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- PDB-5ady: Cryo-EM structures of the 50S ribosome subunit bound with HflX -

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Entry
Database: PDB / ID: 5ady
TitleCryo-EM structures of the 50S ribosome subunit bound with HflX
Components
  • (50S RIBOSOMAL PROTEIN ...) x 31
  • 23S RRNA23S ribosomal RNA
  • 5S RRNA5S ribosomal RNA
  • GTPASE HFLX
KeywordsRIBOSOME / RIBOSOME RESCUE
Function / homology
Function and homology information


ribosome disassembly / peptidyl-serine autophosphorylation / ribosomal large subunit binding / rescue of stalled ribosome / stringent response / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / negative regulation of endoribonuclease activity / translation repressor activity / mature ribosome assembly ...ribosome disassembly / peptidyl-serine autophosphorylation / ribosomal large subunit binding / rescue of stalled ribosome / stringent response / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / negative regulation of endoribonuclease activity / translation repressor activity / mature ribosome assembly / negative regulation of translational initiation / polysomal ribosome / ribosome assembly / assembly of large subunit precursor of preribosome / translational termination / DNA-templated transcription, termination / translation repressor activity, mRNA regulatory element binding / DNA-binding transcription repressor activity / regulation of cell growth / response to reactive oxygen species / large ribosomal subunit rRNA binding / ribosome biogenesis / large ribosomal subunit / cytosolic large ribosomal subunit / ribosomal large subunit assembly / ribosome binding / 5S rRNA binding / protein-DNA complex / response to radiation / response to heat / tRNA binding / transferase activity / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / ATPase activity / translation / GTPase activity / mRNA binding / response to antibiotic / GTP binding / negative regulation of transcription, DNA-templated / zinc ion binding / ATP binding / metal ion binding / cytosol / cytoplasm
Ribosomal protein L13, conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein L1, conserved site / Ribosomal protein L1-like / GTPase HflX, N-terminal / Ribosomal protein L28/L24 / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L21-like / Ribosomal protein L25 ...Ribosomal protein L13, conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein L1, conserved site / Ribosomal protein L1-like / GTPase HflX, N-terminal / Ribosomal protein L28/L24 / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L21-like / Ribosomal protein L25 / HflX-type guanine nucleotide-binding (G) domain / Ribosomal protein L15 / Ribosomal protein L5, N-terminal / Ribosomal protein L2 signature. / GTP-binding protein, middle domain / L28p-like / Ribosomal protein L20, C-terminal / EF-G domain III/V-like / Ribosomal protein L36 superfamily / Ribosomal protein L29/L35 superfamily / L21-like superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L10 / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L33, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein L3, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L14P, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L25, short-form / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L9, C-terminal / Ribosomal protein L9, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein L5 domain superfamily / Ribosomal protein L11, N-terminal / Ribosomal protein L11, conserved site / Ribosomal protein L16, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L35 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L22/L17, conserved site / Ribosomal L25p family / ribosomal L5P family C-terminus / Ribosomal protein L1p/L10e family / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal prokaryotic L21 protein / Ribosomal L28 family / Ribosomal L29 protein / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal L27 protein / Ribosomal protein L17 / Ribosomal protein L19 / Ribosomal protein L9, N-terminal domain / Ribosomal protein L35 / Ribosomal protein L13 / Ribosomal L32p protein family / 50S ribosome-binding GTPase / Ribosomal protein L11, N-terminal domain / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L9, C-terminal domain / GTP-binding GTPase N-terminal / GTP-binding GTPase Middle Region / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L14 signature. / Ribosomal protein L23 signature. / Ribosomal protein L5 signature. / Ribosomal protein L4/L1 family / Ribosomal protein L33 / Ribosomal protein L14 superfamily / Ribosomal protein L22p/L17e / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein L19 superfamily / Ribosomal Protein L26/L24, KOW domain / GTPase HflX, N-terminal domain superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L14p/L23e / Ribosomal protein L34 / Ribosomal protein L16p/L10e / Ribosomal protein L23
50S ribosomal protein L16 / GTPase HflX / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 50S ribosomal protein L24 / 50S ribosomal protein L2 / 50S ribosomal protein L3 ...50S ribosomal protein L16 / GTPase HflX / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 50S ribosomal protein L24 / 50S ribosomal protein L2 / 50S ribosomal protein L3 / 50S ribosomal protein L4 / 50S ribosomal protein L22 / 50S ribosomal protein L5 / 50S ribosomal protein L25 / gb:507148446: / 50S ribosomal protein L23 / 50S ribosomal protein L20 / 50S ribosomal protein L14 / 50S ribosomal protein L28 / 50S ribosomal protein L15 / 50S ribosomal protein L10 / 50S ribosomal protein L11 / 50S ribosomal protein L19 / 50S ribosomal protein L1 / 50S ribosomal protein L27 / 50S ribosomal protein L29 / 50S ribosomal protein L13 / 50S ribosomal protein L32 / 50S ribosomal protein L33 / 50S ribosomal protein L34 / 50S ribosomal protein L35 / 50S ribosomal protein L36 / 50S ribosomal protein L9 / gb:507148266:
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsZhang, Y. / Mandava, C.S. / Cao, W. / Li, X. / Zhang, D. / Li, N. / Zhang, Y. / Zhang, X. / Qin, Y. / Mi, K. / Lei, J. / Sanyal, S. / Gao, N.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2015
Title: HflX is a ribosome-splitting factor rescuing stalled ribosomes under stress conditions.
Authors: Yanqing Zhang / Chandra Sekhar Mandava / Wei Cao / Xiaojing Li / Dejiu Zhang / Ningning Li / Yixiao Zhang / Xiaoxiao Zhang / Yan Qin / Kaixia Mi / Jianlin Lei / Suparna Sanyal / Ning Gao /
Abstract: Adverse cellular conditions often lead to nonproductive translational stalling and arrest of ribosomes on mRNAs. Here, we used fast kinetics and cryo-EM to characterize Escherichia coli HflX, a ...Adverse cellular conditions often lead to nonproductive translational stalling and arrest of ribosomes on mRNAs. Here, we used fast kinetics and cryo-EM to characterize Escherichia coli HflX, a GTPase with unknown function. Our data reveal that HflX is a heat shock-induced ribosome-splitting factor capable of dissociating vacant as well as mRNA-associated ribosomes with deacylated tRNA in the peptidyl site. Structural data demonstrate that the N-terminal effector domain of HflX binds to the peptidyl transferase center in a strikingly similar manner as that of the class I release factors and induces dramatic conformational changes in central intersubunit bridges, thus promoting subunit dissociation. Accordingly, loss of HflX results in an increase in stalled ribosomes upon heat shock. These results suggest a primary role of HflX in rescuing translationally arrested ribosomes under stress conditions.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Aug 2, 2017Group: Data collection / Derived calculations / Category: em_image_scans / em_software / struct_conn / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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
Revision 1.5Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type

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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
5: 50S RIBOSOMAL PROTEIN L1
6: GTPASE HFLX
7: 50S RIBOSOMAL PROTEIN L10
A: 5S RRNA
B: 23S 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 L11
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)1,448,69336
Polymers1,448,14634
Non-polymers5472
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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50S RIBOSOMAL PROTEIN ... , 31 types, 31 molecules 0123457CDEFGHIJKLMNOPQRSTUVWXYZ

#1: Protein/peptide 50S RIBOSOMAL PROTEIN L32 /


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7N4
#2: Protein/peptide 50S RIBOSOMAL PROTEIN L33 /


Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7N9
#3: Protein/peptide 50S RIBOSOMAL PROTEIN L34 /


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7P5
#4: Protein/peptide 50S RIBOSOMAL PROTEIN L35 / / RIBOSOMAL PROTEIN A


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7Q1
#5: Protein/peptide 50S RIBOSOMAL PROTEIN L36 / / RIBOSOMAL PROTEIN B


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7Q6
#6: Protein/peptide 50S RIBOSOMAL PROTEIN L1 /


Mass: 24765.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7L0
#8: Protein/peptide 50S RIBOSOMAL PROTEIN L10 / / 50S RIBOSOMAL PROTEIN L8


Mass: 17736.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7J3
#11: Protein/peptide 50S RIBOSOMAL PROTEIN L2 /


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P60422
#12: Protein/peptide 50S RIBOSOMAL PROTEIN L3 /


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P60438
#13: Protein/peptide 50S RIBOSOMAL PROTEIN L4 /


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P60723
#14: Protein/peptide 50S RIBOSOMAL PROTEIN L5 /


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P62399
#15: Protein/peptide 50S RIBOSOMAL PROTEIN L6 /


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0AG55
#16: Protein/peptide 50S RIBOSOMAL PROTEIN L9 /


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7R1
#17: Protein/peptide 50S RIBOSOMAL PROTEIN L11 /


Mass: 14894.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7J7
#18: Protein/peptide 50S RIBOSOMAL PROTEIN L13 /


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0AA10
#19: Protein/peptide 50S RIBOSOMAL PROTEIN L14 /


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0ADY3
#20: Protein/peptide 50S RIBOSOMAL PROTEIN L15 /


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P02413
#21: Protein/peptide 50S RIBOSOMAL PROTEIN L16 /


Mass: 15312.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0ADY7
#22: Protein/peptide 50S RIBOSOMAL PROTEIN L17 /


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0AG44
#23: Protein/peptide 50S RIBOSOMAL PROTEIN L18 /


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0C018
#24: Protein/peptide 50S RIBOSOMAL PROTEIN L19 /


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7K6
#25: Protein/peptide 50S RIBOSOMAL PROTEIN L20 /


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7L3
#26: Protein/peptide 50S RIBOSOMAL PROTEIN L21 /


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0AG48
#27: Protein/peptide 50S RIBOSOMAL PROTEIN L22 /


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P61175
#28: Protein/peptide 50S RIBOSOMAL PROTEIN L23 /


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0ADZ0
#29: Protein/peptide 50S RIBOSOMAL PROTEIN L24 /


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P60624
#30: Protein/peptide 50S RIBOSOMAL PROTEIN L25 /


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P68919
#31: Protein/peptide 50S RIBOSOMAL PROTEIN L27 /


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7L8
#32: Protein/peptide 50S RIBOSOMAL PROTEIN L28 /


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7M2
#33: Protein/peptide 50S RIBOSOMAL PROTEIN L29 /


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0A7M6
#34: Protein/peptide 50S RIBOSOMAL PROTEIN L30 /


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P0AG51

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Protein/peptide , 1 types, 1 molecules 6

#7: Protein/peptide GTPASE HFLX / GTP-BINDING PROTEIN HFLX


Mass: 48392.988 Da / Num. of mol.: 1
Details: A GMPPNP AND A MAGNESIUM ION ARE INCLUDED IN THIS CHAIN.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P25519

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RNA chain , 2 types, 2 molecules AB

#9: RNA chain 5S RRNA / 5S ribosomal RNA


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: GenBank: 507148446
#10: RNA chain 23S RRNA / 23S ribosomal RNA


Mass: 941306.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: GenBank: 507148266

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Non-polymers , 2 types, 2 molecules

#35: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp (GMPPNP, energy-carrying molecule analogue) *YM
#36: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Magnesium

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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: 50S-HFLX COMPLEX / Type: RIBOSOME
Buffer solutionName: 20MM TRIS-HCL, 100MM NH4CL, 10MM MGCL2 / pH: 7.5 / Details: 20MM TRIS-HCL, 100MM NH4CL, 10MM MGCL2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jan 7, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k)

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Processing

EM software
IDNameCategory
1RELION3D reconstruction
2SPIDER3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: SINGLE PARTICLE RECONSTRUCTIONSingle particle analysis
Resolution: 4.5 Å / Num. of particles: 384206 / Nominal pixel size: 1.1659 Å / Actual pixel size: 1.1659 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -3133. (DEPOSITION ID: 13705).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--MDFF REFINEMENT PROTOCOL--FLEXIBLE
Atomic model buildingPDB-ID: 3FIK
RefinementHighest resolution: 4.5 Å
Refinement stepCycle: LAST / Highest resolution: 4.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32510 64821 33 0 97364

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