[English] 日本語
Yorodumi
- PDB-5o61: The complete structure of the Mycobacterium smegmatis 70S ribosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o61
TitleThe complete structure of the Mycobacterium smegmatis 70S ribosome
Components
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 31
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • Conserved domain protein
  • LSU ribosomal protein L28P
  • P/P-site Phe-tRNA(Phe)
  • mRNA fragment
KeywordsRIBOSOME / translation
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / 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 / RNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 ...Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 / : / : / Ribosomal protein S14, type Z / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / 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 protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / 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 S14/S29 / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / 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 L36 superfamily / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / 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 L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35
Similarity search - Domain/homology
PHENYLALANINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S6 / Conserved domain protein / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL11 ...PHENYLALANINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S6 / Conserved domain protein / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / 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 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS9 / Uncharacterized protein / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein bS18B / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL15
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsHentschel, J. / Burnside, C. / Mignot, I. / Leibundgut, M. / Boehringer, D. / Ban, N.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_163478 Switzerland
NCCR RNA and disease program, SNSF51NF40_141735 Switzerland
CitationJournal: Cell Rep / Year: 2017
Title: The Complete Structure of the Mycobacterium smegmatis 70S Ribosome.
Authors: Jendrik Hentschel / Chloe Burnside / Ingrid Mignot / Marc Leibundgut / Daniel Boehringer / Nenad Ban /
Abstract: The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death ...The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance. Here, we present the 3.3-Å cryo-EM structure of the 70S ribosome of Mycobacterium smegmatis, a close relative to the human pathogen Mycobacterium tuberculosis. The structure reveals two additional ribosomal proteins and localizes them to the vicinity of drug-target sites in both the catalytic center and the decoding site of the ribosome. Furthermore, we visualized actinobacterium-specific rRNA and protein expansions that extensively remodel the ribosomal surface with implications for polysome organization. Our results provide a foundation for understanding the idiosyncrasies of mycobacterial translation and reveal atomic details of the structure that will facilitate the design of anti-tubercular therapeutics.
History
DepositionJun 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0May 15, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_validate_torsion / struct_conf / struct_conn
Item: _atom_site.auth_seq_id / _database_2.pdbx_DOI ..._atom_site.auth_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_torsion.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_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_asym_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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-3751
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-3751
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
3: 50S ribosomal protein bL37
A: 23S rRNA
B: 5S rRNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
I: 50S ribosomal protein L10
J: 50S ribosomal protein L11
K: 50S ribosomal protein L13
L: 50S ribosomal protein L14
M: 50S ribosomal protein L15
N: 50S ribosomal protein L16
O: 50S ribosomal protein L17
P: 50S ribosomal protein L18
Q: 50S ribosomal protein L19
R: 50S ribosomal protein L20
S: 50S ribosomal protein L21
T: 50S ribosomal protein L22
U: 50S ribosomal protein L23
V: 50S ribosomal protein L24
W: 50S ribosomal protein L25
X: 50S ribosomal protein L27
Y: LSU ribosomal protein L28P
Z: 50S ribosomal protein L29
a: 50S ribosomal protein L30
b: 50S ribosomal protein L32
c: 50S ribosomal protein L33 1
d: 50S ribosomal protein L34
e: 50S ribosomal protein L35
f: 50S ribosomal protein L36
g: 50S ribosomal protein L31
BA: 16S rRNA
BB: Conserved domain protein
BC: 30S ribosomal protein S3
BD: 30S ribosomal protein S4
BE: 30S ribosomal protein S5
BF: 30S ribosomal protein S6
BG: 30S ribosomal protein S7
BH: 30S ribosomal protein S8
BI: 30S ribosomal protein S9
BJ: 30S ribosomal protein S10
BK: 30S ribosomal protein S11
BL: 30S ribosomal protein S12
BM: 30S ribosomal protein S13
BN: 30S ribosomal protein S14 type Z
BO: 30S ribosomal protein S15
BP: 30S ribosomal protein S16
BQ: 30S ribosomal protein S17
BR: 30S ribosomal protein S18 2
BS: 30S ribosomal protein S19
BT: 30S ribosomal protein S20
BV: 30S ribosomal protein S2
BW: P/P-site Phe-tRNA(Phe)
BX: mRNA fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,322,204689
Polymers2,306,45557
Non-polymers15,748632
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area268650 Å2
ΔGint-2235 kcal/mol
Surface area826670 Å2
MethodPISA

-
Components

+
50S ribosomal protein ... , 31 types, 31 molecules 3CDEFGHIJKLMNOPQRSTUVWXZabcdefg

#1: Protein/peptide 50S ribosomal protein bL37 / bl37


Mass: 2841.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QTP4
#4: Protein 50S ribosomal protein L2 / uL2


Mass: 30425.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD4
#5: Protein 50S ribosomal protein L3 / uL3


Mass: 23011.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD1
#6: Protein 50S ribosomal protein L4 / uL4


Mass: 22920.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD2
#7: Protein 50S ribosomal protein L5 / uL5


Mass: 21152.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSG1
#8: Protein 50S ribosomal protein L6 / uL6


Mass: 19483.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSG4
#9: Protein 50S ribosomal protein L9 / bL9


Mass: 15949.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 44-73 modeled as poly-alanine
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R7F6
#10: Protein 50S ribosomal protein L10 / uL10


Mass: 18035.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QS62
#11: Protein 50S ribosomal protein L11 / uL11


Mass: 15023.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QS45
#12: Protein 50S ribosomal protein L13 / uL13


Mass: 16146.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSP8
#13: Protein 50S ribosomal protein L14 / uL14


Mass: 13400.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSF9
#14: Protein 50S ribosomal protein L15 / uL15


Mass: 15602.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: I7G436, UniProt: A0QSG8*PLUS
#15: Protein 50S ribosomal protein L16 / uL16


Mass: 15774.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD8
#16: Protein 50S ribosomal protein L17 / bL17


Mass: 21892.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSL9
#17: Protein 50S ribosomal protein L18 / uL18


Mass: 13711.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSG5
#18: Protein 50S ribosomal protein L19 / bL19


Mass: 12892.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QV42
#19: Protein 50S ribosomal protein L20 / bL20


Mass: 14494.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QYU6
#20: Protein 50S ribosomal protein L21 / bL21


Mass: 11055.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R151
#21: Protein 50S ribosomal protein L22 / uL22


Mass: 16353.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD6
#22: Protein 50S ribosomal protein L23 / uL23


Mass: 11047.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD3
#23: Protein 50S ribosomal protein L24 / uL24


Mass: 11228.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 48-55 not modeled
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSG0
#24: Protein 50S ribosomal protein L25 / bL25


Mass: 22571.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R3D2
#25: Protein 50S ribosomal protein L27 / bL27


Mass: 9249.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R150
#27: Protein 50S ribosomal protein L29 / uL29


Mass: 8790.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD9
#28: Protein 50S ribosomal protein L30 / uL30


Mass: 7022.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSG7
#29: Protein 50S ribosomal protein L32 / bL32


Mass: 6467.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R3I9
#30: Protein 50S ribosomal protein L33 1 / bL33


Mass: 6468.501 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QS39
#31: Protein/peptide 50S ribosomal protein L34 / bL34


Mass: 5522.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R7K0
#32: Protein 50S ribosomal protein L35 / bL35


Mass: 7298.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QYU7
#33: Protein/peptide 50S ribosomal protein L36 / bL36


Mass: 4341.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSL4
#34: Protein 50S ribosomal protein L31 / bL31


Mass: 8312.485 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: residues 49-55 not modeled, intersubunit bridge forming protein
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R215

-
RNA chain , 5 types, 5 molecules ABBABWBX

#2: RNA chain 23S rRNA


Mass: 1012140.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: GenBank: 118168627
#3: RNA chain 5S rRNA


Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: GenBank: 118168627
#35: RNA chain 16S rRNA


Mass: 495373.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: GenBank: 118168627
#56: RNA chain P/P-site Phe-tRNA(Phe)


Mass: 24485.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Model and sequence adopted from Escherichia coli tRNA(Phe)
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
#57: RNA chain mRNA fragment


Mass: 1791.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)

-
30S ribosomal protein ... , 19 types, 19 molecules BCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBV

#37: Protein 30S ribosomal protein S3 / uS3


Mass: 30191.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD7
#38: Protein 30S ribosomal protein S4 / uS4


Mass: 23415.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSL7
#39: Protein 30S ribosomal protein S5 / uS5


Mass: 21946.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSG6
#40: Protein 30S ribosomal protein S6 / bS6


Mass: 10991.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0A0D6J3X3
#41: Protein 30S ribosomal protein S7 / uS7


Mass: 17660.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QS97
#42: Protein 30S ribosomal protein S8 / uS8


Mass: 14492.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSG3
#43: Protein 30S ribosomal protein S9 / uS9


Mass: 16794.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSP9
#44: Protein 30S ribosomal protein S10 / uS10


Mass: 11454.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD0
#45: Protein 30S ribosomal protein S11 / uS11


Mass: 14671.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSL6
#46: Protein 30S ribosomal protein S12 / uS12


Mass: 13896.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QS96
#47: Protein 30S ribosomal protein S13 / uS13


Mass: 14249.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSL5
#48: Protein 30S ribosomal protein S14 type Z / uS14


Mass: 6976.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSG2
#49: Protein 30S ribosomal protein S15 / uS15


Mass: 10368.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QVQ3
#50: Protein 30S ribosomal protein S16 / bS16


Mass: 16795.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QV37
#51: Protein 30S ribosomal protein S17 / uS17


Mass: 11127.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSE0
#52: Protein 30S ribosomal protein S18 2 / bS18


Mass: 9524.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R7F7
#53: Protein 30S ribosomal protein S19 / uS19


Mass: 10800.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD5
#54: Protein 30S ribosomal protein S20 / bS20


Mass: 9556.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R102
#55: Protein 30S ribosomal protein S2 / uS2


Mass: 30145.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QVB8

-
Protein / Protein/peptide , 2 types, 2 molecules YBB

#26: Protein LSU ribosomal protein L28P / bL28


Mass: 6891.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: I7FJ52, UniProt: A0QV03*PLUS
#36: Protein/peptide Conserved domain protein / bS22


Mass: 4164.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QR10

-
Non-polymers , 3 types, 632 molecules

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


Mass: 24.305 Da / Num. of mol.: 625 / Source method: obtained synthetically / Formula: Mg
#59: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#60: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C9H11NO2
Details: Model and sequence adopted from Escherichia coli tRNA(Phe)
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 70S ribosome / Type: RIBOSOME / Entity ID: #1-#57 / Source: NATURAL
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE-PROPANE / Humidity: 96 %

-
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 FIELD / Calibrated magnification: 100719 X
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Details: FEI EPU data collection
Image scansMovie frames/image: 7

-
Processing

EM software
IDNameVersionCategory
1EMAN Boxer1.9particle selection
4CTFFIND3CTF correction
9PHENIXmodel refinement
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
13RELION1.43D reconstruction
CTF correctionDetails: CTF correction in Relion / Type: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224584 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more