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- PDB-7p7q: E. faecalis 70S ribosome bound by PoxtA-EQ2, high-resolution comb... -

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Basic information

Entry
Database: PDB / ID: 7p7q
TitleE. faecalis 70S ribosome bound by PoxtA-EQ2, high-resolution combined volume
Components
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 28
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • ARE-ABC-F family resistance factor PoxtA
  • fMet-tRNA
  • mRNAMessenger RNA
KeywordsRIBOSOME / Enterococcus faecalis / PoxtA / ABCF / antibiotic resistance protein
Function / homology
Function and homology information


large ribosomal subunit / regulation of translation / small ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation ...large ribosomal subunit / regulation of translation / small ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Ribosomal protein L31 type B / Ribosomal protein L1, bacterial-type / Ribosomal protein S14, type Z / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family ...Ribosomal protein L31 type B / Ribosomal protein L1, bacterial-type / Ribosomal protein S14, type Z / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / 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, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein S14/S29 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / 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 S3, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 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 / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / 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 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / 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 protein S15, bacterial-type / 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 S6 / Ribosomal protein S6
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / 1,4-DIAMINOBUTANE / SPECTINOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL33C ...ADENOSINE-5'-TRIPHOSPHATE / : / 1,4-DIAMINOBUTANE / SPECTINOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL33C / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL31B / Large ribosomal subunit protein bL32C / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL17 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14C / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / 50S ribosomal protein L13
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsCrowe-McAuliffe, C. / Wilson, D.N.
Funding support Germany, Sweden, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)WI3285/8-1 Germany
Swedish Research Council2017-03783 Sweden
Citation
Journal: Nat Commun / Year: 2022
Title: Structural basis for PoxtA-mediated resistance to phenicol and oxazolidinone antibiotics.
Authors: Caillan Crowe-McAuliffe / Victoriia Murina / Kathryn Jane Turnbull / Susanne Huch / Marje Kasari / Hiraku Takada / Lilit Nersisyan / Arnfinn Sundsfjord / Kristin Hegstad / Gemma C Atkinson / ...Authors: Caillan Crowe-McAuliffe / Victoriia Murina / Kathryn Jane Turnbull / Susanne Huch / Marje Kasari / Hiraku Takada / Lilit Nersisyan / Arnfinn Sundsfjord / Kristin Hegstad / Gemma C Atkinson / Vicent Pelechano / Daniel N Wilson / Vasili Hauryliuk /
Abstract: PoxtA and OptrA are ATP binding cassette (ABC) proteins of the F subtype (ABCF). They confer resistance to oxazolidinone and phenicol antibiotics, such as linezolid and chloramphenicol, which stall ...PoxtA and OptrA are ATP binding cassette (ABC) proteins of the F subtype (ABCF). They confer resistance to oxazolidinone and phenicol antibiotics, such as linezolid and chloramphenicol, which stall translating ribosomes when certain amino acids are present at a defined position in the nascent polypeptide chain. These proteins are often encoded on mobile genetic elements, facilitating their rapid spread amongst Gram-positive bacteria, and are thought to confer resistance by binding to the ribosome and dislodging the bound antibiotic. However, the mechanistic basis of this resistance remains unclear. Here we refine the PoxtA spectrum of action, demonstrate alleviation of linezolid-induced context-dependent translational stalling, and present cryo-electron microscopy structures of PoxtA in complex with the Enterococcus faecalis 70S ribosome. PoxtA perturbs the CCA-end of the P-site tRNA, causing it to shift by ∼4 Å out of the ribosome, corresponding to a register shift of approximately one amino acid for an attached nascent polypeptide chain. We postulate that the perturbation of the P-site tRNA by PoxtA thereby alters the conformation of the attached nascent chain to disrupt the drug binding site.
#1: Journal: Biorxiv / Year: 2021
Title: Structural basis for PoxtA-mediated resistance to Phenicol and Oxazolidinone antibiotics
Authors: Crowe-McAuliffe, C. / Murina, V. / Kasari, M. / Takada, H. / Turnbull, K.J. / Sundsfjord, A. / Hegstad, K. / Atkinson, G.C. / Wilson, D.N. / Hauryliuk, V.
#2: Journal: mSphere / Year: 2018
Title: The Enterococcus Cassette Chromosome, a Genomic Variation Enabler in Enterococci.
Authors: A Sivertsen / J Janice / T Pedersen / T M Wagner / J Hegstad / K Hegstad /
Abstract: has a highly variable genome prone to recombination and horizontal gene transfer. Here, we have identified a novel genetic island with an insertion locus and mobilization genes similar to those of ... has a highly variable genome prone to recombination and horizontal gene transfer. Here, we have identified a novel genetic island with an insertion locus and mobilization genes similar to those of staphylococcus cassette chromosome elements SCC This novel element termed the enterococcus cassette chromosome (ECC) element was located in the 3' region of and encoded large serine recombinases similar to SCC Horizontal transfer of an ECC element termed ECC:: containing a knock-in chloramphenicol resistance determinant occurred in the presence of a conjugative plasmid. We determined the ECC:: insertion site in the 3' region of in the recipient by long-read sequencing. ECC:: also mobilized by homologous recombination through sequence identity between flanking insertion sequence (IS) elements in ECC:: and the conjugative plasmid. The genes were found in 69 of 516 genomes in GenBank. Full-length ECC elements were retrieved from 32 of these genomes. ECCs were flanked by and sites of approximately 50 bp. The sequences were found by PCR and sequencing of circularized ECCs in three strains. The genes in ECCs contained an amalgam of common and rare genes. Taken together, our data imply that ECC elements act as hot spots for genetic exchange and contribute to the large variation of accessory genes found in is a bacterium found in a great variety of environments, ranging from the clinic as a nosocomial pathogen to natural habitats such as mammalian intestines, water, and soil. They are known to exchange genetic material through horizontal gene transfer and recombination, leading to great variability of accessory genes and aiding environmental adaptation. Identifying mobile genetic elements causing sequence variation is important to understand how genetic content variation occurs. Here, a novel genetic island, the enterococcus cassette chromosome, is shown to contain a wealth of genes, which may aid in adapting to new environments. The transmission mechanism involves the only two conserved genes within ECC, , large serine recombinases that insert ECC into the host genome similarly to SCC elements found in staphylococci.
History
DepositionJul 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / em_entity_assembly / em_entity_assembly_naturalsource / em_entity_assembly_recombinant / em_imaging / entity_src_gen / entity_src_nat
Item: _em_entity_assembly_recombinant.entity_assembly_id / _em_imaging.nominal_defocus_max ..._em_entity_assembly_recombinant.entity_assembly_id / _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _entity_src_gen.gene_src_common_name / _entity_src_nat.common_name
Revision 2.0Dec 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / citation ...atom_site / citation / em_entity_assembly / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _citation.journal_id_ISSN / _em_entity_assembly.entity_id_list / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 2.1Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
0: ARE-ABC-F family resistance factor PoxtA
1: 50S ribosomal protein L29
2: 50S ribosomal protein L30
3: 50S ribosomal protein L31 type B
4: 50S ribosomal protein L32-3
5: 50S ribosomal protein L33 3
6: 50S ribosomal protein L34
7: 50S ribosomal protein L35
8: 50S ribosomal protein L36
A: 23S rRNA
B: 5S rRNA
D: fMet-tRNA
F: 50S ribosomal protein L1
G: 50S ribosomal protein L2
H: 50S ribosomal protein L3
I: 50S ribosomal protein L4
J: 50S ribosomal protein L5
K: 50S ribosomal protein L6
M: 50S ribosomal protein L13
N: 50S ribosomal protein L14
O: 50S ribosomal protein L15
P: 50S ribosomal protein L16
Q: 50S ribosomal protein L17
R: 50S ribosomal protein L18
S: 50S ribosomal protein L19
T: 50S ribosomal protein L20
U: 50S ribosomal protein L21
V: 50S ribosomal protein L22
W: 50S ribosomal protein L23
X: 50S ribosomal protein L24
Y: 50S ribosomal protein L27
Z: 50S ribosomal protein L28
a: 16S rRNA
b: mRNA
c: 30S ribosomal protein S2
d: 30S ribosomal protein S3
e: 30S ribosomal protein S4
f: 30S ribosomal protein S5
g: 30S ribosomal protein S6
h: 30S ribosomal protein S7
i: 30S ribosomal protein S8
j: 30S ribosomal protein S9
k: 30S ribosomal protein S10
l: 30S ribosomal protein S11
m: 30S ribosomal protein S12
n: 30S ribosomal protein S13
o: 30S ribosomal protein S14 type Z
p: 30S ribosomal protein S15
q: 30S ribosomal protein S16
r: 30S ribosomal protein S17
s: 30S ribosomal protein S18
t: 30S ribosomal protein S19
u: 30S ribosomal protein S20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,244,009412
Polymers2,231,39053
Non-polymers12,619359
Water64,8723601
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 1 molecules 0

#1: Protein ARE-ABC-F family resistance factor PoxtA


Mass: 67890.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: poxtA / Production host: Enterococcus faecalis (bacteria)

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50S ribosomal protein ... , 28 types, 28 molecules 12345678FGHIJKMNOPQRSTUVWXYZ

#2: Protein 50S ribosomal protein L29 /


Mass: 7342.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839F6
#3: Protein 50S ribosomal protein L30 /


Mass: 6365.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839E6
#4: Protein 50S ribosomal protein L31 type B / Ribosome


Mass: 10138.101 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q836E3
#5: Protein 50S ribosomal protein L32-3 / Ribosome


Mass: 6548.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q836R0
#6: Protein/peptide 50S ribosomal protein L33 3 / Ribosome


Mass: 6052.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: P59628
#7: Protein/peptide 50S ribosomal protein L34 /


Mass: 5373.507 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q82YU9
#8: Protein 50S ribosomal protein L35 /


Mass: 7727.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q837C8
#9: Protein/peptide 50S ribosomal protein L36 /


Mass: 4440.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839E1
#13: Protein 50S ribosomal protein L1 /


Mass: 24495.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q830Q6
#14: Protein 50S ribosomal protein L2 /


Mass: 30161.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839G1
#15: Protein 50S ribosomal protein L3 /


Mass: 22758.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839G4
#16: Protein 50S ribosomal protein L4 /


Mass: 22549.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839G3
#17: Protein 50S ribosomal protein L5 /


Mass: 20123.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839F2
#18: Protein 50S ribosomal protein L6 /


Mass: 19437.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839E9
#19: Protein 50S ribosomal protein L13 /


Mass: 16325.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: R3K7G5
#20: Protein 50S ribosomal protein L14 /


Mass: 13165.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839F4
#21: Protein 50S ribosomal protein L15 /


Mass: 15602.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839E5
#22: Protein 50S ribosomal protein L16 /


Mass: 16261.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839F7
#23: Protein 50S ribosomal protein L17 /


Mass: 14503.704 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839D8
#24: Protein 50S ribosomal protein L18 /


Mass: 12937.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839E8
#25: Protein 50S ribosomal protein L19 /


Mass: 13244.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q833P5
#26: Protein 50S ribosomal protein L20 /


Mass: 13674.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q837C7
#27: Protein 50S ribosomal protein L21 /


Mass: 11166.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q836X6
#28: Protein 50S ribosomal protein L22 /


Mass: 12473.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839F9
#29: Protein 50S ribosomal protein L23 /


Mass: 11089.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839G2
#30: Protein 50S ribosomal protein L24 /


Mass: 11137.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839F3
#31: Protein 50S ribosomal protein L27 /


Mass: 10175.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q836X4
#32: Protein 50S ribosomal protein L28 /


Mass: 7005.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q82ZE4

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RNA chain , 5 types, 5 molecules ABDab

#10: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 943422.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria)
#11: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 37433.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: GenBank: CP002621.1
#12: RNA chain fMet-tRNA


Mass: 24811.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria)
#33: RNA chain 16S rRNA /


Mass: 504278.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria)
#34: RNA chain mRNA / Messenger RNA


Mass: 6219.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Sequence unknown. Likely a mix of many different mRNAs.
Source: (natural) Enterococcus faecalis (bacteria)

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30S ribosomal protein ... , 19 types, 19 molecules cdefghijklmnopqrstu

#35: Protein 30S ribosomal protein S2 /


Mass: 29500.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q831U9
#36: Protein 30S ribosomal protein S3 /


Mass: 24415.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839F8
#37: Protein 30S ribosomal protein S4 /


Mass: 23273.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q82ZI6
#38: Protein 30S ribosomal protein S5 /


Mass: 17444.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839E7
#39: Protein 30S ribosomal protein S6 /


Mass: 11621.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839Z0
#40: Protein 30S ribosomal protein S7 /


Mass: 17864.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839H0
#41: Protein 30S ribosomal protein S8 /


Mass: 14936.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839F0
#42: Protein 30S ribosomal protein S9 /


Mass: 14271.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q82Z47
#43: Protein 30S ribosomal protein S10 /


Mass: 11731.739 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839G5
#44: Protein 30S ribosomal protein S11 /


Mass: 13740.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839E0
#45: Protein 30S ribosomal protein S12 /


Mass: 15309.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839H1
#46: Protein 30S ribosomal protein S13 /


Mass: 13595.774 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: P59754
#47: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 7172.593 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839F1
#48: Protein 30S ribosomal protein S15 /


Mass: 10668.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q82ZJ1
#49: Protein 30S ribosomal protein S16 /


Mass: 10356.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q834F9
#50: Protein 30S ribosomal protein S17 /


Mass: 10332.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839F5
#51: Protein 30S ribosomal protein S18 /


Mass: 9262.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839Y8
#52: Protein 30S ribosomal protein S19 /


Mass: 10586.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q839G0
#53: Protein 30S ribosomal protein S20 /


Mass: 8972.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / References: UniProt: Q831Q7

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Non-polymers , 7 types, 3960 molecules

#54: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#55: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 196 / Source method: obtained synthetically / Formula: Mg
#56: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 153 / Source method: obtained synthetically / Formula: K
#57: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#58: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE / Putrescine


Mass: 88.151 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12N2
#59: Chemical ChemComp-SCM / SPECTINOMYCIN / ACTINOSPECTACIN / ESPECTINOMICINA / CHX-3101 / Spectinomycin


Mass: 332.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C14H24N2O7 / Comment: antibiotic*YM
#60: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3601 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Complex of PoxtA-EQ2 bound to the 70S ribosome from E. faecalis (initiation complex), state I.COMPLEXObtained by affinity purification of FLAG-tagged PoxtA.#1-#43, #45-#530MULTIPLE SOURCES
2PoxACOMPLEXARE-ABC-F family resistance factor PoxtA#11RECOMBINANT
370S RibosomeRibosomeRIBOSOME70S ribosome#2-#43, #45-#531NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Enterococcus faecalis (bacteria)1351
33Enterococcus faecalis (bacteria)1351
Source (recombinant)Organism: Enterococcus faecalis (bacteria)
Buffer solutionpH: 9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Grid was prepared by four applications of elution fraction from affinity purification.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 165000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingAverage exposure time: 5 sec. / Electron dose: 30.255 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3639
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

Software
NameVersionClassification
phenix.real_space_refinedev_4373refinement
PHENIXdev_4373refinement
EM software
IDNameVersionCategory
4CTFFINDCTF correction
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 203231
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112877 / Num. of class averages: 2 / Symmetry type: POINT

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