKQGRGKK ITVFTYKRRK NSKRKKGHR QPYTKLTIDK INA

Macromolecule #17: 50S ribosomal protein L22

• Macromolecule: Name: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 12.328358 KDa

Sequence

String:

MEAKAVARTI RIAPRKVRLV LDLIRGKNAA EAIAILKLTN KASSPVIEKV LMSALANAEH NYDMNTDELV VKEAYANEGP TLKRFRPRA QGRASAINKR TSHITIVVSD GKE

Macromolecule #18: 50S ribosomal protein L23

• Macromolecule: Name: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 10.3801 KDa

Sequence

String:

EARDILKRPV ITEKSSEAMA EDKYTFDVDT RVNKTQVKMA VEEIFNVKVA SVNIMNYKPK KKRMGRYQGY TNKRRKAIVT LKEGSIDLF

Macromolecule #19: 50S ribosomal protein L24

• Macromolecule: Name: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 11.316205 KDa

Sequence

String:

HIKKGDNVKV IAGKDKGKEG KVIATLPKKD RVVVEGVNIM KKHQKPTQLN PEGGILETEA AIHVSNVQLL DPKTNEPTRV GYKFVDGKK VRIAKKSGEE IKSN

Macromolecule #20: 50S ribosomal protein L25

• Macromolecule: Name: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 10.4622 KDa

Sequence

String:

ASLKSIIRQG KQTRSDLKQL RKSGKVPAVV YGYGTKNVSV KVDEVEFIKV IREVGRNGVI ELGVGSKTIK VMVADYQFDP LKNQITHID FLAIN

Macromolecule #21: 50S ribosomal protein L27

• Macromolecule: Name: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 8.595688 KDa

Sequence

String:

VSSTKNGRDS ESKRLGAKRA DGQFVTGGSI LYRQRGTKIY PGENVGRGGD DTLFAKIDGV VKFERKGRDK KQVSVYAVA

Macromolecule #22: 50S ribosomal protein L28

• Macromolecule: Name: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 5.499432 KDa

Sequence

String:

ASTGNRRSHA LNSTKRRWNA NLQKVRILVD GKPKKVWVSA RALKSGKVT

Macromolecule #23: 50S ribosomal protein L29

• Macromolecule: Name: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 7.845942 KDa

Sequence

String:

KAKEIRDLTT SEIEEQIKSS KEELFNLRFQ LATGQLEETA RIRTVRKTIA RLKTVARERE IEQSKAN

Macromolecule #24: 50S ribosomal protein L30

• Macromolecule: Name: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 6.434487 KDa

Sequence

String:

AKLQITLTRS VIGRPETQRK TVEALGLKKT NSSVVVEDNP AIRGQINKVK HLVTVEEK

Macromolecule #25: 50S ribosomal protein L32

• Macromolecule: Name: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 5.569565 KDa

Sequence

String:

AVPKRRTSKT RKNKRRTHFK ISVPGMTECP NCGEYKLSHR VCKNCGSY

Macromolecule #26: 50S ribosomal protein L33

• Macromolecule: Name: 50S ribosomal protein L33 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 5.684561 KDa

Sequence

String:

RVNVTLACTE CGDRNYITTK NKRNNPERIE MKKYCPRLNK YTLHRET

Macromolecule #27: 50S ribosomal protein L34

• Macromolecule: Name: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 5.252369 KDa

Sequence

String:

VKRTYQPNKR KHSKVHGFRK RMSTKNGRKV LARRRRKGRK VLS

Macromolecule #28: 50S ribosomal protein L35

• Macromolecule: Name: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 7.461992 KDa

Sequence

String:

PKMKTHRGAA KRVKRTASGQ LKRSRAFTSH LFANKSTKQK RQLRKARLVS KSDMKRVKQL LAYK

Macromolecule #29: 50S ribosomal protein L36

• Macromolecule: Name: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 4.318422 KDa

Sequence

String:

MKVRPSVKPI CEKCKVIKRK GKVMVICENP KHKQRQG

Macromolecule #30: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 30 / Number of copies: 237 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Experimental details

Structure determination

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

Sample preparation

• Concentration: 1 mg/mL
• Buffer: pH: 7.6
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
• Image recording: Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Ų
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Initial angle assignment: Type: OTHER
• Final angle assignment: Type: OTHER
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 211046