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- PDB-7f0d: Cryo-EM structure of Mycobacterium tuberculosis 50S ribosome subu... -

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Basic information

Entry
Database: PDB / ID: 7f0d
TitleCryo-EM structure of Mycobacterium tuberculosis 50S ribosome subunit bound with clarithromycin
Components
  • (50S ribosomal protein ...) x 29
  • 23S rRNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / Mycobacterium tuberculosis / 50S ribosomal subunit / gate site A2062 / clarithromycin / dynamic interaction / Cryo-EM / drug resistance
Function / homology
Function and homology information


large ribosomal subunit / 5S rRNA binding / transferase activity / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation ...large ribosomal subunit / 5S rRNA binding / transferase activity / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 ...Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / : / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / 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 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 L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / 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 L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L16 / : / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L21 / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L32p / Ribosomal protein L24 / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L23/L25, conserved site
Similarity search - Domain/homology
CLARITHROMYCIN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 ...CLARITHROMYCIN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL5 / 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 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL13 / 50S ribosomal protein L36 / 50S ribosomal protein L34 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL21
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Ra (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhang, W. / Sun, Y. / Gao, N. / Li, Z.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)11179012 China
National Natural Science Foundation of China (NSFC)31725007 China
National Basic Research Program of China (973 Program)2011CB710800 China
CitationJournal: Emerg Microbes Infect / Year: 2022
Title: Cryo-EM structure of 50S ribosomal subunit bound with clarithromycin reveals dynamic and specific interactions with macrolides.
Authors: Wen Zhang / ZhiFei Li / Yufan Sun / Peng Cui / Jianhua Liang / Qinghe Xing / Jing Wu / Yanhui Xu / Wenhong Zhang / Ying Zhang / Lin He / Ning Gao /
Abstract: Tuberculosis (TB) is the leading infectious disease caused by (). Clarithromycin (CTY), an analog of erythromycin (ERY), is more potent against multidrug-resistance (MDR) TB. ERY and CTY were ...Tuberculosis (TB) is the leading infectious disease caused by (). Clarithromycin (CTY), an analog of erythromycin (ERY), is more potent against multidrug-resistance (MDR) TB. ERY and CTY were previously reported to bind to the nascent polypeptide exit tunnel (NPET) near peptidyl transferase center (PTC), but the only available CTY structure in complex with () ribosome could be misinterpreted due to resolution limitation. To date, the mechanism of specificity and efficacy of CTY for remains elusive since the ribosome-CTY complex structure is still unknown. Here, we employed new sample preparation methods and solved the ribosome-CTY complex structure at 3.3Å with cryo-EM technique, where the crucial gate site A2062 ( numbering) is located at the CTY binding site within NPET. Two alternative conformations of A2062, a novel -conformation as well as a swayed conformation bound with water molecule at interface, may play a role in coordinating the binding of specific drug molecules. The previously overlooked C-H hydrogen bond (H-bond) and π interaction may collectively contribute to the enhanced binding affinity. Together, our structure data provide a structural basis for the dynamic binding as well as the specificity of CTY and explain of how a single methyl group in CTY improves its potency, which provides new evidence to reveal previously unclear mechanism of translational modulation for future drug design and anti-TB therapy. Furthermore, our sample preparation method may facilitate drug discovery based on the complexes with low water solubility drugs by cryo-EM technique.
History
DepositionJun 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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 ribosomal RNA
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: 50S ribosomal protein L21
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,458,90433
Polymers1,458,13131
Non-polymers7722
Water543
1


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

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Components

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50S ribosomal protein ... , 29 types, 29 molecules 012346CDEFGHJKLMNOPQRSTUVWXYZ

#1: Protein 50S ribosomal protein L32


Mass: 6525.757 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rpmF, rpmF_1, rpmF_2 / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rpmG2, rpmG / Production host: Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HU86
#3: Protein/peptide 50S ribosomal protein L34


Mass: 5643.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rpmH / Production host: Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A3E0V610
#4: Protein 50S ribosomal protein L35


Mass: 7241.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rpmI / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rpmJ / Production host: Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A3E0V5U0
#6: Protein 50S ribosomal protein L31


Mass: 8770.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rpmE / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rplB / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rplC / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rplD / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rplE / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rplF / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rplI / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rplM / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rplN / Production host: Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HTP7
#17: Protein 50S ribosomal protein L15


Mass: 15534.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rplO / Production host: Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A654TTE7
#18: Protein 50S ribosomal protein L16


Mass: 15724.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rplP / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rplQ / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rplR / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rplS / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rplT / Production host: Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045KJ85
#23: Protein 50S ribosomal protein L21


Mass: 11173.147 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rplU / Production host: Mycobacterium tuberculosis (bacteria) / References: UniProt: P9WHC3
#24: Protein 50S ribosomal protein L22


Mass: 20424.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rplV / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rplW / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rplX / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rplY / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rpmA / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rpmB / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rpmC / Production host: 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 genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: rpmD / Production host: Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045H4J2

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RNA chain , 2 types, 2 molecules AB

#7: RNA chain 23S rRNA


Mass: 1017792.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Production host: Mycobacterium tuberculosis (bacteria) / References: GenBank: 1251771536
#8: RNA chain 5S ribosomal RNA


Mass: 37097.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Production host: Mycobacterium tuberculosis (bacteria) / References: GenBank: 1251771551

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Non-polymers , 3 types, 5 molecules

#32: Chemical ChemComp-CTY / CLARITHROMYCIN


Mass: 747.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H69NO13 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#33: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#34: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Source detailsThe source provided by authors are used.

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Mycobacterium tuberculosis ribosome 50S subunitRIBOSOME#1-#310RECOMBINANT
250S ribosomal subunitRIBOSOME#1-#6, #9-#311RECOMBINANT
Source (natural)Organism: Mycobacterium tuberculosis H37Ra (bacteria)
Source (recombinant)Organism: Mycobacterium tuberculosis (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 IS (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameCategory
7Cootmodel fitting
8UCSF Chimeramodel fitting
14PHENIXmodel refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34912 / Symmetry type: POINT
Atomic model buildingPDB-ID: 5V7Q

5v7q


Accession code: 5V7Q / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009103039
ELECTRON MICROSCOPYf_angle_d1.036155325
ELECTRON MICROSCOPYf_dihedral_angle_d15.73654387
ELECTRON MICROSCOPYf_chiral_restr0.05519991
ELECTRON MICROSCOPYf_plane_restr0.0077673

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