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- EMDB-37258: Structure of YchF with 50S ribosomal subunit (local map) -

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Basic information

Entry
Database: EMDB / ID: EMD-37258
TitleStructure of YchF with 50S ribosomal subunit (local map)
Map data
Sample
  • Complex: Complex of 50S subunit with YchF
    • Complex: YchF
      • Protein or peptide: Ribosome-binding ATPase YchF
    • Complex: 50S subunit
      • RNA: 23S rRNA (partial)
      • Protein or peptide: 50S ribosomal protein L14
      • Protein or peptide: 50S ribosomal protein L19
  • Ligand: MAGNESIUM ION
KeywordsYchF / OLA1 / Ribosome
Function / homology
Function and homology information


ribosomal large subunit binding / enzyme inhibitor activity / ribosome binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / response to oxidative stress / cytoplasmic translation / structural constituent of ribosome / GTP binding ...ribosomal large subunit binding / enzyme inhibitor activity / ribosome binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / response to oxidative stress / cytoplasmic translation / structural constituent of ribosome / GTP binding / protein homodimerization activity / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosome-binding ATPase YchF/Obg-like ATPase 1 / YchF, C-terminal domain / TGS-like domain superfamily / YchF, N-terminal / Protein of unknown function (DUF933) / TGS-like / TGS domain profile. / TGS / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. ...Ribosome-binding ATPase YchF/Obg-like ATPase 1 / YchF, C-terminal domain / TGS-like domain superfamily / YchF, N-terminal / Protein of unknown function (DUF933) / TGS-like / TGS domain profile. / TGS / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / Beta-grasp domain superfamily / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. / Ribosomal protein L14p/L23e / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e / Translation protein SH3-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Large ribosomal subunit protein bL19 / Ribosome-binding ATPase YchF / Large ribosomal subunit protein uL14
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsYu T / Li X / Zeng F
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171200 China
Guangdong Basic and Applied Basic Research Foundation2021A1515010805 China
Shenzhen Science and Technology ProgramJCYJ20220530115210023 China
CitationJournal: To Be Published
Title: Structure basis of translation regulation by YchF bound to ribosome
Authors: Li X / Yu T / Li Q / Zeng F
History
DepositionAug 23, 2023-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateAug 28, 2024-
Current statusAug 28, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37258.png

Downloads & links

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Map

FileDownload / File: emd_37258.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 256 pix.
= 268.8 Å		1.05 Å/pix.
x 256 pix.
= 268.8 Å		1.05 Å/pix.
x 256 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.029832287 - 0.0728835
Average (Standard dev.)0.00001966856 (±0.0014963724)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37258_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37258_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of 50S subunit with YchF

EntireName: Complex of 50S subunit with YchF
Components
  • Complex: Complex of 50S subunit with YchF
    • Complex: YchF
      • Protein or peptide: Ribosome-binding ATPase YchF
    • Complex: 50S subunit
      • RNA: 23S rRNA (partial)
      • Protein or peptide: 50S ribosomal protein L14
      • Protein or peptide: 50S ribosomal protein L19
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of 50S subunit with YchF

SupramoleculeName: Complex of 50S subunit with YchF / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #2: YchF

SupramoleculeName: YchF / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

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Supramolecule #3: 50S subunit

SupramoleculeName: 50S subunit / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#4

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Macromolecule #1: Ribosome-binding ATPase YchF

MacromoleculeName: Ribosome-binding ATPase YchF / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 41.651305 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHEN LYFQGHMGFK CGIVGLPNVG KSTLFNALTK AGIEAANFPF CTIEPNTGVV PMPDPRLDQL AEIVKPQRTL PTTMEFVDI AGLVKGASKG EGLGNQFLTN IRETEAIGHV VRCFENDNII AVSGKVNPAD DIEVINTELA LADLDTCERA I HRVQKKAK ...String:
MGHHHHHHEN LYFQGHMGFK CGIVGLPNVG KSTLFNALTK AGIEAANFPF CTIEPNTGVV PMPDPRLDQL AEIVKPQRTL PTTMEFVDI AGLVKGASKG EGLGNQFLTN IRETEAIGHV VRCFENDNII AVSGKVNPAD DIEVINTELA LADLDTCERA I HRVQKKAK GGDKDAKAEL AVLEKCLPQL ENAGMLRALD LSAEEKAAIR YLSFLTLKPT MYIANVNEDG FENNPYLDQV RE IAAKEGS VVVPVCAAVE ADIAELDDEE RDEFMQELGL EEPGLNRVIR AGYKLLNLQT YFTAGVKEVR AWTIPVGATA PQA AGKIHT DFEKGFIRAQ TISFEDFITY KGEQGAKEAG KMRAEGKDYI VKDGDVMNFL FNV

UniProtKB: Ribosome-binding ATPase YchF

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Macromolecule #3: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.565067 KDa
SequenceString:
MIQEQTMLNV ADNSGARRVM CIKVLGGSHR RYAGVGDIIK ITIKEAIPRG KVKKGDVLKA VVVRTKKGVR RPDGSVIRFD GNACVLLNN NSEQPIGTRI FGPVTRELRS EKFMKIISLA PEVL

UniProtKB: Large ribosomal subunit protein uL14

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Macromolecule #4: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.159278 KDa
SequenceString:
MSNIIKQLEQ EQMKQDVPSF RPGDTVEVKV WVVEGSKKRL QAFEGVVIAI RNRGLHSAFT VRKISNGEGV ERVFQTHSPV VDSISVKRR GAVRKAKLYY LRERTGKAAR IKERLN

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #2: 23S rRNA (partial)

MacromoleculeName: 23S rRNA (partial) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 941.663438 KDa
SequenceString: GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGA UAUGAACCGU UAUAACCGGC GAUUUCCGAA UGGGGAAACC CAGUGUGUUU CGACACACUA UCAUUAACUG A AUCCAUAG ...String:
GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGA UAUGAACCGU UAUAACCGGC GAUUUCCGAA UGGGGAAACC CAGUGUGUUU CGACACACUA UCAUUAACUG A AUCCAUAG GUUAAUGAGG CGAACCGGGG GAACUGAAAC AUCUAAGUAC CCCGAGGAAA AGAAAUCAAC CGAGAUUCCC CC AGUAGCG GCGAGCGAAC GGGGAGCAGC CCAGAGCCUG AAUCAGUGUG UGUGUUAGUG GAAGCGUCUG GAAAGGCGCG CGA UACAGG GUGACAGCCC CGUACACAAA AAUGCACAUG CUGUGAGCUC GAUGAGUAGG GCGGGACACG UGGUAUCCUG UCUG AAUAU GGGGGGACCA UCCUCCAAGG CUAAAUACUC CUGACUGACC GAUAGUGAAC CAGUACCGUG AGGGAAAGGC GAAAA GAAC CCCGGCGAGG GGAGUGAAAA AGAACCUGAA ACCGUGUACG UACAAGCAGU GGGAGCACGC UUAGGCGUGU GACUGC GUA CCUUUUGUAU AAUGGGUCAG CGACUUAUAU UCUGUAGCAA GGUUAACCGA AUAGGGGAGC CGAAGGGAAA CCGAGUC UU AACUGGGCGU UAAGUUGCAG GGUAUAGACC CGAAACCCGG UGAUCUAGCC AUGGGCAGGU UGAAGGUUGG GUAACACU A ACUGGAGGAC CGAACCGACU AAU(1MG)UUGAAA AAUUAGCGGA UGACUUGUGG CUGGGGGUGA AAGGCCAAUC AAACC GGGA GAUAGCUGGU UCUCCCCGAA AGCUAUUUAG GUAGCGCCUC GUGAAUUCAU CUCCGGGGGU AGAGCACUGU UUCGGC AAG GGGGUCAACC CGACUUACCA ACCCGAUGCA AACUGCGAAU ACCGGAGAAU GUUAUCACGG GAGACACACG GCGGGUG CU AACGUCCGUC GUGAAGAGGG AAACAACCCA GACCGCCAGC UAAGGUCCCA AAGUCAUGGU UAAGUGGGAA ACGAUGUG G GAAGGCCCAG ACAGCCAGGA UGUUGGCUUA GAAGCAGCCA UCAUUUAAAG AAAGCGUAAU AGCUCACUGG UCGAGUCGG CCUGCGCGGA AGAUGUAACG GGGCUAAACC AUGCACCGAA GCUGCGGCAG CGACGCUUAU GCGUUGUUGG GUAGGGGAGC GUUCUGUAA GCCUGCGAAG GUGUGCUGUG AGGCAUGCUG GAGGUAUCAG AAGUGCGAAU GCUGACAUAA GUAACGAUAA A GCGGGUGA AAAGCCCGCU CGCCGGAAGA CCAAGGGUUC CUGUCCAACG UUAAUCGGGG CAGGGUGAGU CGACCCCUAA GG CGAGGCC GAAAGGCGUA GUCGAUGGGA AACAGGUUAA UAUUCCUGUA CUUGGUGUUA CUGCGAAGGG GGGACGGAGA AGG CUAUGU UGGCCGGGCG ACGGUUGUCC CGGUUUAAGC GUGUAGGCUG GUUUUCCAGG CAAAUCCGGA AAAUCAAGGC UGAG GCGUG AUGACGAGGC ACUACGGUGC UGAAGCAACA AAUGCCCUGC UUCCAGGAAA AGCCUCUAAG CAUCAGGUAA CAUCA AAUC GUACCCCAAA CCGACACAGG UGGUCAGGUA GAGAAUACCA AGGCGCUUGA GAGAACUCGG GUGAAGGAAC UAGGCA AAA UGGUGCCGUA ACUUCGGGAG AAGGCACGCU GAUAUGUAGG UGAGGUCCCU CGCGGAUGGA GCUGAAAUCA GUCGAAG AU ACCAGCUGGC UGCAACUGUU UAUUAAAAAC ACAGCACUGU GCAAACACGA AAGUGGACGU AUACGGUGUG ACGCCUGC C CGGUGCCGGA AGGUUAAUUG AUGGGGUUAG CGCAAGCGAA GCUCUUGAUC GAAGCCCCGG UAAACGGCGG CCGUAACUA UAACGGUCCU AAGGUAGCGA AAUUCCUUGU CGGGUAAGUU CCGACCUGCA CGAAUGGCGU AAUGAUGGCC AGGCUGUCUC CACCCGAGA CUCAGUGAAA UUGAACUCGC UGUGAAGAUG CAGUGUACCC GCGGCAAGAC GGAAAGACCC CGUGAACCUU U ACUAUAGC UUGACACUGA ACAUUGAGCC UUGAUGUGUA GGAUAGGUGG GAGGCUUUGA AGUGUGGACG CCAGUCUGCA UG GAGCCGA CCUUGAAAUA CCACCCUUUA AUGUUUGAUG UUCUAACGUU GACCCGUAAU CCGGGUUGCG GACAGUGUCU GGU GGGUAG UUUGACUGGG GCGGUCUCCU CCUAAAGAGU AACGGAGGAG CACGAAGGUU GGCUAAUCCU GGUCGGACAU CAGG AGGUU AGUGCAAUGG CAUAAGCCAG CUUGACUGCG AGCGUGACGG CGCGAGCAGG UGCGAAAGCA GGUCAUAGUG AUCCG GUGG UUCUGAAUGG AAGGGCCAUC GCUCAACGGA UAAAAGGUAC UCCGGGGAUA ACAGGCUGAU ACCGCCCAAG AGUUCA UAU CGACGGCGGU GUUUGGCACC UCGAUGUCGG CUCAUCACAU CCUGGGGCUG AAGUAGGUCC CAAGGGUAUG GC(OMU) GUUCGC CAUUUAAAGU GGUACGCGAG C(PSU)GGGUUUAG AACGUCGUGA GACAGUUCGG UCCCUAUCUG CCGUGGGCGC UGGAGAACU GAGGGGGGCU GCUCCUAGUA CGAGAGGACC GGAGUGGACG CAUCACUGGU GUUCGGGUUG UCAUGCCAAU G GCACUGCC CGGUAGCUAA AUGCGGAAGA GAUAAGUGCU GAAAGCAUCU AAGCACGAAA CUUGCCCCGA GAUGAGUUCU CC CUGACCC UUUAAGGGUC CUGAAGGAAC GUUGAAGACG ACGACGUUGA UAGGCCGGGU GUGUAAGCGC AGCGAUGCGU UGA GCUAAC CGGUACUAAU GAACCGUGAG GCUUAACCUU

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 30 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 4 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5u4i

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90708
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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