EMDB-40051: Methyltransferase RmtC bound to the 30S ribosomal subunit

Basic information

Entry

Database: EMDB / ID: EMD-40051

• Title: Methyltransferase RmtC bound to the 30S ribosomal subunit
• Map data: phenix sharpened map

Sample

• Complex: 16S rRNA methyltransferase RmtC bound to the 30S ribosomal subunit
  • Complex: 16S rRNA (guanine(1405)-N(7))-methyltransferase
    • Protein or peptide: x 1 types
  • RNA: x 1 types
  • Protein or peptide: x 13 types
• Ligand: x 1 types

• Keywords: ribosome / 30S / RmtC / 16S rRNA methyltransferase

Function / homology

Function:

16S rRNA (guanine1405-N7)-methyltransferase / rRNA methyltransferase activity / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / membrane / cytoplasm / cytosol

Domain/homology:

Ribosomal RNA aminoglycoside-resistance methyltransferase, Gram-negative bacteria / Ribosomal RNA aminoglycoside-resistance methyltransferase / Ribosomal RNA methyltransferase (FmrO) / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein 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 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. / 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 S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7, conserved site / 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 S5, C-terminal domain / Ribosomal protein S13, conserved site / Ribosomal protein S4/S9 N-terminal domain / 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/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S15 signature. / Ribosomal protein S4/S9 / K homology domain-like, alpha/beta / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal protein S13-like, H2TH / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / S15/NS1, RNA-binding / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Nucleic acid-binding, OB-fold

Component:

Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS5 / 16S rRNA (guanine(1405)-N(7))-methyltransferase / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein bS18

• Biological species: Escherichia coli (E. coli) / Proteus mirabilis (bacteria)
• Method: single particle reconstruction / cryo EM / Resolution: 3.0 Å
• Authors: Srinivas P / Conn GL / Dunham CM

Funding support

United States, 1 items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01AI088025-13	United States

• Citation: Journal: bioRxiv / Year: 2023; Title: 30S subunit recognition and G1405 modification by the aminoglycoside-resistance 16S ribosomal RNA methyltransferase RmtC.; Authors: Pooja Srinivas / Meisam Nosrati / Natalia Zelinskaya / Debayan Dey / Lindsay R Comstock / Christine M Dunham / Graeme L Conn / ; Abstract: Acquired ribosomal RNA (rRNA) methylation has emerged as a significant mechanism of aminoglycoside resistance in pathogenic bacterial infections. Modification of a single nucleotide in the ribosome decoding center by the aminoglycoside-resistance 16S rRNA (m G1405) methyltransferases effectively blocks the action of all 4,6-deoxystreptamine ring-containing aminoglycosides, including the latest generation of drugs. To define the molecular basis of 30S subunit recognition and G1405 modification by these enzymes, we used a S-adenosyl-L-methionine (SAM) analog to trap the complex in a post-catalytic state to enable determination of an overall 3.0 Ã… cryo-electron microscopy structure of the m G1405 methyltransferase RmtC bound to the mature Escherichia coli 30S ribosomal subunit. This structure, together with functional analyses of RmtC variants, identifies the RmtC N-terminal domain as critical for recognition and docking of the enzyme on a conserved 16S rRNA tertiary surface adjacent to G1405 in 16S rRNA helix 44 (h44). To access the G1405 N7 position for modification, a collection of residues across one surface of RmtC, including a loop that undergoes a disorder to order transition upon 30S subunit binding, induces significant distortion of h44. This distortion flips G1405 into the enzyme active site where it is positioned for modification by two almost universally conserved RmtC residues. These studies expand our understanding of ribosome recognition by rRNA modification enzymes and present a more complete structural basis for future development of strategies to inhibit m G1405 modification to re-sensitize bacterial pathogens to aminoglycosides.

History

Deposition	Mar 12, 2023	-
Header (metadata) release	Apr 12, 2023	-
Map release	Apr 12, 2023	-
Update	Jun 19, 2024	-
Current status	Jun 19, 2024	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_40051.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: phenix sharpened map
• Voxel size: X=Y=Z: 0.7984 Å

Density

Contour Level	By AUTHOR: 0.1
Minimum - Maximum	-11.217881999999999 - 26.880155999999999
Average (Standard dev.)	0.000000000000343 (±1.0)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 400 400 400 Spacing 400 400 400
Cell	A=B=C: 319.36 Å α=β=γ: 90.0 °

Supplemental data

Additional map: Relion post processed map

• File: emd_40051_additional_1.map
• Annotation: Relion post processed map

Additional map: 30S body multi body

• File: emd_40051_additional_2.map
• Annotation: 30S body multi body

Additional map: RmtC multibody

• File: emd_40051_additional_3.map
• Annotation: RmtC multibody

Additional map: 30S head multi body

• File: emd_40051_additional_4.map
• Annotation: 30S head multi body

Additional map: multi body map-30S

• File: emd_40051_additional_5.map
• Annotation: multi body map-30S

Additional map: multi body map-h44-rmtc

• File: emd_40051_additional_6.map
• Annotation: multi body map-h44-rmtc

Half map: half map

• File: emd_40051_half_map_1.map
• Annotation: half map

Half map: half map

• File: emd_40051_half_map_2.map
• Annotation: half map

Sample components

Entire : 16S rRNA methyltransferase RmtC bound to the 30S ribosomal subunit

• Entire: Name: 16S rRNA methyltransferase RmtC bound to the 30S ribosomal subunit

Components

• Complex: 16S rRNA methyltransferase RmtC bound to the 30S ribosomal subunit
  • Complex: 16S rRNA (guanine(1405)-N(7))-methyltransferase
    • Protein or peptide: 16S rRNA (guanine(1405)-N(7))-methyltransferase
  • RNA: 16S rRNA
  • 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, non-modified isoform
  • Protein or peptide: 30S ribosomal protein S7
  • Protein or peptide: 30S ribosomal protein S8
  • 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 S20
• Ligand: MAGNESIUM ION

Supramolecule #1: 16S rRNA methyltransferase RmtC bound to the 30S ribosomal subunit

• Supramolecule: Name: 16S rRNA methyltransferase RmtC bound to the 30S ribosomal subunit; type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
• Source (natural): Organism: Escherichia coli (E. coli)

Supramolecule #2: 16S rRNA (guanine(1405)-N(7))-methyltransferase

• Supramolecule: Name: 16S rRNA (guanine(1405)-N(7))-methyltransferase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
• Source (natural): Organism: Proteus mirabilis (bacteria)

Macromolecule #1: 16S rRNA (guanine(1405)-N(7))-methyltransferase

• Macromolecule: Name: 16S rRNA (guanine(1405)-N(7))-methyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 32.146834 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MKTNDNYIEE VTAKVLTSGK YSTLYPPTVR RVTERLFDRY PPKQLEKEVR KKLHQAYGAY IGGIDGKRLE KKIEKIIHEI PNPTTDEAT RTEWEKEICL KILNLHTSTN ERTVAYDELY QKIFEVTGVP TSITDAGCAL NPFSFPFFTE AGMLGQYIGF D LDKGMIEA IEHSLRTLNA PEGIVVKQGD ILSDPSGESD LLLMFKLYTL LDRQEEASGL KILQEWKYKN AVISFPIKTI SG RDVGMEE NYTVKFENDL VGSDLRIMQK LKLGNEMYFI VSRL

UniProtKB: 16S rRNA (guanine(1405)-N(7))-methyltransferase

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 (E. coli)
• Molecular weight: Theoretical: 23.078785 KDa

Sequence

String:

GQKVHPNGIR LGIVKPWNST WFANTKEFAD NLDSDFKVRQ YLTKELAKAS VSRIVIERPA KSIRVTIHTA RPGIVIGKKG EDVEKLRKV VADIAGVPAQ INIAEVRKPE LDAKLVADSI TSQLERRVMF RRAMKRAVQN AMRLGAKGIK VEVSGRLGGA E IARTEWYR EGRVPLHTLR ADIDYNTSEA HTTYGVIGVK VWIFKGEI

UniProtKB: Small ribosomal subunit protein uS3

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 (E. coli)
• Molecular weight: Theoretical: 23.383002 KDa

Sequence

String:

ARYLGPKLKL SRREGTDLFL KSGVRAIDTK CKIEQAPGQH GARKPRLSDY GVQLREKQKV RRIYGVLERQ FRNYYKEAAR LKGNTGENL LALLEGRLDN VVYRMGFGAT RAEARQLVSH KAIMVNGRVV NIASYQVSPN DVVSIREKAK KQSRVKAALE L AEQREKPT WLEVDAGKME GTFKRKPERS DLSADINEHL IVELYSK

UniProtKB: Small ribosomal subunit protein uS4

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 (E. coli)
• Molecular weight: Theoretical: 15.804282 KDa

Sequence

String:

ELQEKLIAVN RVSKTVKGGR IFSFTALTVV GDGNGRVGFG YGKAREVPAA IQKAMEKARR NMINVALNNG TLQHPVKGVH TGSRVFMQP ASEGTGIIAG GAMRAVLEVA GVHNVLAKAY GSTNPINVVR ATIDGLENMN SPEMVAAKRG K

UniProtKB: Small ribosomal subunit protein uS5

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

• Macromolecule: Name: 30S ribosomal protein S6, non-modified isoform / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 11.669371 KDa

Sequence

String:

MRHYEIVFMV HPDQSEQVPG MIERYTAAIT GAEGKIHRLE DWGRRQLAYP INKLHKAHYV LMNVEAPQEV IDELETTFRF NDAVIRSMV MRTKHAVTEA S

UniProtKB: Small ribosomal subunit protein bS6

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 (E. coli)
• Molecular weight: Theoretical: 16.861523 KDa

Sequence

String:

PRRRVIGQRK ILPDPKFGSE LLAKFVNILM VDGKKSTAES IVYSALETLA QRSGKSELEA FEVALENVRP TVEVKSRRVG GSTYQVPVE VRPVRRNALA MRWIVEAARK RGDKSMALRL ANELSDAAEN KGTAVKKRED VHRMAEANKA FA

UniProtKB: Small ribosomal subunit protein uS7

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 (E. coli)
• Molecular weight: Theoretical: 14.015361 KDa

Sequence

String:

SMQDPIADML TRIRNGQAAN KAAVTMPSSK LKVAIANVLK EEGFIEDFKV EGDTKPELEL TLKYFQGKAV VESIQRVSRP GLRIYKRKD ELPKVMAGLG IAVVSTSKGV MTDRAARQAG LGGEIICYVA

UniProtKB: Small ribosomal subunit protein uS8

Macromolecule #9: 30S ribosomal protein S12

• Macromolecule: Name: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 13.636961 KDa

Sequence

String:

ATVNQLVRKP RARKVAKSNV PALEACPQKR GVCTRVYTTT PKKPNSALRK VCRVRLTNGF EVTSYIGGEG HNLQEHSVIL IRGGRVKDL PGVRYHTVRG ALDCSGVKDR KQARSKYGVK RPKA

UniProtKB: Small ribosomal subunit protein uS12

Macromolecule #10: 30S ribosomal protein S13

• Macromolecule: Name: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 10.36013 KDa

Sequence

String:

ARIAGINIPD HKHAVIALTS IYGVGKTRSK AILAAAGIAE DVKIKELSEG QIDTLRDEVA KFVVEGDLRR EISMSIKRLM DLGCYRGLR HRRR

UniProtKB: Small ribosomal subunit protein uS13

Macromolecule #11: 30S ribosomal protein S15

• Macromolecule: Name: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 10.159621 KDa

Sequence

String:

SLSTEATAKI VSEFGRDAND TGSTEVQVAL LTAQINHLQG HFAEHKKDHH SRRGLLRMVS QRRKLLDYLK RKDVARYTQL IERLGLRR

UniProtKB: Small ribosomal subunit protein uS15

Macromolecule #12: 30S ribosomal protein S16

• Macromolecule: Name: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 9.207572 KDa

Sequence

String:

MVTIRLARHG AKKRPFYQVV VADSRNARNG RFIERVGFFN PIASEKEEGT RLDLDRIAHW VGQGATISDR VAALIKEVNK AA

UniProtKB: Small ribosomal subunit protein bS16

Macromolecule #13: 30S ribosomal protein S17

• Macromolecule: Name: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 9.263946 KDa

Sequence

String:

KIRTLQGRVV SDKMEKSIVV AIERFVKHPI YGKFIKRTTK LHVHDENNEC GIGDVVEIRE CRPLSKTKSW TLVRVVEKAV

UniProtKB: Small ribosomal subunit protein uS17

Macromolecule #14: 30S ribosomal protein S18

• Macromolecule: Name: 30S ribosomal protein S18 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 6.466477 KDa

Sequence

String:

EIDYKDIATL KNYITESGKI VPSRITGTRA KYQRQLARAI KRARYLSLLP YTDRH

UniProtKB: Small ribosomal subunit protein bS18

Macromolecule #15: 30S ribosomal protein S20

• Macromolecule: Name: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 9.50619 KDa

Sequence

String:

NIKSAKKRAI QSEKARKHNA SRRSMMRTFI KKVYAAIEAG DKAAAQKAFN EMQPIVDRQA AKGLIHKNKA ARHKANLTAQ INKLA

UniProtKB: Small ribosomal subunit protein bS20

Macromolecule #2: 16S rRNA

• Macromolecule: Name: 16S rRNA / type: rna / ID: 2 / Number of copies: 1
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 496.966562 KDa

Sequence

String:

AAUUGAAGAG UUUGAUCAUG GCUCAGAUUG AACGCUGGCG GCAGGCCUAA CACAUGCAAG UCGAACGGUA ACAGGAAGAA GCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA A ACGGUAGC UAAUACCGCA UAACGUCGCA AGACCAAAGA GGGGGACCUU CGGGCCUCUU GCCAUCGGAU GUGCCCAGAU GG GAUUAGC UAGUAGGUGG GGUAACGGCU CACCUAGGCG ACGAUCCCUA GCUGGUCUGA GAGGAUGACC AGCCACACUG GAA CUGAGA CACGGUCCAG ACUCCUACGG GAGGCAGCAG UGGGGAAUAU UGCACAAUGG GCGCAAGCCU GAUGCAGCCA UGCC GCGUG UAUGAAGAAG GCCUUCGGGU UGUAAAGUAC UUUCAGCGGG GAGGAAGGGA GUAAAGUUAA UACCUUUGCU CAUUG ACGU UACCCGCAGA AGAAGCACCG GCUAACUCCG UGCCAGCAGC CGCGGUAAUA CGGAGGGUGC AAGCGUUAAU CGGAAU UAC UGGGCGUAAA GCGCACGCAG GCGGUUUGUU AAGUCAGAUG UGAAAUCCCC GGGCUCAACC UGGGAACUGC AUCUGAU AC UGGCAAGCUU GAGUCUCGUA GAGGGGGGUA GAAUUCCAGG UGUAGCGGUG AAAUGCGUAG AGAUCUGGAG GAAUACCG G UGGCGAAGGC GGCCCCCUGG ACGAAGACUG ACGCUCAGGU GCGAAAGCGU GGGGAGCAAA CAGGAUUAGA UACCCUGGU AGUCCACGCC GUAAACGAUG UCGACUUGGA GGUUGUGCCC UUGAGGCGUG GCUUCCGGAG CUAACGCGUU AAGUCGACCG CCUGGGGAG UACGGCCGCA AGGUUAAAAC UCAAAUGAAU UGACGGGGGC CCGCACAAGC GGUGGAGCAU GUGGUUUAAU U CGAUGCAA CGCGAAGAAC CUUACCUGGU CUUGACAUCC ACGGAAGUUU UCAGAGAUGA GAAUGUGCCU UCGGGAACCG UG AGACAGG UGCUGCAUGG CUGUCGUCAG CUCGUGUUGU GAAAUGUUGG GUUAAGUCCC GCAACGAGCG CAACCCUUAU CCU UUGUUG CCAGCGGUCC GGCCGGGAAC UCAAAGGAGA CUGCCAGUGA UAAACUGGAG GAAGGUGGGG AUGACGUCAA GUCA UCAUG GCCCUUACGA CCAGGGCUAC ACACGUGCUA CAAUGGCGCA UACAAAGAGA AGCGACCUCG CGAGAGCAAG CGGAC CUCA UAAAGUGCGU CGUAGUCCGG AUUGGAGUCU GCAACUCGAC UCCAUGAAGU CGGAAUCGCU AGUAAUCGUG GAUCAG AAU GCCACGGUGA AUACGUUCCC GGGCCUUGUA CACACAGCCC (ZIV)UCACACCAU GGGAGUGGGU UGCAAAAGAA GUA GGUAGC UUAACCUUCG GGAGGGCGCU UACCACUUUG UGAUUCAUGA CUGGGGUGAA GUCGUAACAA GGUAACCGUA GGGG AACCU GCGGUUGGAU C

Macromolecule #16: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 16 / Number of copies: 83 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Experimental details

Structure determination

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

Sample preparation

• Buffer: pH: 7.6
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Startup model: Type of model: INSILICO MODEL
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 129736
• Initial angle assignment: Type: ANGULAR RECONSTITUTION
• Final angle assignment: Type: ANGULAR RECONSTITUTION