[English] 日本語
Yorodumi
- PDB-4v19: Structure of the large subunit of the mammalian mitoribosome, par... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v19
TitleStructure of the large subunit of the mammalian mitoribosome, part 1 of 2
Components
  • (MITORIBOSOMAL ...Mitochondrial ribosome) x 30
  • TRNATransfer RNA
KeywordsRIBOSOME / TRANSLATION / LARGE RIBOSOMAL SUBUNIT / MITORIBOSOME / MAMMALIAN MITOCHONDRIAL RIBOSOME / CRYO-EM
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / rRNA import into mitochondrion / mitochondrial large ribosomal subunit / mitochondrial translation / organelle membrane / large ribosomal subunit / 5S rRNA binding / rRNA binding / ribosome ...Mitochondrial translation elongation / Mitochondrial translation termination / rRNA import into mitochondrion / mitochondrial large ribosomal subunit / mitochondrial translation / organelle membrane / large ribosomal subunit / 5S rRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / protein domain specific binding / intracellular membrane-bounded organelle / mitochondrion / RNA binding / cytoplasm
Similarity search - Function
Ribosomal Protein L25; Chain P / Mitochondrial ribosomal protein L55 / Ribosomal protein L9, N-terminal domain / Ribosomal protein L10, N-terminal RNA-binding domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L33 / Ribosomal Protein L9; domain 1 / Helix Hairpins - #3980 / Ribosomal protein L17 ...Ribosomal Protein L25; Chain P / Mitochondrial ribosomal protein L55 / Ribosomal protein L9, N-terminal domain / Ribosomal protein L10, N-terminal RNA-binding domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L33 / Ribosomal Protein L9; domain 1 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L4; Chain: A; / Ribosomal protein L4/L1 / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L13 / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Ribosomal protein S11/S14 / Ribosomal protein L35, mitochondrial / Ribosomal Protein L22; Chain A / SH3 type barrels. - #30 / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Other non-globular / Rubrerythrin, domain 2 / : / RRM (RNA recognition motif) domain / Single Sheet / Ribosomal protein L10-like domain superfamily / Nucleic acid-binding proteins / Ribosomal protein L10P / Ribosomal protein L10 / 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 L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L35 / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L21 / 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 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 L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Special / SH3 type barrels. / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 / Ribosomal protein S11 superfamily / Ribosomal protein L15 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L30p/L7e / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L26/L24, KOW domain / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L24 signature. / Ribosomal protein L14p/L23e / Helix Hairpins / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 39S ribosomal protein L18, mitochondrial isoform 1 / 39S ribosomal protein L18, mitochondrial isoform 1 / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL16m / : ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 39S ribosomal protein L18, mitochondrial isoform 1 / 39S ribosomal protein L18, mitochondrial isoform 1 / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL16m / : / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein uL14m / Mitochondrial ribosomal protein L2 / 39S ribosomal protein L15, mitochondrial / 39S ribosomal protein L27, mitochondrial / Large ribosomal subunit protein uL11m / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein bL21m / : / Mitochondrial ribosomal protein L4 / 39S ribosomal protein L18, mitochondrial isoform 1 / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein uL30m / Large ribosomal subunit protein bL35m / : / Large ribosomal subunit protein bL19m / : / Large ribosomal subunit protein bL9m / Large ribosomal subunit protein bL32m / Large ribosomal subunit protein bL34m
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGreber, B.J. / Boehringer, D. / Leibundgut, M. / Bieri, P. / Leitner, A. / Schmitz, N. / Aebersold, R. / Ban, N.
CitationJournal: Nature / Year: 2014
Title: The complete structure of the large subunit of the mammalian mitochondrial ribosome.
Authors: Basil J Greber / Daniel Boehringer / Marc Leibundgut / Philipp Bieri / Alexander Leitner / Nikolaus Schmitz / Ruedi Aebersold / Nenad Ban /
Abstract: Mitochondrial ribosomes (mitoribosomes) are extensively modified ribosomes of bacterial descent specialized for the synthesis and insertion of membrane proteins that are critical for energy ...Mitochondrial ribosomes (mitoribosomes) are extensively modified ribosomes of bacterial descent specialized for the synthesis and insertion of membrane proteins that are critical for energy conversion and ATP production inside mitochondria. Mammalian mitoribosomes, which comprise 39S and 28S subunits, have diverged markedly from the bacterial ribosomes from which they are derived, rendering them unique compared to bacterial, eukaryotic cytosolic and fungal mitochondrial ribosomes. We have previously determined at 4.9 Å resolution the architecture of the porcine (Sus scrofa) 39S subunit, which is highly homologous to the human mitoribosomal large subunit. Here we present the complete atomic structure of the porcine 39S large mitoribosomal subunit determined in the context of a stalled translating mitoribosome at 3.4 Å resolution by cryo-electron microscopy and chemical crosslinking/mass spectrometry. The structure reveals the locations and the detailed folds of 50 mitoribosomal proteins, shows the highly conserved mitoribosomal peptidyl transferase active site in complex with its substrate transfer RNAs, and defines the path of the nascent chain in mammalian mitoribosomes along their idiosyncratic exit tunnel. Furthermore, we present evidence that a mitochondrial tRNA has become an integral component of the central protuberance of the 39S subunit where it architecturally substitutes for the absence of the 5S ribosomal RNA, a ubiquitous component of all cytoplasmic ribosomes.
History
DepositionSep 25, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Nov 19, 2014Group: Database references
Revision 2.0Aug 2, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / diffrn_radiation_wavelength ...atom_site / diffrn_radiation_wavelength / em_image_scans / em_software / entity / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.pdbx_formal_charge / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name / _entity.src_method / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_validate_close_contact.auth_atom_id_1
Revision 2.1Oct 2, 2019Group: Data collection / Derived calculations / Other / Category: atom_sites / cell / struct_conn
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -6-STRANDED BARREL THIS IS REPRESENTED BY A -5-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-2787
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: MITORIBOSOMAL PROTEIN BL27M, MRPL27
1: MITORIBOSOMAL PROTEIN BL28M, MRPL28
2: MITORIBOSOMAL PROTEIN UL29M, MRPL47
3: MITORIBOSOMAL PROTEIN UL30M, MRPL30
4: MITORIBOSOMAL PROTEIN BL31M, MRPL55
5: MITORIBOSOMAL PROTEIN BL32M, MRPL32
6: MITORIBOSOMAL PROTEIN BL33M, MRPL33
7: MITORIBOSOMAL PROTEIN BL34M, MRPL34
8: MITORIBOSOMAL PROTEIN BL35M, MRPL35
9: MITORIBOSOMAL PROTEIN BL36M, MRPL36
A: MITORIBOSOMAL 16S RRNA
B: MITORIBOSOMAL CP TRNA
C: TRNA
D: MITORIBOSOMAL PROTEIN UL2M, MRPL2
E: MITORIBOSOMAL PROTEIN UL3M, MRPL3
F: MITORIBOSOMAL PROTEIN UL4M, MRPL4
I: MITORIBOSOMAL PROTEIN BL9M, MRPL9
J: MITORIBOSOMAL PROTEIN UL10M, MRPL10
K: MITORIBOSOMAL PROTEIN UL11M, MRPL11
N: MITORIBOSOMAL PROTEIN UL13M, MRPL13
O: MITORIBOSOMAL PROTEIN UL14M, MRPL14
P: MITORIBOSOMAL PROTEIN UL15M, MRPL15
Q: MITORIBOSOMAL PROTEIN UL16M, MRPL16
R: MITORIBOSOMAL PROTEIN BL17M, MRPL17
S: MITORIBOSOMAL PROTEIN UL18M, MRPL18
T: MITORIBOSOMAL PROTEIN BL19M, MRPL19
U: MITORIBOSOMAL PROTEIN BL20M, MRPL20
V: MITORIBOSOMAL PROTEIN BL21M, MRPL21
W: MITORIBOSOMAL PROTEIN UL22M, MRPL22
X: MITORIBOSOMAL PROTEIN UL23M, MRPL23
Y: MITORIBOSOMAL PROTEIN UL24M, MRPL24
Z: TRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,176,426203
Polymers1,172,18832
Non-polymers4,238171
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

-
Components

+
MITORIBOSOMAL ... , 30 types, 30 molecules 0123456789ABDEFIJKNOPQRSTUVWXY

#1: Protein MITORIBOSOMAL PROTEIN BL27M, MRPL27


Mass: 15943.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RT79
#2: Protein MITORIBOSOMAL PROTEIN BL28M, MRPL28


Mass: 30148.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RGV8, UniProt: A0A0R4J8D5*PLUS
#3: Protein MITORIBOSOMAL PROTEIN UL29M, MRPL47


Mass: 30085.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1SGC7*PLUS
#4: Protein MITORIBOSOMAL PROTEIN UL30M, MRPL30


Mass: 18585.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1STE5
#5: Protein MITORIBOSOMAL PROTEIN BL31M, MRPL55


Mass: 15156.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: I3LQ65
#6: Protein MITORIBOSOMAL PROTEIN BL32M, MRPL32


Mass: 21537.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: I3LTC4
#7: Protein MITORIBOSOMAL PROTEIN BL33M, MRPL33


Mass: 7508.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#8: Protein MITORIBOSOMAL PROTEIN BL34M, MRPL34


Mass: 10871.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: W5IDC1
#9: Protein MITORIBOSOMAL PROTEIN BL35M, MRPL35


Mass: 21548.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1SVC5
#10: Protein MITORIBOSOMAL PROTEIN BL36M, MRPL36


Mass: 10841.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: I3LDE8
#11: RNA chain MITORIBOSOMAL 16S RRNA


Mass: 504538.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: GenBank: 4220565
#12: RNA chain MITORIBOSOMAL CP TRNA


Mass: 18446.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#14: Protein MITORIBOSOMAL PROTEIN UL2M, MRPL2


Mass: 33270.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RRN2
#15: Protein MITORIBOSOMAL PROTEIN UL3M, MRPL3


Mass: 38427.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#16: Protein MITORIBOSOMAL PROTEIN UL4M, MRPL4


Mass: 33251.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1S3J8
#17: Protein MITORIBOSOMAL PROTEIN BL9M, MRPL9


Mass: 30373.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: I3LR45
#18: Protein MITORIBOSOMAL PROTEIN UL10M, MRPL10


Mass: 29449.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RWJ0
#19: Protein MITORIBOSOMAL PROTEIN UL11M, MRPL11


Mass: 20809.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RU54
#20: Protein MITORIBOSOMAL PROTEIN UL13M, MRPL13


Mass: 20633.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1S286
#21: Protein MITORIBOSOMAL PROTEIN UL14M, MRPL14


Mass: 15955.632 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RQV7
#22: Protein MITORIBOSOMAL PROTEIN UL15M, MRPL15


Mass: 33481.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RSH0
#23: Protein MITORIBOSOMAL PROTEIN UL16M, MRPL16


Mass: 28680.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RI89
#24: Protein MITORIBOSOMAL PROTEIN BL17M, MRPL17


Mass: 19268.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RMQ4
#25: Protein MITORIBOSOMAL PROTEIN UL18M, MRPL18


Mass: 20582.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1SB64, UniProt: A0A0R4J8D5*PLUS
#26: Protein MITORIBOSOMAL PROTEIN BL19M, MRPL19


Mass: 33441.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: I3LNJ0
#27: Protein MITORIBOSOMAL PROTEIN BL20M, MRPL20


Mass: 17554.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RJD0
#28: Protein MITORIBOSOMAL PROTEIN BL21M, MRPL21


Mass: 23154.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RY70
#29: Protein MITORIBOSOMAL PROTEIN UL22M, MRPL22


Mass: 24313.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#30: Protein MITORIBOSOMAL PROTEIN UL23M, MRPL23


Mass: 17643.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#31: Protein MITORIBOSOMAL PROTEIN UL24M, MRPL24


Mass: 24893.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RHJ1

-
RNA chain , 1 types, 2 molecules CZ

#13: RNA chain TRNA / Transfer RNA


Mass: 894.612 Da / Num. of mol.: 2 / Fragment: CCA-3' END / Source method: isolated from a natural source / Details: CHAIN C IS P-SITE TRNA AND CHAIN Z IS A-SITE TRNA / Source: (natural) SUS SCROFA (pig) / Organ: LIVER

-
Non-polymers , 3 types, 375 molecules

#32: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#33: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 169 / Source method: obtained synthetically / Formula: Mg
#34: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsZINC ION (ZN): ZN IONS COORDINATED BY ZINC FINGER PROTEINS PYRIMIDINE RIBOSIDE-5'-MONOPHOSPHATE ...ZINC ION (ZN): ZN IONS COORDINATED BY ZINC FINGER PROTEINS PYRIMIDINE RIBOSIDE-5'-MONOPHOSPHATE (Y5P): UNASSIGNED PYRIMIDINES IN CP-TRNA POLYNUCLEOTIDE PURINE RIBOSIDE-5'-MONOPHOSPHATE (P5P): UNASSIGNED PURINES IN CP-TRNA POLYNUCLEOTIDE CYS J64 FORMS A MIXED ZINC FINGER TOGETHER WITH RESIDUES CYS x70, CYS x73 AND CYS x108 OF SPLIT ENTRY 4V1A
Sequence detailsA-SITE TRNA, UNIVERSALLY CONSERVED CCA-3' END P-SITE TRNA, UNIVERSALLY CONSERVED CCA-3' END ...A-SITE TRNA, UNIVERSALLY CONSERVED CCA-3' END P-SITE TRNA, UNIVERSALLY CONSERVED CCA-3' END UNASSIGNED PURINE-PYRIMIDINE POLYNUCLEOTIDE OF CP-TRNA. PURINES BUILT AS P5P, PYRIMIDINES BUILT AS Y5P. G NUCLEOTIDE INSERTION AT POSITION 127A RELATIVE TO MINIMAL REFERENCE SEQUENCE AJ002189.1 GENBANK REFERENCE FOR CHAIN 2 XP_003132595.1 GENBANK REFERENCE FOR CHAIN 6 XP_003125332.1 GENBANK REFERENCE FOR CHAIN E AY609899.1 GENBANK REFERENCE FOR CHAIN W AK392578.1 GENBANK REFERENCE FOR CHAIN X AK392218.1

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: SUS SCROFA 55S MITOCHONDRIAL RIBOSOME / Type: RIBOSOME
Details: QUANTIFOIL HOLEY CARBON GRIDS WERE COATED WITH A THIN CARBON FILM
Buffer solutionName: 20 MM HEPES-KOH, 50 MM KCL, 40 MM MGCL2, 1 MM DTT / pH: 7.4 / Details: 20 MM HEPES-KOH, 50 MM KCL, 40 MM MGCL2, 1 MM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE / Details: MIXTURE OF LIQUID ETHANE AND PROPANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: May 30, 2014
Details: IMAGES WERE ACQUIRED IN 2 SESSIONS ON A FEI TITAN KRIOS IN MAY 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 100000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderTemperature: 85 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameVersionCategory
1CTFFINDCTF correction
2Cootmodel fitting
3Omodel fitting
4UCSF Chimeramodel fitting
5EMAN1.93D reconstruction
6RELION3D reconstruction
CTF correctionDetails: PER DETECTOR FRAME
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: MAXIMUM LIKELIHOOD BASED REFINEMENT IMPLEMENTED IN RELION
Resolution: 3.4 Å / Num. of particles: 141675 / Actual pixel size: 1.4 Å
Details: FOR VISUALIZATION PURPOSES THE FINAL MAP WAS FILTERED AND AMPLITUDE CORRECTED IN RELION SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2787. (DEPOSITION ID: 12830). THE COMBINED ...Details: FOR VISUALIZATION PURPOSES THE FINAL MAP WAS FILTERED AND AMPLITUDE CORRECTED IN RELION SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2787. (DEPOSITION ID: 12830). THE COMBINED COORDINATES (SPLIT ENTRIES 4V19 AND 4V1A) WERE REFINED IN RECIPROCAL SPACE USING PHENIX.REFINE AGAINST THE MLHL TARGET. FOR THIS, THE CRYO-EM MAPS (EMD-2787) WERE CONVERTED TO RECIPROCAL SPACE STRUCTURE FACTORS.
Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementHighest resolution: 3.4 Å
Refinement stepCycle: LAST / Highest resolution: 3.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35452 33582 171 204 69409

+
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