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- PDB-8g2d: Crystal structure of the wild-type Thermus thermophilus 70S ribos... -

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Basic information

Entry
Database: PDB / ID: 8g2d
TitleCrystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with tylosin, mRNA, deacylated A- and E-site tRNAphe, and deacylated P-site tRNAmet at 2.70A resolution
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S Ribosomal RNA
  • 23S Ribosomal RNA
  • 5S Ribosomal RNA
  • A-site and E-site Deacylated tRNAphe
  • MF-mRNA
  • P-site Deacylated tRNAmet
KeywordsRIBOSOME / CFR / methyltransferase / multidrug / antibiotic / resistance / methylation / A2503 / 23S rRNA / 70S ribosome / inhibition of translation / peptidyl transferase center / nascent peptide exit tunnel / iboxamycin / tylosin
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 type A ...30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / 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 S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S14/S29 / Ribosomal protein S6 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein L28/L24 / Ribosomal protein S18 signature. / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / : / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein L27 / Ribosomal protein S6 superfamily / Ribosomal L27 protein / Ribosomal protein S12, bacterial-type / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19
Similarity search - Domain/homology
: / IRON/SULFUR CLUSTER / TYLOSIN / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) ...: / IRON/SULFUR CLUSTER / TYLOSIN / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Thermus thermophilus HB8 (bacteria)
Escherichia phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAleksandrova, E.V. / Wu, K.J.Y. / Tresco, B.I.C. / Syroegin, E.A. / Killeavy, E.E. / Balasanyants, S.M. / Svetlov, M.S. / Gregory, S.T. / Atkinson, G.C. / Myers, A.G. / Polikanov, Y.S.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM132302 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21-AI163466 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI168228 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM094157 United States
National Science Foundation (NSF, United States)MCB-1907273 United States
United States Department of Agriculture (USDA)Hatch Project 1016013 United States
Other governmentUniversity of Illinois Startup Funds
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Structural basis of Cfr-mediated antimicrobial resistance and mechanisms to evade it.
Authors: Aleksandrova, E.V. / Wu, K.J.Y. / Tresco, B.I.C. / Syroegin, E.A. / Killeavy, E.E. / Balasanyants, S.M. / Svetlov, M.S. / Gregory, S.T. / Atkinson, G.C. / Myers, A.G. / Polikanov, Y.S.
History
DepositionFeb 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 10, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 19, 2025Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp_atom.atom_id / _chem_comp_atom.pdbx_aromatic_flag ..._chem_comp_atom.atom_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1A: 23S Ribosomal RNA
1B: 5S Ribosomal RNA
1D: 50S ribosomal protein L2
1E: 50S ribosomal protein L3
1F: 50S ribosomal protein L4
1G: 50S ribosomal protein L5
1H: 50S ribosomal protein L6
1I: 50S ribosomal protein L9
1N: 50S ribosomal protein L13
1O: 50S ribosomal protein L14
1P: 50S ribosomal protein L15
1Q: 50S ribosomal protein L16
1R: 50S ribosomal protein L17
1S: 50S ribosomal protein L18
1T: 50S ribosomal protein L19
1U: 50S ribosomal protein L20
1V: 50S ribosomal protein L21
1W: 50S ribosomal protein L22
1X: 50S ribosomal protein L23
1Y: 50S ribosomal protein L24
1Z: 50S ribosomal protein L25
10: 50S ribosomal protein L27
11: 50S ribosomal protein L28
12: 50S ribosomal protein L29
13: 50S ribosomal protein L30
14: 50S ribosomal protein L31
15: 50S ribosomal protein L32
16: 50S ribosomal protein L33
17: 50S ribosomal protein L34
18: 50S ribosomal protein L35
19: 50S ribosomal protein L36
1a: 16S Ribosomal RNA
1b: 30S ribosomal protein S2
1c: 30S ribosomal protein S3
1d: 30S ribosomal protein S4
1e: 30S ribosomal protein S5
1f: 30S ribosomal protein S6
1g: 30S ribosomal protein S7
1h: 30S ribosomal protein S8
1i: 30S ribosomal protein S9
1j: 30S ribosomal protein S10
1k: 30S ribosomal protein S11
1l: 30S ribosomal protein S12
1m: 30S ribosomal protein S13
1n: 30S ribosomal protein S14 type Z
1o: 30S ribosomal protein S15
1p: 30S ribosomal protein S16
1q: 30S ribosomal protein S17
1r: 30S ribosomal protein S18
1s: 30S ribosomal protein S19
1t: 30S ribosomal protein S20
1u: 30S ribosomal protein Thx
1v: MF-mRNA
1w: A-site and E-site Deacylated tRNAphe
1x: P-site Deacylated tRNAmet
1y: A-site and E-site Deacylated tRNAphe
2A: 23S Ribosomal RNA
2B: 5S Ribosomal RNA
2D: 50S ribosomal protein L2
2E: 50S ribosomal protein L3
2F: 50S ribosomal protein L4
2G: 50S ribosomal protein L5
2H: 50S ribosomal protein L6
2I: 50S ribosomal protein L9
2N: 50S ribosomal protein L13
2O: 50S ribosomal protein L14
2P: 50S ribosomal protein L15
2Q: 50S ribosomal protein L16
2R: 50S ribosomal protein L17
2S: 50S ribosomal protein L18
2T: 50S ribosomal protein L19
2U: 50S ribosomal protein L20
2V: 50S ribosomal protein L21
2W: 50S ribosomal protein L22
2X: 50S ribosomal protein L23
2Y: 50S ribosomal protein L24
2Z: 50S ribosomal protein L25
20: 50S ribosomal protein L27
21: 50S ribosomal protein L28
22: 50S ribosomal protein L29
23: 50S ribosomal protein L30
24: 50S ribosomal protein L31
25: 50S ribosomal protein L32
26: 50S ribosomal protein L33
27: 50S ribosomal protein L34
28: 50S ribosomal protein L35
29: 50S ribosomal protein L36
2a: 16S Ribosomal RNA
2b: 30S ribosomal protein S2
2c: 30S ribosomal protein S3
2d: 30S ribosomal protein S4
2e: 30S ribosomal protein S5
2f: 30S ribosomal protein S6
2g: 30S ribosomal protein S7
2h: 30S ribosomal protein S8
2i: 30S ribosomal protein S9
2j: 30S ribosomal protein S10
2k: 30S ribosomal protein S11
2l: 30S ribosomal protein S12
2m: 30S ribosomal protein S13
2n: 30S ribosomal protein S14 type Z
2o: 30S ribosomal protein S15
2p: 30S ribosomal protein S16
2q: 30S ribosomal protein S17
2r: 30S ribosomal protein S18
2s: 30S ribosomal protein S19
2t: 30S ribosomal protein S20
2u: 30S ribosomal protein Thx
2v: MF-mRNA
2w: A-site and E-site Deacylated tRNAphe
2x: P-site Deacylated tRNAmet
2y: A-site and E-site Deacylated tRNAphe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,572,0272919
Polymers4,500,842112
Non-polymers71,1852807
Water71,3753962
1
1A: 23S Ribosomal RNA
1B: 5S Ribosomal RNA
1D: 50S ribosomal protein L2
1E: 50S ribosomal protein L3
1F: 50S ribosomal protein L4
1G: 50S ribosomal protein L5
1H: 50S ribosomal protein L6
1I: 50S ribosomal protein L9
1N: 50S ribosomal protein L13
1O: 50S ribosomal protein L14
1P: 50S ribosomal protein L15
1Q: 50S ribosomal protein L16
1R: 50S ribosomal protein L17
1S: 50S ribosomal protein L18
1T: 50S ribosomal protein L19
1U: 50S ribosomal protein L20
1V: 50S ribosomal protein L21
1W: 50S ribosomal protein L22
1X: 50S ribosomal protein L23
1Y: 50S ribosomal protein L24
1Z: 50S ribosomal protein L25
10: 50S ribosomal protein L27
11: 50S ribosomal protein L28
12: 50S ribosomal protein L29
13: 50S ribosomal protein L30
14: 50S ribosomal protein L31
15: 50S ribosomal protein L32
16: 50S ribosomal protein L33
17: 50S ribosomal protein L34
18: 50S ribosomal protein L35
19: 50S ribosomal protein L36
1a: 16S Ribosomal RNA
1b: 30S ribosomal protein S2
1c: 30S ribosomal protein S3
1d: 30S ribosomal protein S4
1e: 30S ribosomal protein S5
1f: 30S ribosomal protein S6
1g: 30S ribosomal protein S7
1h: 30S ribosomal protein S8
1i: 30S ribosomal protein S9
1j: 30S ribosomal protein S10
1k: 30S ribosomal protein S11
1l: 30S ribosomal protein S12
1m: 30S ribosomal protein S13
1n: 30S ribosomal protein S14 type Z
1o: 30S ribosomal protein S15
1p: 30S ribosomal protein S16
1q: 30S ribosomal protein S17
1r: 30S ribosomal protein S18
1s: 30S ribosomal protein S19
1t: 30S ribosomal protein S20
1u: 30S ribosomal protein Thx
1v: MF-mRNA
1w: A-site and E-site Deacylated tRNAphe
1x: P-site Deacylated tRNAmet
1y: A-site and E-site Deacylated tRNAphe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,289,8901619
Polymers2,250,42156
Non-polymers39,4691563
Water82946
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
2A: 23S Ribosomal RNA
2B: 5S Ribosomal RNA
2D: 50S ribosomal protein L2
2E: 50S ribosomal protein L3
2F: 50S ribosomal protein L4
2G: 50S ribosomal protein L5
2H: 50S ribosomal protein L6
2I: 50S ribosomal protein L9
2N: 50S ribosomal protein L13
2O: 50S ribosomal protein L14
2P: 50S ribosomal protein L15
2Q: 50S ribosomal protein L16
2R: 50S ribosomal protein L17
2S: 50S ribosomal protein L18
2T: 50S ribosomal protein L19
2U: 50S ribosomal protein L20
2V: 50S ribosomal protein L21
2W: 50S ribosomal protein L22
2X: 50S ribosomal protein L23
2Y: 50S ribosomal protein L24
2Z: 50S ribosomal protein L25
20: 50S ribosomal protein L27
21: 50S ribosomal protein L28
22: 50S ribosomal protein L29
23: 50S ribosomal protein L30
24: 50S ribosomal protein L31
25: 50S ribosomal protein L32
26: 50S ribosomal protein L33
27: 50S ribosomal protein L34
28: 50S ribosomal protein L35
29: 50S ribosomal protein L36
2a: 16S Ribosomal RNA
2b: 30S ribosomal protein S2
2c: 30S ribosomal protein S3
2d: 30S ribosomal protein S4
2e: 30S ribosomal protein S5
2f: 30S ribosomal protein S6
2g: 30S ribosomal protein S7
2h: 30S ribosomal protein S8
2i: 30S ribosomal protein S9
2j: 30S ribosomal protein S10
2k: 30S ribosomal protein S11
2l: 30S ribosomal protein S12
2m: 30S ribosomal protein S13
2n: 30S ribosomal protein S14 type Z
2o: 30S ribosomal protein S15
2p: 30S ribosomal protein S16
2q: 30S ribosomal protein S17
2r: 30S ribosomal protein S18
2s: 30S ribosomal protein S19
2t: 30S ribosomal protein S20
2u: 30S ribosomal protein Thx
2v: MF-mRNA
2w: A-site and E-site Deacylated tRNAphe
2x: P-site Deacylated tRNAmet
2y: A-site and E-site Deacylated tRNAphe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,282,1371300
Polymers2,250,42156
Non-polymers31,7161244
Water70339
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.360, 449.770, 616.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 6 types, 14 molecules 1A2A1B2B1a2a1v2v1w1y2w2y1x2x

#1: RNA chain 23S Ribosomal RNA


Mass: 948021.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#2: RNA chain 5S Ribosomal RNA


Mass: 39188.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: AP008226.1
#32: RNA chain 16S Ribosomal RNA


Mass: 493863.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#53: RNA chain MF-mRNA


Mass: 7804.735 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic 24-nt M-F-Stop mRNA / Source: (synth.) Escherichia phage T4 (virus)
#54: RNA chain
A-site and E-site Deacylated tRNAphe


Mass: 24644.873 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Deacylated phenylalanine-specific tRNAphe / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE-600 / Production host: Escherichia coli (E. coli) / Strain (production host): MRE-600 / References: GenBank: 1850831943
#55: RNA chain P-site Deacylated tRNAmet


Mass: 24846.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Deacylated initiator tRNAmet / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE-600 / Production host: Escherichia coli (E. coli) / Strain (production host): MRE-600 / References: GenBank: 732678099

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50S ribosomal protein ... , 29 types, 58 molecules 1D2D1E2E1F2F1G2G1H2H1I2I1N2N1O2O1P2P1Q2Q1R2R1S2S1T2T1U2U1V2V...

#3: Protein 50S ribosomal protein L2


Mass: 30532.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60405
#4: Protein 50S ribosomal protein L3


Mass: 22450.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN8
#5: Protein 50S ribosomal protein L4 / L1e


Mass: 23271.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN9
#6: Protein 50S ribosomal protein L5


Mass: 21061.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ0
#7: Protein 50S ribosomal protein L6


Mass: 19568.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P0DOY8
#8: Protein 50S ribosomal protein L9


Mass: 16422.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SLQ1
#9: Protein 50S ribosomal protein L13


Mass: 15927.903 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60488
#10: Protein 50S ribosomal protein L14


Mass: 13323.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP8
#11: Protein 50S ribosomal protein L15


Mass: 16319.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ7
#12: Protein 50S ribosomal protein L16


Mass: 15993.909 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60489
#13: Protein 50S ribosomal protein L17


Mass: 13750.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q9Z9H5
#14: Protein 50S ribosomal protein L18 / TL24


Mass: 12639.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ4
#15: Protein 50S ribosomal protein L19


Mass: 17188.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60490
#16: Protein 50S ribosomal protein L20


Mass: 13779.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60491
#17: Protein 50S ribosomal protein L21


Mass: 11069.153 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60492
#18: Protein 50S ribosomal protein L22


Mass: 12808.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP3
#19: Protein 50S ribosomal protein L23


Mass: 10759.808 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP0
#20: Protein 50S ribosomal protein L24


Mass: 12085.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP9
#21: Protein 50S ribosomal protein L25 / TL5


Mass: 23238.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHZ1
#22: Protein 50S ribosomal protein L27


Mass: 9529.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60493
#23: Protein 50S ribosomal protein L28


Mass: 11004.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60494
#24: Protein 50S ribosomal protein L29


Mass: 8670.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP6
#25: Protein 50S ribosomal protein L30


Mass: 6799.126 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ6
#26: Protein 50S ribosomal protein L31


Mass: 8300.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJE1
#27: Protein 50S ribosomal protein L32


Mass: 6722.050 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80339
#28: Protein 50S ribosomal protein L33


Mass: 6632.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P35871
#29: Protein/peptide 50S ribosomal protein L34


Mass: 6132.449 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80340
#30: Protein 50S ribosomal protein L35


Mass: 7506.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SKU1
#31: Protein/peptide 50S ribosomal protein L36 / Ribosomal protein B


Mass: 4435.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHR2

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30S ribosomal protein ... , 20 types, 40 molecules 1b2b1c2c1d2d1e2e1f2f1g2g1h2h1i2i1j2j1k2k1l2l1m2m1n2n1o2o1p2p...

#33: Protein 30S ribosomal protein S2


Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80371
#34: Protein 30S ribosomal protein S3


Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80372
#35: Protein 30S ribosomal protein S4


Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80373
#36: Protein 30S ribosomal protein S5


Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ5
#37: Protein 30S ribosomal protein S6 / TS9


Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SLP8
#38: Protein 30S ribosomal protein S7


Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P17291
#39: Protein 30S ribosomal protein S8


Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P0DOY9
#40: Protein 30S ribosomal protein S9


Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80374
#41: Protein 30S ribosomal protein S10


Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN7
#42: Protein 30S ribosomal protein S11


Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80376
#43: Protein 30S ribosomal protein S12


Mass: 14683.476 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN3
#44: Protein 30S ribosomal protein S13


Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80377
#45: Protein 30S ribosomal protein S14 type Z


Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P0DOY6
#46: Protein 30S ribosomal protein S15


Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJ76
#47: Protein 30S ribosomal protein S16


Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJH3
#48: Protein 30S ribosomal protein S17


Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P0DOY7
#49: Protein 30S ribosomal protein S18


Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SLQ0
#50: Protein 30S ribosomal protein S19


Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP2
#51: Protein 30S ribosomal protein S20


Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80380
#52: Protein/peptide 30S ribosomal protein Thx / S31


Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SIH3

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Non-polymers , 6 types, 6769 molecules

#56: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2789 / Source method: obtained synthetically / Formula: Mg
#57: Chemical ChemComp-TYK / TYLOSIN


Mass: 916.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C46H77NO17 / Feature type: SUBJECT OF INVESTIGATION
#58: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#59: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#60: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#61: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3962 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

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Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 62.21 % / Description: Long needles
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.6
Details: 0.1-0.2 M Arginine-HCl, 0.1M Tris-HCl pH 7.6, 2.5% PEG-20K, 7-12% MPD, 0.5 mM BME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 5, 2019 / Details: S/N E-32-0124
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→254.37 Å / Num. obs: 1527540 / % possible obs: 97.2 % / Redundancy: 4.111 % / Biso Wilson estimate: 48.177 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.163 / Rrim(I) all: 0.186 / Χ2: 1.046 / Net I/σ(I): 7.32 / Num. measured all: 6279665 / Scaling rejects: 11286
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.773.5381.1590.993865721158221092670.2051.35694.3
2.77-2.853.60.9211.243904191127781084390.2851.07696.2
2.85-2.933.5010.6861.653638341097261039370.4140.80494.7
2.93-3.024.0330.5222.364194471066731040080.5750.59997.5
3.02-3.124.1120.3863.254164081034221012660.7140.44297.9
3.12-3.234.1520.3014.2540845399962983740.8040.34498.4
3.23-3.354.1870.255.2239917996526953300.8580.28598.8
3.35-3.494.1330.2215.9537816993015914980.8850.25398.4
3.49-3.644.0040.1956.8334574889141863410.9050.22496.9
3.64-3.824.4760.1698.5537939285340847630.9390.19299.3
3.82-4.024.4390.1519.8535772981248805840.9510.17199.2
4.02-4.274.3580.13710.933127176886760170.960.15598.9
4.27-4.564.2060.12112.0529742072249707140.9680.13997.9
4.56-4.934.1580.10813.1326916367361647400.9740.12496.1
4.93-5.44.4930.09814.5927406462143609970.9820.11198.2
5.4-6.044.50.0915.0424697556266548790.9850.10297.5
6.04-6.974.290.08214.7420312349802473480.9870.09395.1
6.97-8.544.6220.06517.0918812742219407010.9920.07396.4
8.54-12.074.6630.04919.4914721932945315740.9960.05595.8
12.07-254.374.5910.04221.997695318594167630.9940.04890.2

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Coot0.8.2model building
PDB_EXTRACT3.28data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XHW

6xhw


Resolution: 2.7→254.37 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2773 76638 5.02 %
Rwork0.2241 1450574 -
obs0.2268 1527212 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.05 Å2 / Biso mean: 53.7852 Å2 / Biso min: 9.9 Å2
Refinement stepCycle: final / Resolution: 2.7→254.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms90996 201989 2947 3969 299901
Biso mean--44.21 36.67 -
Num. residues----20959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004321747
X-RAY DIFFRACTIONf_angle_d0.838481012
X-RAY DIFFRACTIONf_chiral_restr0.04160609
X-RAY DIFFRACTIONf_plane_restr0.00525482
X-RAY DIFFRACTIONf_dihedral_angle_d16.99148834
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.730.390823530.341455664791992
2.73-2.760.377424740.3349476165009096
2.76-2.80.370925710.3198476015017296
2.8-2.830.370725090.3156476485015796
2.83-2.870.360925740.3095471864976095
2.87-2.910.359424900.3078462484873894
2.91-2.950.382324970.3292480055050297
2.95-2.990.364225200.3014483715089198
2.99-3.040.336525640.2795483795094398
3.04-3.090.33825550.27485225107798
3.09-3.140.32125480.2596487195126798
3.14-3.20.314925980.2545488625146099
3.2-3.260.313125330.2523489555148899
3.26-3.330.307425470.2452489985154599
3.33-3.40.295625110.2416490645157599
3.4-3.480.289925810.2364487605134198
3.48-3.570.292325880.2354475445013296
3.57-3.660.283726010.2233488885148998
3.66-3.770.274325800.2168493605194099
3.77-3.890.272725600.2157494185197899
3.89-4.030.264625760.2124493865196299
4.03-4.190.256726650.207492015186699
4.19-4.390.248425800.2027489705155098
4.39-4.620.256226020.2009484375103997
4.62-4.910.246125580.1904479435050196
4.91-5.290.236525670.1833491415170898
5.29-5.820.2326240.1772489425156698
5.82-6.660.22825750.1746485715114697
6.66-8.390.221425800.171479495052995
8.39-254.370.216125570.1865483245088194

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