EMDB-55947: Staphylococcus aureus 50S ribosome in complex with RRF, EF-G and ...

Basic information

Entry

Database: EMDB / ID: EMD-55947

• Title: Staphylococcus aureus 50S ribosome in complex with RRF, EF-G and fusidic acid (50S-RRF-EF-G-FA)
• Map data: Sharpened map using phenix.auto_sharpen with local sharpening providing the half maps

Sample

• Complex: S. aureus 50S ribosome in complex with ribosome recycling factor (RRF) and Elongation factor G (EF-G)
  • Protein or peptide: x 30 types
  • RNA: x 2 types
• Ligand: x 4 types

• Keywords: RRF / EF-G / Ribosome / Recycling

Function / homology

Function:

ribosome disassembly / ribosomal large subunit binding / translation elongation factor activity / translational termination / large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / GTPase activity / GTP binding / RNA binding / cytoplasm

Domain/homology:

Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Ribosomal protein L31 type B / Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / : / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / : / Ribosomal protein L20 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / Ribosomal protein L16 / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / : / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L34

Component:

Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / 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 bL31B / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL33A / Ribosome-recycling factor / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Elongation factor G / Large ribosomal subunit protein bL25

• Biological species: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Method: single particle reconstruction / cryo EM / Resolution: 2.18 Å
• Authors: Gonzalez-Lopez A / Selmer M

Funding support

Sweden, 3 items

Organization	Grant number	Country
Sven och Lilly Lawskis fond for naturvetenskaplig forskning		Sweden
Uppsala Antibiotic Center		Sweden
Swedish Research Council	2022-04511	Sweden

• Citation: Journal: To Be Published; Title: Structural mechanism of ribosome recycling inhibited by fusidic acid; Authors: Gonzalez-Lopez A / Larsson DSD / Selmer M

History

Deposition	Dec 5, 2025	-
Header (metadata) release	Jul 22, 2026	-
Map release	Jul 22, 2026	-
Update	Jul 22, 2026	-
Current status	Jul 22, 2026	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_55947.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Sharpened map using phenix.auto_sharpen with local sharpening providing the half maps
• Voxel size: X=Y=Z: 0.672 Å

Density

Contour Level	By AUTHOR: 2.4
Minimum - Maximum	-18.545522999999999 - 43.008740000000003
Average (Standard dev.)	-0.0027983552 (±0.9266852)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order Z Y X Origin 0 0 0 Dimensions 600 600 600 Spacing 600 600 600
Cell	A=B=C: 403.19998 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_55947_msk_1.map

Mask #2

• File: emd_55947_msk_2.map

Mask #3

• File: emd_55947_msk_3.map

Mask #4

• File: emd_55947_msk_4.map

Additional map: Raw map out of the refinement

• File: emd_55947_additional_1.map
• Annotation: Raw map out of the refinement

Half map: Half map A

• File: emd_55947_half_map_1.map
• Annotation: Half map A

Half map: Half map B

• File: emd_55947_half_map_2.map
• Annotation: Half map B

Sample components

Entire : S. aureus 50S ribosome in complex with ribosome recycling factor ...

• Entire: Name: S. aureus 50S ribosome in complex with ribosome recycling factor (RRF) and Elongation factor G (EF-G)

Components

• Complex: S. aureus 50S ribosome in complex with ribosome recycling factor (RRF) and Elongation factor G (EF-G)
  • 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 L31 type B
  • Protein or peptide: Large ribosomal subunit protein bL32
  • Protein or peptide: Large ribosomal subunit protein bL33A
  • Protein or peptide: 50S ribosomal protein L34
  • Protein or peptide: 50S ribosomal protein L35
  • Protein or peptide: 50S ribosomal protein L36
  • RNA: 23S rRNA
  • RNA: 5S rRNA
  • Protein or peptide: Ribosome-recycling factor
  • Protein or peptide: Elongation factor G
  • 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: Large ribosomal subunit protein uL6
  • 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
• Ligand: ZINC ION
• Ligand: MAGNESIUM ION
• Ligand: GUANOSINE-5'-DIPHOSPHATE
• Ligand: FUSIDIC ACID

Supramolecule #1: S. aureus 50S ribosome in complex with ribosome recycling factor ...

• Supramolecule: Name: S. aureus 50S ribosome in complex with ribosome recycling factor (RRF) and Elongation factor G (EF-G); type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#32
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 2.3 MDa

Macromolecule #1: 50S ribosomal protein L28

• Macromolecule: Name: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 6.995289 KDa

Sequence

String:

MGKQCFVTGR KASTGNRRSH ALNSTKRRWN ANLQKVRILV DGKPKKVWVS ARALKSGKVT RV

UniProtKB: Large ribosomal subunit protein bL28

Macromolecule #2: 50S ribosomal protein L29

• Macromolecule: Name: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 8.105266 KDa

Sequence

String:

MKAKEIRDLT TSEIEEQIKS SKEELFNLRF QLATGQLEET ARIRTVRKTI ARLKTVARER EIEQSKANQ

UniProtKB: Large ribosomal subunit protein uL29

Macromolecule #3: 50S ribosomal protein L30

• Macromolecule: Name: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 6.565683 KDa

Sequence

String:

MAKLQITLTR SVIGRPETQR KTVEALGLKK TNSSVVVEDN PAIRGQINKV KHLVTVEEK

UniProtKB: Large ribosomal subunit protein uL30

Macromolecule #4: 50S ribosomal protein L31 type B

• Macromolecule: Name: 50S ribosomal protein L31 type B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 9.737912 KDa

Sequence

String:

MKQGIHPEYH QVIFLDTTTN FKFLSGSTKT SSEMMEWEDG KEYPVIRLDI SSDSHPFYTG RQKFAAADGR VERFNKKFGL KSNN

UniProtKB: Large ribosomal subunit protein bL31B

Macromolecule #5: Large ribosomal subunit protein bL32

• Macromolecule: Name: Large ribosomal subunit protein bL32 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 6.500609 KDa

Sequence

String:

MAVPKRRTSK TRKNKRRTHF KISVPGMTEC PNCGEYKLSH RVCKNCGSYN GEEVAAK

UniProtKB: Large ribosomal subunit protein bL32

Macromolecule #6: Large ribosomal subunit protein bL33A

• Macromolecule: Name: Large ribosomal subunit protein bL33A / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 5.944937 KDa

Sequence

String:

MRVNVTLACT ECGDRNYITT KNKRNNPERI EMKKYCPRLN KYTLHRETK

UniProtKB: Large ribosomal subunit protein bL33A

Macromolecule #7: 50S ribosomal protein L34

• Macromolecule: Name: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 5.454642 KDa

Sequence

String:

MVKRTYQPNK RKHSKVHGFR KRMSTKNGRK VLARRRRKGR KVLSA

UniProtKB: Large ribosomal subunit protein bL34

Macromolecule #8: 50S ribosomal protein L35

• Macromolecule: Name: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 7.722368 KDa

Sequence

String:

MPKMKTHRGA AKRVKRTASG QLKRSRAFTS HLFANKSTKQ KRQLRKARLV SKSDMKRVKQ LLAYKK

UniProtKB: Large ribosomal subunit protein bL35

Macromolecule #9: 50S ribosomal protein L36

• Macromolecule: Name: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 4.318422 KDa

Sequence

String:

MKVRPSVKPI CEKCKVIKRK GKVMVICENP KHKQRQG

UniProtKB: Large ribosomal subunit protein bL36

Macromolecule #12: Ribosome-recycling factor

• Macromolecule: Name: Ribosome-recycling factor / 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: 20.576188 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

String:

GHMSDIINET KSRMQKSIES LSRELANISA GRANSNLLNG VTVDYYGAPT PVQQLASINV PEARLLVISP YDKTSVADIE KAIIAANLG VNPTSDGEVI RIAVPALTEE RRKERVKDVK KIGEEAKVSV RNIRRDMNDQ LKKDEKNGDI TEDELRSGTE D VQKATDNS IKEIDQMIAD KEKDIMSV

UniProtKB: Ribosome-recycling factor

Macromolecule #13: Elongation factor G

• Macromolecule: Name: Elongation factor G / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 76.699289 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

String:

MAREFSLEKT RNIGIMAHID AGKTTTTERI LYYTGRIHKI GETHEGASQM DWMEQEQDRG ITITSAATTA AWEGHRVNII DTPGHVDFT VEVERSLRVL DGAVTVLDAQ SGVEPQTETV WRQATTYGVP RIVFVNKMDK LGANFEYSVS TLHDRLQANA A PIQLPIGA EDEFEAIIDL VEMKCFKYTN DLGTEIEEIE IPEDHLDRAE EARASLIEAV AETSDELMEK YLGDEEISVS EL KEAIRQA TTNVEFYPVL CGTAFKNKGV QLMLDAVIDY LPSPLDVKPI IGHRASNPEE EVIAKADDSA EFAALAFKVM TDP YVGKLT FFRVYSGTMT SGSYVKNSTK GKRERVGRLL QMHANSRQEI DTVYSGDIAA AVGLKDTGTG DTLCGEKNDI ILES MEFPE PVIHLSVEPK SKADQDKMTQ ALVKLQEEDP TFHAHTDEET GQVIIGGMGE LHLDILVDRM KKEFNVECNV GAPMV SYRE TFKSSAQVQG KFSRQSGGRG QYGDVHIEFT PNETGAGFEF ENAIVGGVVP REYIPSVEAG LKDAMENGVL AGYPLI DVK AKLYDGSYHD VDSSEMAFKI AASLALKEAA KKCDPVILEP MMKVTIEMPE EYMGDIMGDV TSRRGRVDGM EPRGNAQ VV NAYVPLSEMF GYATSLRSNT QGRGTYTMYF DHYAEVPKSI AEDIIKKNKG E

UniProtKB: Elongation factor G

Macromolecule #14: 50S ribosomal protein L2

• Macromolecule: Name: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 30.217164 KDa

Sequence

String:

MAIKKYKPIT NGRRNMTSLD FAEITKTTPE KSLLKPLPKK AGRNNQGKLT VRHHGGGHKR QYRVIDFKRN KDGINAKVDS IQYDPNRSA NIALVVYADG EKRYIIAPKG LEVGQIVESG AEADIKVGNA LPLQNIPVGT VVHNIELKPG KGGQIARSAG A SAQVLGKE GKYVLIRLRS GEVRMILSTC RATIGQVGNL QHELVNVGKA GRSRWKGIRP TVRGSVMNPN DHPHGGGEGR AP IGRPSPM SPWGKPTLGK KTRRGKKSSD KLIVRGRKKK

UniProtKB: Large ribosomal subunit protein uL2

Macromolecule #15: 50S ribosomal protein L3

• Macromolecule: Name: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 23.760256 KDa

Sequence

String:

MTKGILGRKI GMTQVFGENG ELIPVTVVEA KENVVLQKKT VEVDGYNAIQ VGFEDKKAYK KDAKSNKYAN KPAEGHAKKA DAAPKRFIR EFRNVDVDAY EVGQEVSVDT FVAGDVIDVT GVSKGKGFQG AIKRHGQSRG PMSHGSHFHR APGSVGMASD A SRVFKGQK MPGRMGGNTV TVQNLEVVQV DTENKVILVK GNVPGPKKGL VEIRTSIKKG NK

UniProtKB: Large ribosomal subunit protein uL3

Macromolecule #16: 50S ribosomal protein L4

• Macromolecule: Name: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 22.495697 KDa

Sequence

String:

MANYDVLKLD GTKSGSIELS DAVFGIEPNN SVLFEAINLQ RASLRQGTHA VKNRSAVSGG GRKPWKQKGT GRARQGTIRA PQWRGGGIV FGPTPRSYAY KMPKKMRRLA LRSALSFKAQ ENGLTVVDAF NFEAPKTKEF KNVLSTLEQP KKVLVVTENE D VNVELSAR NIPGVQVTTA QGLNVLDITN ADSLVITEAA AKKVEEVLG

UniProtKB: Large ribosomal subunit protein uL4

Macromolecule #17: 50S ribosomal protein L5

• Macromolecule: Name: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 20.296637 KDa

Sequence

String:

MNRLKEKFNT EVTENLMKKF NYSSVMEVPK IDKIVVNMGV GDAVQNSKVL DNAVEELELI TGQKPLVTKA KKSIATFRLR EGMPIGAKV TLRGERMYEF LDKLISVSLP RVRDFQGVSK KAFDGRGNYT LGVKEQLIFP EIDYDKVSKV RGMDIVIVTT A NTDEEARE LLANFGMPFR K

UniProtKB: Large ribosomal subunit protein uL5

Macromolecule #18: Large ribosomal subunit protein uL6

• Macromolecule: Name: Large ribosomal subunit protein uL6 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 19.81858 KDa

Sequence

String:

MSRVGKKIID IPSDVTVTFD GNHVTVKGPK GELSRTLNER MTFKQEENTI EVVRPSDSKE DRTNHGTTRA LLNNMVQGVS QGYVKVLEL VGVGYRAQMQ GKDLILNVGY SHPVEIKAEE NITFSVEKNT VVKVEGISKE QVGALASNIR SVRPPEPYKG K GIRYQGEY VRRKEGKTGK

UniProtKB: Large ribosomal subunit protein uL6

Macromolecule #19: 50S ribosomal protein L13

• Macromolecule: Name: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 16.359427 KDa

Sequence

String:

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

UniProtKB: Large ribosomal subunit protein uL13

Macromolecule #20: 50S ribosomal protein L14

• Macromolecule: Name: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 13.157342 KDa

Sequence

String:

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

UniProtKB: Large ribosomal subunit protein uL14

Macromolecule #21: 50S ribosomal protein L15

• Macromolecule: Name: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 15.62889 KDa

Sequence

String:

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

UniProtKB: Large ribosomal subunit protein uL15

Macromolecule #22: 50S ribosomal protein L16

• Macromolecule: Name: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 16.274049 KDa

Sequence

String:

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

UniProtKB: Large ribosomal subunit protein uL16

Macromolecule #23: 50S ribosomal protein L17

• Macromolecule: Name: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 13.771773 KDa

Sequence

String:

MGYRKLGRTS DQRKAMLRDL ATSLIISERI ETTEARAKEV RSVVEKLITL GKKGDLASRR NAAKTLRNVE ILNEDETTQT ALQKLFGEI AERYTERQGG YTRILKQGPR RGDGAESVII ELV

UniProtKB: Large ribosomal subunit protein bL17

Macromolecule #24: 50S ribosomal protein L18

• Macromolecule: Name: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 13.124093 KDa

Sequence

String:

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

UniProtKB: Large ribosomal subunit protein uL18

Macromolecule #25: 50S ribosomal protein L19

• Macromolecule: Name: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 13.392771 KDa

Sequence

String:

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

UniProtKB: Large ribosomal subunit protein bL19

Macromolecule #26: 50S ribosomal protein L20

• Macromolecule: Name: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 13.720295 KDa

Sequence

String:

MPRVKGGTVT RARRKKTIKL AKGYFGSKHT LYKVAKQQVM KSGQYAFRDR RQRKRDFRKL WITRINAAAR QHEMSYSRLM NGLKKAGID INRKMLSEIA ISDEKAFAQL VTKAKDALK

UniProtKB: Large ribosomal subunit protein bL20

Macromolecule #27: 50S ribosomal protein L21

• Macromolecule: Name: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 11.354081 KDa

Sequence

String:

MFAIIETGGK QIKVEEGQEI FVEKLDVNEG DTFTFDKVLF VGGDSVKVGA PTVEGATVTA TVNKQGRGKK ITVFTYKRRK NSKRKKGHR QPYTKLTIDK INA

UniProtKB: Large ribosomal subunit protein bL21

Macromolecule #28: 50S ribosomal protein L22

• Macromolecule: Name: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 12.857922 KDa

Sequence

String:

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

UniProtKB: Large ribosomal subunit protein uL22

Macromolecule #29: 50S ribosomal protein L23

• Macromolecule: Name: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 10.625398 KDa

Sequence

String:

MEARDILKRP VITEKSSEAM AEDKYTFDVD TRVNKTQVKM AVEEIFNVKV ASVNIMNYKP KKKRMGRYQG YTNKRRKAIV TLKEGSIDL FN

UniProtKB: Large ribosomal subunit protein uL23

Macromolecule #30: 50S ribosomal protein L24

• Macromolecule: Name: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 11.561504 KDa

Sequence

String:

MHIKKGDNVK VIAGKDKGKE GKVIATLPKK DRVVVEGVNI MKKHQKPTQL NPEGGILETE AAIHVSNVQL LDPKTNEPTR VGYKFVDGK KVRIAKKSGE EIKSNN

UniProtKB: Large ribosomal subunit protein uL24

Macromolecule #31: 50S ribosomal protein L25

• Macromolecule: Name: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 23.810609 KDa

Sequence

String:

MASLKSIIRQ GKQTRSDLKQ LRKSGKVPAV VYGYGTKNVS VKVDEVEFIK VIREVGRNGV IELGVGSKTI KVMVADYQFD PLKNQITHI DFLAINMSEE RTVEVPVQLV GEAVGAKEGG VVEQPLFNLE VTATPDNIPE AIEVDITELN INDSLTVADV K VTGDFKIE NDSAESVVTV VAPTEEPTEE EIEAMEGEQQ TEEPEVVGES KEDEEKTEE

UniProtKB: Large ribosomal subunit protein bL25

Macromolecule #32: 50S ribosomal protein L27

• Macromolecule: Name: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 10.334798 KDa

Sequence

String:

MLKLNLQFFA SKKGVSSTKN GRDSESKRLG AKRADGQFVT GGSILYRQRG TKIYPGENVG RGGDDTLFAK IDGVVKFERK GRDKKQVSV YAVAE

UniProtKB: Large ribosomal subunit protein bL27

Macromolecule #10: 23S rRNA

• Macromolecule: Name: 23S rRNA / type: rna / ID: 10 / Number of copies: 1
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 946.811688 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 GUAAC(3TD)AUAA CGGUCCUAAG GUAGCGAAA(5MU) UCCUUGUCGG GUAAGUUCCG AC CCGCACG AAAGGCGUAA CGAUUUGGGC ACUGUCUCAA CGAGAGACUC GGUGAAAUCA UAGUACCUGU GAAGAUGCAG GUU ACCCGC GACAGGACGG AAAGACCCCG UGGAGCUUUA CUGUAGCCUG AUAUUGAAAU UCGGCACAGC UUGUACAGGA UAGG UAGGA GCCUUUGAAA CGUGAGCGCU AGCUUACGUG GAGGCGCUGG UGGGAUACUA CCCUAGCUGU GUUGGCUUUC UAACC CGCA CCACUUAUCG UGGUGGGAGA CAGUGUCAGG CGGGCAGUUU GACUG(OMG)GGCG GUCGCCUCCU AAAAGGUAAC GG AGGCGCU CAAAGGUUCC CUCAGAAUGG UUGGAAAUCA UUCAUAGAGU GUAAAGGCAU AAGGGAGCUU GACUGCGAGA CCU ACAAGU CGAGCAGGGU CGAAAGACGG ACUUAGUGAU CCGGUGGUUC CGCAUGGAAG GGCCAUCGCU CAACGGAUAA AAGC UACCC CG(2MG)GGA(H2U)AAC AGGCUUAUCU CCCCCAAGAG UUCACAUCGA CGGGGAGGUU UGGCACCUCG (2MA)UG UCGGCU CAUCGCAUCC UGGGGCUGUA GUCGGUCCCA AGGGUUGGGC U(OMG)UUCGCCCA UUAAAGCGGU AC(G7M)CGA GCU GGGUUCAGAA CGUCGUGAGA CAGUUCGGUC CCUAUCCGUC GUGGGCGUAG GAAAUUUGAG AGGAGCUGUC CUUAGUA CG AGAGGACCGG GAUGGACAUA CCUCUGGUGU ACCAGUUGUC GUGCCAACGG CAUAGCUGGG UAGCUAUGUG UGGACGGG A UAAGUGCUGA AAGCAUCUAA GCAUGAAGCC CCCCUCAAGA UGAGAUUUCC CAACUUCGGU UAUAAGAUCC CUCAAAGAU GAUGAGGUUA AUAGGUUCGA GGUGGAAGCA UGGUGACAUG UGGAGCUGAC GAAUACUAAU CGAUCGAAGA CUUAAUCAA

Macromolecule #11: 5S rRNA

• Macromolecule: Name: 5S rRNA / type: rna / ID: 11 / Number of copies: 1
• Source (natural): Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
• Molecular weight: Theoretical: 36.974945 KDa

Sequence

String:

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

GENBANK: GENBANK: CP000253.1

Macromolecule #33: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 33 / Number of copies: 2 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Macromolecule #34: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 34 / Number of copies: 115 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Macromolecule #35: GUANOSINE-5'-DIPHOSPHATE

• Macromolecule: Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 35 / Number of copies: 1 / Formula: GDP
• Molecular weight: Theoretical: 443.201 Da

Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

Macromolecule #36: FUSIDIC ACID

• Macromolecule: Name: FUSIDIC ACID / type: ligand / ID: 36 / Number of copies: 1 / Formula: FUA
• Molecular weight: Theoretical: 516.709 Da

Chemical component information

ChemComp-FUA:
FUSIDIC ACID / antibiotic, Antimicrobial*YM

Experimental details

Structure determination

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

Sample preparation

Buffer

pH: 7.5
Component:

Concentration	Formula	Name
20.0 mM	C8H18N2O4S-KOH	HEPES-KOH
95.0 mM	KCl	Potassium chloride
5.0 mM	NH4Cl	Ammonium chloride
5.0 mM	Mg(OAc)2	Magnesium acetate
0.5 mM	CaCl2	Calcium chloride
8.0 mM	(CH2)4(NH2)2	Putrescine
1.0 mM	C7H19N3	Spermidine
5.0 mM	C2H6OS	Beta-mercaptoethanol

• Grid: Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

Electron microscopy

• Microscope: TFS KRIOS
• Specialist optics: Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 56478 / Average exposure time: 0.45 sec. / Average electron dose: 30.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 165000
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 2556350
• CTF correction: Software - Name: cryoSPARC (ver. 4.7.1-cuda12+250814) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• Startup model: Type of model: NONE
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 2.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1-cuda12+250814) / Number images used: 77333
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1-cuda12+250814)
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1-cuda12+250814)
• Final 3D classification: Software - Name: cryoSPARC (ver. 4.7.1-cuda12+250814)

Atomic model buiding 1

Initial model

PDB ID	Chain	Details
9ghg	source_name: PDB, initial_model_type: experimental model
	source_name: AlphaFold, initial_model_type: in silico model	chain C

Output model

PDB-9ti8:
Staphylococcus aureus 50S ribosome in complex with RRF, EF-G and fusidic acid (50S-RRF-EF-G-FA)