[English] 日本語
Yorodumi
- EMDB-4370: Unique features of mammalian mitochondrial translation initiation... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 4370
TitleUnique features of mammalian mitochondrial translation initiation revealed by cryo-EM. This file contains the 39S ribosomal subunit.
Map data
Samplemammalian mitochondrial translation initiation complex
  • mammalian mitochondrial ribosome
  • (Translation initiation factor IF-2, ...) x 2
  • tRNATransfer RNA
  • (Mitochondrial ribosomal protein ...) x 42
  • ('Mitochondrial ribosomal protein ...) x 3
  • Ribosomal protein
  • (nucleic-acidNucleic acid) x 3
  • ICT1
  • Mrpl34
  • mL53, MRPL53
  • Uncharacterized protein
  • mL65, MRPS30
  • unassigned secondary structure elements
  • (ligand) x 8
Function / homology39S ribosomal protein L52, mitochondrial / Mitochondrial ribosomal protein L48 / Ribosomal protein L46, N-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Translation initiation factor IF- 2, domain 3 / Ribosomal protein L4 domain superfamily / Ribosomal protein L28/L24 / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S10 domain ...39S ribosomal protein L52, mitochondrial / Mitochondrial ribosomal protein L48 / Ribosomal protein L46, N-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Translation initiation factor IF- 2, domain 3 / Ribosomal protein L4 domain superfamily / Ribosomal protein L28/L24 / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S10 domain / Ribosomal protein L21-like / Ribosomal protein L18e/L15P / Ribosomal protein L15 / NTF2-like domain superfamily / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein L17 / L28p-like / Ribosomal protein L20, C-terminal / Phosphatidylethanolamine-binding protein, eukaryotic / Ribosomal protein L36 superfamily / Ribosomal protein L35 / Ribosomal protein L11, N-terminal / Ribosomal L18e/L15P superfamily / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Double-stranded RNA-binding domain / Ribosomal protein L2, domain 2 / Translation initiation factor IF- 2 / NUDIX hydrolase-like domain superfamily / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L10e/L16 / Ribosomal protein 63, mitochondrial / Ribosomal protein L50, mitochondria / Ribosomal protein L11, C-terminal / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Ribosomal protein L55, mitochondrial / Ribosomal protein L27/L41, mitochondrial / Ribosomal protein L28/L40, mitochondrial / Ribosomal protein L35, mitochondrial / Ribosomal protein S32, mitochondrial / Ribosomal protein L51, mitochondrial / Ribosomal protein L9, N-terminal / L21-like superfamily / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L34 / Ribosomal protein L23 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L30p/L7e / Ribosomal protein S10p/S20e / Ribosomal protein L36 / Ribosomal protein L20 / Ribosomal protein L10 / KOW motif / Ribosomal protein L33 / Ribosomal protein L22p/L17e / RF-1 domain / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein L4/L1 family / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal prokaryotic L21 protein / Ribosomal L28 family / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal L27 protein / Ribosomal protein L16p/L10e / Ribosomal Proteins L2, RNA binding domain / Thioredoxin-like superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L17 superfamily / Ribonuclease III, endonuclease domain superfamily / Ribosomal protein L22/L17 superfamily / PEBP-like superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L10e/L16 superfamily / Elongation factor Tu GTP binding domain / Translation initiation factor IF-2, domain 3 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L35 superfamily / MRP-L47 superfamily, mitochondrial / Ribosomal protein L33 superfamily / 39S ribosomal protein L40, mitochondrial / Ribosomal protein L37, mitochondrial / Ribosomal protein L25/L23 / Phosphatidylethanolamine-binding protein / Ribosomal Proteins L2, C-terminal domain / Mitochondrial ribosomal protein L37 / Mitochondrial 28S ribosomal protein S30 (PDCD9) / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial large subunit ribosomal protein (Img2) / Tim44-like domain / Ribosomal protein L11, N-terminal domain / Mitochondrial ribosomal protein L27 / Ribosomal protein L35 / Ribosomal protein L9, N-terminal domain
Function and homology information
SourceSus scrofa (pig) / Homo sapiens (human) / Pig (pig)
Methodsingle particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsKummer E / Leibundgut M / Boehringer D / Ban N
CitationJournal: Nature / Year: 2018
Title: Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM.
Authors: Eva Kummer / Marc Leibundgut / Oliver Rackham / Richard G Lee / Daniel Boehringer / Aleksandra Filipovska / Nenad Ban
Validation ReportPDB-ID: 6gb2

SummaryFull reportAbout validation report
DateDeposition: Apr 13, 2018 / Header (metadata) release: May 23, 2018 / Map release: Aug 8, 2018 / Last update: Aug 22, 2018

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6gb2
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_4370.map.gz (map file in CCP4 format, 88753 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
281 pix
1.39 Å/pix.
= 390.59 Å
281 pix
1.39 Å/pix.
= 390.59 Å
281 pix
1.39 Å/pix.
= 390.59 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density
Contour Level:0.12 (by author), 0.12 (movie #1):
Minimum - Maximum-0.3282438 - 0.65797997
Average (Standard dev.)0.0017977863 (0.0235527)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions281281281
Origin0.0.0.
Limit280.280.280.
Spacing281281281
CellA=B=C: 390.59 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z281281281
origin x/y/z0.0000.0000.000
length x/y/z390.590390.590390.590
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS281281281
D min/max/mean-0.3280.6580.002

-
Supplemental data

-
Mask #1

Fileemd_4370_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

-
Sample components

+
Entire mammalian mitochondrial translation initiation complex

EntireName: mammalian mitochondrial translation initiation complex
Number of components: 68

+
Component #1: protein, mammalian mitochondrial translation initiation complex

ProteinName: mammalian mitochondrial translation initiation complex
Recombinant expression: No
MassTheoretical: 2.85 MDa

+
Component #2: protein, mammalian mitochondrial ribosome

ProteinName: mammalian mitochondrial ribosome / Recombinant expression: No
SourceSpecies: Sus scrofa (pig)

+
Component #3: protein, Translation initiation factor IF-2, mitochondrial

ProteinName: Translation initiation factor IF-2, mitochondrial / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #4: protein, tRNA

ProteinName: tRNATransfer RNA / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: synthetic construct (others)

+
Component #5: protein, Mitochondrial ribosomal protein L12

ProteinName: Mitochondrial ribosomal protein L12
Details: Unassigned residues have been built as poly-alanine.
Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 21.268975 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #6: protein, Mitochondrial ribosomal protein L27

ProteinName: Mitochondrial ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.943688 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #7: protein, Mitochondrial ribosomal protein L28

ProteinName: Mitochondrial ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.148953 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #8: protein, Mitochondrial ribosomal protein L47

ProteinName: Mitochondrial ribosomal protein L47 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.085088 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #9: protein, 'Mitochondrial ribosomal protein L30

ProteinName: 'Mitochondrial ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.58584 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #10: protein, 'Mitochondrial ribosomal protein L55

ProteinName: 'Mitochondrial ribosomal protein L55 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.156537 kDa
SourceSpecies: Pig (pig)

+
Component #11: protein, Mitochondrial ribosomal protein L32

ProteinName: Mitochondrial ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.53793 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #12: protein, Mitochondrial ribosomal protein L33

ProteinName: Mitochondrial ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.508097 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #13: protein, Mitochondrial ribosomal protein L34

ProteinName: Mitochondrial ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.871729 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #14: protein, Mitochondrial ribosomal protein L35

ProteinName: Mitochondrial ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.548543 kDa
SourceSpecies: Pig (pig)

+
Component #15: protein, Ribosomal protein

ProteinName: Ribosomal protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.841016 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #16: nucleic-acid, 16S ribosomal RNA, mitochondrial

Nucleic-acidName: 16S ribosomal RNA, mitochondrial / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
ACCAAAGCUA GCUCAACAUA CUAAACAAAU ACAAAAAUAC ACCAAAAUAA AAUAAAACAU UCACCUAACA UUAAAGUAUA GGAGAUAGAA AUUUUUAUCC UGACGCUAUA GAGAUAGUAC CGUAAGGGAA AGAUGAAAGA AUAAAAUAAA AGUAAAAAAA AGCAAAGAUU ACCCCUUCUA CCUUUUGCAU AAUGGUUUAA CCAGAAAAAA UCUAACAAAG AGAACUUUAG CUAGAUACCC CGAAACCAGA CGAGCUACCC AUGAGCAGUU UAAAAGAACC AACUCAUCUA UGUGGCAAAA UAGUGAGAAG ACUUGUAGGU AGAGGUGAAA AGCCUAACGA GCCUGGUGAU AGCUGGUUGU CCGAGAAAGA AUUUUAGUUC AACCUUAAAA AUACCCCAAA AACCCUAAAU UCCAAUGUAU UUUUAAGAGA UAGUCUAAAA AGGUACAGCU UUUUAGAAAC GGAUACAACC UUGACUAGAG AGUAAAAUCU UAAUACUACC AUAGUAGGCC UAAAAGCAGC CAUCAAUUGA GAAAGCGUUA AAGCUCAACA AAUUCACCAA CAUAAUCCCA AAAACUAAUA ACAAACUCCU AGCCCAAUAC CGGACUAAUC UAUUGAAACA UAGAAGCAAU AAUGUUAAUA UGAGUAACAA GAAGCCUUUC UCCUCGCACA CGCUUACAUC AGUAACUAAU AAUAUACUGA UAAUUAACAA CCAAUAAACC AAAACAACAC UAAAACGUUU AUUAAUUACA UUGUUAACCC AACACAGGAG UGCACCAAGG AAAGAUUAAA AGAAGUAAAA GGAACUCGGC AAACACAAAC CCCGCCUGUU UACCAAAAAC AUCACCUCUA GCAUUACUAG UAUUAGAGGC AAUGCCUGCC CAGUGACACC AGUUUAACGG CCGCGGUAUU CUGACCGUGC AAAGGUAGCA UAAUCACUUG UUCUCCAAAU AAGGACUUGU AUGAAUGGCC ACACGAGGGU UUUACUGUCU CUUACUUCCA AUCAGUGAAA UUAACCUUCC CGUGAAGAGG CGGGAAUAAA AAAAUAAGAC GAGAAGACCC UAUGGAGCUU UAAUUAACUA UUCCAAAAGU UAAACAACUC AACCACAAAG GGAUAAAACA UAACUUAACA UGGACUAGCA AUUUCGGUUG GGGUGACCUC GGAGUACAAA AAACCCUCCG AGUGAUUUUA AUCUAGACAA ACCAGUCAAA AUAACCAUAA CAUCACUUAU UGAUCCAAAA UUUUGAUCAA CGGAACAAGU UACCCUAGGG AUAACAGCGC AAUCCUGUUC UAGAGUUCCU AUCGACAAUA GGGUUUACGA CCUCGAUGUU GGAUCAGGAC ACCCAAAUGG UGCAACCGCU AUUAAAGGUU CGUUUGUUCA ACGAUUAAAG UCCUACGUGA UCUGAGUUCA GACCGGAGCA AUCCAGGUCG GUUUCUAUCU AUUAUAAAUU UCUCCCAGUA CGAAAGGACA AGAGAAAUGG GACCAACCUC ACAAACGCGU CUCAGAGAUA AUUAAUGAUU UAAUCUUAAC CUAAUUAACU CAUAAUAAAU CCAGCCCUAG AACAGGGCAC A
MassTheoretical: 504.852031 kDa
SourceSpecies: Sus scrofa (pig)

+
Component #17: nucleic-acid, CP tRNAPhe, mitochondrial

Nucleic-acidName: CP tRNAPhe, mitochondrial / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUUAAUGUAG CUUAAAUUAU CAAAGCAAGG CACUGAAAAU GCCUAGAUGA GCCUCACAGC UCCAUAAACA CCA
MassTheoretical: 23.402018 kDa
SourceSpecies: Sus scrofa (pig)

+
Component #18: protein, Translation initiation factor IF-2, mitochondrial

ProteinName: Translation initiation factor IF-2, mitochondrial
Details: Unassigned residues have been built as poly-alanine.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 72.811219 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #19: protein, Mitochondrial ribosomal protein L2

ProteinName: Mitochondrial ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.270934 kDa
SourceSpecies: Pig (pig)

+
Component #20: protein, ICT1

ProteinName: ICT1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.427199 kDa
SourceSpecies: Pig (pig)

+
Component #21: protein, Mitochondrial ribosomal protein L4

ProteinName: Mitochondrial ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.251469 kDa
SourceSpecies: Pig (pig)

+
Component #22: protein, Mitochondrial ribosomal protein L9

ProteinName: Mitochondrial ribosomal protein L9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.373449 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #23: protein, Mitochondrial ribosomal protein L10

ProteinName: Mitochondrial ribosomal protein L10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.449689 kDa
SourceSpecies: Pig (pig)

+
Component #24: protein, Mitochondrial ribosomal protein L11

ProteinName: Mitochondrial ribosomal protein L11
Details: Unassigned residues have been built as poly-alanine.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.809271 kDa
SourceSpecies: Pig (pig)

+
Component #25: protein, Mitochondrial ribosomal protein L13

ProteinName: Mitochondrial ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.633801 kDa
SourceSpecies: Pig (pig)

+
Component #26: protein, Mitochondrial ribosomal protein L14

ProteinName: Mitochondrial ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.955632 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #27: protein, Mitochondrial ribosomal protein L15

ProteinName: Mitochondrial ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.481723 kDa
SourceSpecies: Pig (pig)

+
Component #28: protein, Mitochondrial ribosomal protein L16

ProteinName: Mitochondrial ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.680531 kDa
SourceSpecies: Pig (pig)

+
Component #29: protein, Mitochondrial ribosomal protein L17

ProteinName: Mitochondrial ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.268178 kDa
SourceSpecies: Pig (pig)

+
Component #30: protein, Mitochondrial ribosomal protein L18

ProteinName: Mitochondrial ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.582568 kDa
SourceSpecies: Pig (pig)

+
Component #31: protein, Mitochondrial ribosomal protein L19

ProteinName: Mitochondrial ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.441539 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #32: protein, Mitochondrial ribosomal protein L20

ProteinName: Mitochondrial ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.554793 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #33: protein, Mitochondrial ribosomal protein L21

ProteinName: Mitochondrial ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.154861 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #34: protein, Mitochondrial ribosomal protein L22

ProteinName: Mitochondrial ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.313357 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #35: protein, Mitochondrial ribosomal protein L23

ProteinName: Mitochondrial ribosomal protein L23
Details: Unassigned residues have been built as poly-alanine.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.643205 kDa
SourceSpecies: Pig (pig)

+
Component #36: protein, Mitochondrial ribosomal protein L24

ProteinName: Mitochondrial ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.893529 kDa
SourceSpecies: Pig (pig)

+
Component #37: protein, Mitochondrial ribosomal protein L37

ProteinName: Mitochondrial ribosomal protein L37 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.917988 kDa
SourceSpecies: Pig (pig)

+
Component #38: protein, Mitochondrial ribosomal protein L38

ProteinName: Mitochondrial ribosomal protein L38 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 44.656387 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #39: protein, Mitochondrial ribosomal protein L39

ProteinName: Mitochondrial ribosomal protein L39 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.523422 kDa
SourceSpecies: Pig (pig)

+
Component #40: protein, Mitochondrial ribosomal protein L40

ProteinName: Mitochondrial ribosomal protein L40 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.075658 kDa
SourceSpecies: Pig (pig)

+
Component #41: protein, Mitochondrial ribosomal protein L41

ProteinName: Mitochondrial ribosomal protein L41 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.073404 kDa
SourceSpecies: Pig (pig)

+
Component #42: protein, Mitochondrial ribosomal protein L42

ProteinName: Mitochondrial ribosomal protein L42
Details: Unassigned residues have been built as poly-alanine.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.680178 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #43: protein, Mitochondrial ribosomal protein L43

ProteinName: Mitochondrial ribosomal protein L43 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.728109 kDa
SourceSpecies: Pig (pig)

+
Component #44: protein, Mitochondrial ribosomal protein L44

ProteinName: Mitochondrial ribosomal protein L44 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.527195 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #45: protein, Mitochondrial ribosomal protein L45

ProteinName: Mitochondrial ribosomal protein L45 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.331805 kDa
SourceSpecies: Pig (pig)

+
Component #46: protein, Mitochondrial ribosomal protein L46

ProteinName: Mitochondrial ribosomal protein L46 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.215998 kDa
SourceSpecies: Pig (pig)

+
Component #47: protein, Mitochondrial ribosomal protein L48

ProteinName: Mitochondrial ribosomal protein L48 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.749512 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #48: protein, Mrpl34

ProteinName: Mrpl34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.957779 kDa
SourceSpecies: Pig (pig)

+
Component #49: protein, Mitochondrial ribosomal protein L50

ProteinName: Mitochondrial ribosomal protein L50 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.351 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #50: protein, Mitochondrial ribosomal protein L51

ProteinName: Mitochondrial ribosomal protein L51 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.249048 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #51: protein, Mitochondrial ribosomal protein L52

ProteinName: Mitochondrial ribosomal protein L52 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.813705 kDa
SourceSpecies: Pig (pig)

+
Component #52: protein, mL53, MRPL53

ProteinName: mL53, MRPL53 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.015747 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #53: protein, Uncharacterized protein

ProteinName: Uncharacterized protein
Details: Unassigned residues have been built as poly-alanine.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.957357 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #54: protein, Mitochondrial ribosomal protein L57

ProteinName: Mitochondrial ribosomal protein L57 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.001915 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #55: protein, Mitochondrial ribosomal protein L58

ProteinName: Mitochondrial ribosomal protein L58
Details: Unassigned residues have been built as poly-alanine.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.545873 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #56: protein, 'Mitochondrial ribosomal protein L59

ProteinName: 'Mitochondrial ribosomal protein L59 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.815031 kDa
SourceSpecies: Pig (pig)

+
Component #57: protein, mL65, MRPS30

ProteinName: mL65, MRPS30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.100504 kDa
SourceSpecies: Pig (pig)

+
Component #58: protein, Mitochondrial ribosomal protein S18A

ProteinName: Mitochondrial ribosomal protein S18A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.273084 kDa
SourceSpecies: Pig (pig)

+
Component #59: protein, unassigned secondary structure elements

ProteinName: unassigned secondary structure elements
Details: Unassigned secondary structure elements have been built as poly-alanine.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.846387 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: liver

+
Component #60: nucleic-acid, P-site fMet-tRNAMet, mitochondrial

Nucleic-acidName: P-site fMet-tRNAMet, mitochondrial / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AGUAAGGUCA GCUAAAUAAG CUAUCGGGCC CAUACCCCGA AAAUGUUGGU UAUACCCUUC CCGUACUACC A
MassTheoretical: 22.664498 kDa
SourceSpecies: Homo sapiens (human)

+
Component #61: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 216 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #62: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #63: ligand, GUANOSINE-5'-MONOPHOSPHATE

LigandName: GUANOSINE-5'-MONOPHOSPHATE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.363221 kDa

+
Component #64: ligand, SPERMINE

LigandName: SPERMINE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.20234 kDa

+
Component #65: ligand, 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE

LigandName: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.539246 kDa

+
Component #66: ligand, SODIUM ION

LigandName: SODIUM IONSodium / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.29905 MDa

+
Component #67: ligand, N-FORMYLMETHIONINE

LigandName: N-FORMYLMETHIONINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.177221 kDa

+
Component #68: ligand, water

LigandName: water / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.171 mg/ml / pH: 7.6
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 13936

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 75666
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Modeling #1Refinement space: RECIPROCAL / Overall bvalue: 56.899999999999999
Output model

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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