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- PDB-5v93: Cryo-EM structure of the 70S ribosome from Mycobacterium tubercul... -

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Entry
Database: PDB / ID: 5v93
TitleCryo-EM structure of the 70S ribosome from Mycobacterium tuberculosis bound with Capreomycin
Components
  • (30S ribosomal protein ...) x 18
  • (50S ribosomal protein ...) x 28
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • Capreomycin
  • LSU ribosomal protein L21p
  • Mitochondrial domain of uncharacterised function (DUF1713)
KeywordsRIBOSOME / RNA complex
Function / homology
Function and homology information


large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex ...large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / 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 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 S16, conserved site ...Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / 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 S16, conserved site / Ribosomal protein S16 signature. / 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 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 S14/S29 / 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 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 L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6 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 L14P, bacterial-type / Ribosomal protein S4, bacterial-type / 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 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 L20 / Ribosomal protein L20, C-terminal / Ribosomal protein S16 domain superfamily / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein S15, bacterial-type / Ribosomal protein L17
Similarity search - Domain/homology
Capreomycin 1B / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 ...Capreomycin 1B / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL33 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein uS17 / Mitochondrial domain of uncharacterized function (DUF1713) / 50S ribosomal protein L15 / Large ribosomal subunit protein uL13 / 50S ribosomal protein L14 / : / : / : / 50S ribosomal protein L15 / Small ribosomal subunit protein uS12
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Streptomyces puniceus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsYang, K. / Chang, J.-Y. / Cui, Z. / Li, X. / Meng, R. / Duan, L. / Thongchol, J. / Jakana, J. / Huwe, C. / Sacchettini, J. / Zhang, J.
CitationJournal: Nucleic Acids Res / Year: 2017
Title: Structural insights into species-specific features of the ribosome from the human pathogen Mycobacterium tuberculosis.
Authors: Kailu Yang / Jeng-Yih Chang / Zhicheng Cui / Xiaojun Li / Ran Meng / Lijun Duan / Jirapat Thongchol / Joanita Jakana / Christoph M Huwe / James C Sacchettini / Junjie Zhang /
Abstract: Ribosomes from Mycobacterium tuberculosis (Mtb) possess species-specific ribosomal RNA (rRNA) expansion segments and ribosomal proteins (rProtein). Here, we present the near-atomic structures of the ...Ribosomes from Mycobacterium tuberculosis (Mtb) possess species-specific ribosomal RNA (rRNA) expansion segments and ribosomal proteins (rProtein). Here, we present the near-atomic structures of the Mtb 50S ribosomal subunit and the complete Mtb 70S ribosome, solved by cryo-electron microscopy. Upon joining of the large and small ribosomal subunits, a 100-nt long expansion segment of the Mtb 23S rRNA, named H54a or the 'handle', switches interactions from with rRNA helix H68 and rProtein uL2 to with rProtein bS6, forming a new intersubunit bridge 'B9'. In Mtb 70S, bridge B9 is mostly maintained, leading to correlated motions among the handle, the L1 stalk and the small subunit in the rotated and non-rotated states. Two new protein densities were discovered near the decoding center and the peptidyl transferase center, respectively. These results provide a structural basis for studying translation in Mtb as well as developing new tuberculosis drugs.
History
DepositionMar 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Aug 12, 2020Group: Database references / Derived calculations / Structure summary
Category: pdbx_molecule_features / struct_conn / struct_ref
Item: _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id ..._struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.db_name / _struct_ref.pdbx_db_accession

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Structure visualization

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Assembly

Deposited unit
0: 50S ribosomal protein L32
1: 50S ribosomal protein L33
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
6: 50S ribosomal protein L31
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
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: LSU ribosomal protein L21p
S: 50S ribosomal protein L22
T: 50S ribosomal protein L23
U: 50S ribosomal protein L24
V: 50S ribosomal protein L25
W: 50S ribosomal protein L27
X: 50S ribosomal protein L28
Y: 50S ribosomal protein L29
Z: 50S ribosomal protein L30
a: 16S rRNA
b: Capreomycin
c: 30S ribosomal protein S3
d: 30S ribosomal protein S4
e: 30S ribosomal protein S5
f: 30S ribosomal protein S6
g: 30S ribosomal protein S7
h: 30S ribosomal protein S8
i: 30S ribosomal protein S9
j: 30S ribosomal protein S10
k: 30S ribosomal protein S11
l: 30S ribosomal protein S12
m: 30S ribosomal protein S13
n: 30S ribosomal protein S14 type Z
o: 30S ribosomal protein S15
p: 30S ribosomal protein S16
q: 30S ribosomal protein S17
r: 30S ribosomal protein S18
s: 30S ribosomal protein S19
t: 30S ribosomal protein S20
x: Mitochondrial domain of uncharacterised function (DUF1713)


Theoretical massNumber of molelcules
Total (without water)2,231,03852
Polymers2,231,03852
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area239170 Å2
ΔGint-1996 kcal/mol
Surface area800080 Å2
MethodPISA

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Components

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50S ribosomal protein ... , 28 types, 28 molecules 012346CDEFGHJKLMNOPQSTUVWXYZ

#1: Protein 50S ribosomal protein L32 /


Mass: 6525.757 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IMI5
#2: Protein 50S ribosomal protein L33 /


Mass: 6512.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HU86
#3: Protein/peptide 50S ribosomal protein L34 /


Mass: 5611.632 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A1L6JUG3
#4: Protein 50S ribosomal protein L35 /


Mass: 7241.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045KKY9
#5: Protein/peptide 50S ribosomal protein L36 /


Mass: 4323.239 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A1L6JSF4
#6: Protein 50S ribosomal protein L31 /


Mass: 8770.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HLX7
#9: Protein 50S ribosomal protein L2 /


Mass: 30644.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045H5T7
#10: Protein 50S ribosomal protein L3 /


Mass: 23127.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HU18
#11: Protein 50S ribosomal protein L4 /


Mass: 23779.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045J9H1
#12: Protein 50S ribosomal protein L5 /


Mass: 21052.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HUU0
#13: Protein 50S ribosomal protein L6 /


Mass: 19408.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JJU1
#14: Protein 50S ribosomal protein L9 /


Mass: 16196.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JW48
#15: Protein 50S ribosomal protein L13 /


Mass: 16333.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A0T9D5H2
#16: Protein 50S ribosomal protein L14 /


Mass: 13419.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A0U0S3A8
#17: Protein 50S ribosomal protein L15 /


Mass: 15534.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A0T7M0A0, UniProt: A0A654TTE7*PLUS
#18: Protein 50S ribosomal protein L16 /


Mass: 15724.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IWV9
#19: Protein 50S ribosomal protein L17 /


Mass: 19512.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IVA2
#20: Protein 50S ribosomal protein L18 /


Mass: 13211.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JK28
#21: Protein 50S ribosomal protein L19 /


Mass: 13041.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IDD2
#22: Protein 50S ribosomal protein L20 /


Mass: 14557.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045KJ85
#24: Protein 50S ribosomal protein L22 /


Mass: 20424.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045H760
#25: Protein 50S ribosomal protein L23 /


Mass: 10976.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045J9M3
#26: Protein 50S ribosomal protein L24 /


Mass: 11500.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IXU4
#27: Protein 50S ribosomal protein L25 / / General stress protein CTC


Mass: 22466.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JAK4
#28: Protein 50S ribosomal protein L27 /


Mass: 8987.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045K0G1
#29: Protein 50S ribosomal protein L28 /


Mass: 6920.075 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IDB8
#30: Protein 50S ribosomal protein L29 /


Mass: 8872.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IQ64
#31: Protein 50S ribosomal protein L30 /


Mass: 7361.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045H4J2

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RNA chain , 3 types, 3 molecules ABa

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


Mass: 1017792.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: GenBank: 984989958
#8: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 37097.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: GenBank: 1092945381
#32: RNA chain 16S rRNA /


Mass: 498260.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: GenBank: 1050844762

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Protein , 1 types, 1 molecules R

#23: Protein LSU ribosomal protein L21p / Ribosomal protein L21 (BL20)


Mass: 11173.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A1N6MHB1

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Protein/peptide , 2 types, 2 molecules bx

#33: Protein/peptide Capreomycin


Type: Cyclic peptide / Class: Inhibitor / Mass: 670.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces puniceus (bacteria) / References: NOR: NOR00639, Capreomycin 1B
#52: Protein/peptide Mitochondrial domain of uncharacterised function (DUF1713)


Mass: 4164.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A0T5Y2Y4

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30S ribosomal protein ... , 18 types, 18 molecules cdefghijklmnopqrst

#34: Protein 30S ribosomal protein S3 /


Mass: 30038.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045H4H6
#35: Protein 30S ribosomal protein S4 /


Mass: 23515.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045GRS4
#36: Protein 30S ribosomal protein S5 /


Mass: 22925.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JKV0
#37: Protein 30S ribosomal protein S6 /


Mass: 10952.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JVY9
#38: Protein 30S ribosomal protein S7 /


Mass: 17633.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JMN7
#39: Protein 30S ribosomal protein S8 /


Mass: 14432.563 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IWX2
#40: Protein 30S ribosomal protein S9 /


Mass: 16465.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045I839
#41: Protein 30S ribosomal protein S10 /


Mass: 11420.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HTN2
#42: Protein 30S ribosomal protein S11 /


Mass: 14815.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045I821
#43: Protein 30S ribosomal protein S12 /


Mass: 13882.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: M9TET4
#44: Protein 30S ribosomal protein S13 /


Mass: 14383.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045GT82
#45: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 6841.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HUG3
#46: Protein 30S ribosomal protein S15 /


Mass: 10500.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JF49
#47: Protein 30S ribosomal protein S16 /


Mass: 17466.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JER3
#48: Protein 30S ribosomal protein S17 /


Mass: 14776.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A0E9AP91
#49: Protein 30S ribosomal protein S18 /


Mass: 9565.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JW21
#50: Protein 30S ribosomal protein S19 /


Mass: 10830.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IXT2
#51: Protein 30S ribosomal protein S20 /


Mass: 9396.876 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045GXQ2

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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

ComponentName: Ribosome from human pathogen Mycobacterium tuberculosis
Type: RIBOSOME / Entity ID: #1-#51 / Source: NATURAL
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.27 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 184330 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01156396
ELECTRON MICROSCOPYf_angle_d1.089234911
ELECTRON MICROSCOPYf_dihedral_angle_d10.08883128
ELECTRON MICROSCOPYf_chiral_restr0.05430106
ELECTRON MICROSCOPYf_plane_restr0.00912133

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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

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