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- PDB-9ojm: Human mitochondrial 28S PIC with tRNA and mtIF2 -

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Basic information

Entry
Database: PDB / ID: 9ojm
TitleHuman mitochondrial 28S PIC with tRNA and mtIF2
Components
  • (28S ribosomal protein ...) x 11
  • (Small ribosomal subunit protein ...) x 18
  • 12S mitochondrial RNA
  • Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
  • RNA (71-MER)
  • Translation initiation factor IF-2, mitochondrial
  • mRNA (5'-R(P*AP*UP*GP*U)-3')
KeywordsRIBOSOME / Mitochondrial Ribosome 28S pre-initiation complex
Function / homology
Function and homology information


mitochondrial translational initiation / translation factor activity, RNA binding / formation of translation preinitiation complex / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation initiation / Mitochondrial ribosome-associated quality control / Mitochondrial translation termination / mitochondrial ribosome / ribosome disassembly ...mitochondrial translational initiation / translation factor activity, RNA binding / formation of translation preinitiation complex / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation initiation / Mitochondrial ribosome-associated quality control / Mitochondrial translation termination / mitochondrial ribosome / ribosome disassembly / mitochondrial small ribosomal subunit / mitochondrial translation / apoptotic mitochondrial changes / positive regulation of proteolysis / ribosomal small subunit binding / sperm head-tail coupling apparatus / translation initiation factor activity / Mitochondrial protein degradation / apoptotic signaling pathway / fibrillar center / regulation of translation / small ribosomal subunit / small ribosomal subunit rRNA binding / nuclear membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / tRNA binding / cell population proliferation / mitochondrial inner membrane / rRNA binding / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / mRNA binding / GTPase activity / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / : / Elongation factor G domain 2 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 ...Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / : / Elongation factor G domain 2 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / Cysteine alpha-hairpin motif superfamily / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / 28S ribosomal protein S27, mitochondrial / MRPS27/PTCD2 / Mitochondrial 28S ribosomal protein S27 / Ribosomal protein S22, mitochondrial / : / Mitochondrial 28S ribosomal protein S22 / Ribosomal protein S29, mitochondrial / Ribosomal protein S28, mitochondrial / 28S ribosomal protein S10, mitochondrial / Mitochondrial ribosomal protein MRP-S35 / 28S ribosomal protein S24, mitochondrial / Mitochondrial 28S ribosomal protein S34 / Pentatricopeptide repeat domain-containing protein 3 / 28S ribosomal protein S17, mitochondrial / : / : / Mitochondrial ribosome subunit S24 / Mitochondrial 28S ribosomal protein S34 / Small ribosomal subunit protein uS5m, N-terminal / Small ribosomal subunit protein mS39, PPR / 28S ribosomal protein S25, mitochondrial / Pentatricopeptide repeat domain / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / Pentatricopeptide (PPR) repeat profile. / Pentatricopeptide repeat / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / CHCH / CHCH domain / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S2 signature 1. / Small GTP-binding protein domain / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S10p/S20e / Ribosomal S11, conserved site / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S11 signature. / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S11 / Ribosomal protein S12 signature. / Ribosomal protein S11 / Ribosomal protein S5/S7 / Ribosomal protein S7 domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) ...ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS12m / Small ribosomal subunit protein uS14m / Translation initiation factor IF-2, mitochondrial / Small ribosomal subunit protein mS29 / Small ribosomal subunit protein mS22 / Small ribosomal subunit protein mS25 / Small ribosomal subunit protein uS10m / Small ribosomal subunit protein mS35 / Small ribosomal subunit protein uS5m / Small ribosomal subunit protein uS11m / Small ribosomal subunit protein uS15m / Small ribosomal subunit protein bS21m / Small ribosomal subunit protein mS34 / Small ribosomal subunit protein bS6m / Small ribosomal subunit protein uS9m / Small ribosomal subunit protein mS27 / Small ribosomal subunit protein mS37 / Small ribosomal subunit protein uS3m / Small ribosomal subunit protein mS39 / Small ribosomal subunit protein mS26 / Small ribosomal subunit protein bS22, mitochondrial / Small ribosomal subunit protein mS33 / Small ribosomal subunit protein bS1m / Small ribosomal subunit protein uS17m / Small ribosomal subunit protein uS7m / Small ribosomal subunit protein uS2m / Small ribosomal subunit protein bS16m
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsKober, D.L. / Wang, J.
Funding support United States, 4items
OrganizationGrant numberCountry
Welch FoundationI-2218-20240404 United States
Welch FoundationI-2246-20250403 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00GM141261 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM155152 United States
CitationJournal: Nat Commun / Year: 2026
Title: Mechanisms of human mitochondrial leaderless mRNA translation initiation.
Authors: Shuangjie Shen / Yinghua Xu / Daniel L Kober / Jinfan Wang /
Abstract: Mitochondrial translation is essential for cellular function, and its dysregulation is associated with mitochondrial disorders and cancer. However, the mechanisms by which human mitochondrial ...Mitochondrial translation is essential for cellular function, and its dysregulation is associated with mitochondrial disorders and cancer. However, the mechanisms by which human mitochondrial ribosomes initiate translation remain poorly understood, particularly because mitochondrial mRNAs generally lack the 5' untranslated regions that guide translation initiation in bacterial and cytoplasmic systems. Using real-time single-molecule fluorescence measurements, biochemical assays, and cryo-EM analysis, we show that human mitochondrial translation initiation occurs through two parallel pathways. In one pathway, leaderless mRNA first loads onto the 28S small subunit, followed by recruitment of the 39S large subunit to form the 55S initiation complex. In the second pathway, a preassembled 55S monosome directly loads onto leaderless mRNA. Both pathways require recruitment of mtIF2 and fMet-tRNA before mRNA binding. However, the monosome-loading pathway tolerates non-formylated Met-tRNA and is suppressed by mtIF3. Together, these findings define the heterogeneous pathways of human mitochondrial translation initiation on leaderless mRNAs.
History
DepositionMay 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Small ribosomal subunit protein mS34
1: Small ribosomal subunit protein mS35
2: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
3: Small ribosomal subunit protein mS38
4: Small ribosomal subunit protein mS39
5: RNA (71-MER)
6: mRNA (5'-R(P*AP*UP*GP*U)-3')
7: Translation initiation factor IF-2, mitochondrial
A: 12S mitochondrial RNA
B: Small ribosomal subunit protein uS2m
C: 28S ribosomal protein S24, mitochondrial
D: 28S ribosomal protein S5, mitochondrial
E: 28S ribosomal protein S6, mitochondrial
F: 28S ribosomal protein S7, mitochondrial
G: Small ribosomal subunit protein uS9m
H: Small ribosomal subunit protein uS10m
I: Small ribosomal subunit protein uS11m
J: 28S ribosomal protein S12, mitochondrial
K: 28S ribosomal protein S14, mitochondrial
L: Small ribosomal subunit protein uS15m
M: Small ribosomal subunit protein bS16m
N: Small ribosomal subunit protein uS17m
O: 28S ribosomal protein S18b, mitochondrial
P: 28S ribosomal protein S18c, mitochondrial
Q: 28S ribosomal protein S21, mitochondrial
R: Small ribosomal subunit protein mS22
S: 28S ribosomal protein S23, mitochondrial
T: Small ribosomal subunit protein mS25
U: Small ribosomal subunit protein mS26
V: Small ribosomal subunit protein mS27
W: Small ribosomal subunit protein bS1m
X: Small ribosomal subunit protein mS29
Y: 28S ribosomal protein S27, mitochondrial
Z: Small ribosomal subunit protein mS33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,069,941132
Polymers1,065,51834
Non-polymers4,42398
Water25,2031399
1


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

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Components

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Small ribosomal subunit protein ... , 18 types, 18 molecules 0134BGHILMNRTUVWXZ

#1: Protein Small ribosomal subunit protein mS34 / 28S ribosomal protein S34 / mitochondrial / MRP-S34 / S34mt


Mass: 25336.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82930
#2: Protein Small ribosomal subunit protein mS35 / 28S ribosomal protein S28 / mitochondrial / MRP-S28 / S28mt / 28S ribosomal protein S35 / MRP-S35 / S35mt


Mass: 32156.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82673
#4: Protein Small ribosomal subunit protein mS38 / 28S ribosomal protein S38 / mitochondrial / MRP-S38 / Aurora kinase A-interacting protein / AURKA- ...28S ribosomal protein S38 / mitochondrial / MRP-S38 / Aurora kinase A-interacting protein / AURKA-interacting protein


Mass: 8936.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NWT8
#5: Protein Small ribosomal subunit protein mS39 / 28S ribosomal protein S39 / mitochondrial / MRP-S39 / Pentatricopeptide repeat domain-containing ...28S ribosomal protein S39 / mitochondrial / MRP-S39 / Pentatricopeptide repeat domain-containing protein 3 / Transformation-related gene 15 protein / TRG-15


Mass: 70984.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EY7
#10: Protein Small ribosomal subunit protein uS2m / 28S ribosomal protein S2 / mitochondrial / MRP-S2 / S2mt


Mass: 25988.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y399
#15: Protein Small ribosomal subunit protein uS9m / 28S ribosomal protein S9 / mitochondrial / MRP-S9 / S9mt


Mass: 40136.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82933
#16: Protein Small ribosomal subunit protein uS10m / 28S ribosomal protein S10 / mitochondrial / MRP-S10 / S10mt


Mass: 16360.981 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82664
#17: Protein Small ribosomal subunit protein uS11m / 28S ribosomal protein S11 / mitochondrial / MRP-S11 / S11mt / Cervical cancer proto-oncogene 2 protein / HCC-2


Mass: 14509.841 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82912
#20: Protein Small ribosomal subunit protein uS15m / 28S ribosomal protein S15 / mitochondrial / MRP-S15 / S15mt


Mass: 20729.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82914
#21: Protein Small ribosomal subunit protein bS16m / 28S ribosomal protein S16 / mitochondrial / MRP-S16 / S16mt


Mass: 13438.712 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3D3
#22: Protein Small ribosomal subunit protein uS17m / 28S ribosomal protein S17 / mitochondrial / MRP-S17 / S17mt


Mass: 12349.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2R5
#26: Protein Small ribosomal subunit protein mS22 / 28S ribosomal protein S22 / mitochondrial / MRP-S22 / S22mt


Mass: 34251.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82650
#28: Protein Small ribosomal subunit protein mS25 / 28S ribosomal protein S25 / mitochondrial / MRP-S25 / S25mt


Mass: 19585.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82663
#29: Protein Small ribosomal subunit protein mS26 / 28S ribosomal protein S13 / mitochondrial / MRP-S13 / S13mt / 28S ribosomal protein S26 / MRP-S26 / S26mt


Mass: 21183.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYN8
#30: Protein Small ribosomal subunit protein mS27 / 28S ribosomal protein S27 / mitochondrial / MRP-S27 / S27mt / Mitochondrial ribosomal protein S27


Mass: 43969.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92552
#31: Protein Small ribosomal subunit protein bS1m / 28S ribosomal protein S28 / mitochondrial / MRP-S28 / S28mt / 28S ribosomal protein S35 / MRP-S35 / S35mt


Mass: 11263.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2Q9
#32: Protein Small ribosomal subunit protein mS29 / 28S ribosomal protein S29 / mitochondrial / MRP-S29 / S29mt / Death-associated protein 3 / DAP-3 / ...28S ribosomal protein S29 / mitochondrial / MRP-S29 / S29mt / Death-associated protein 3 / DAP-3 / Ionizing radiation resistance conferring protein


Mass: 40421.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P51398, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#34: Protein Small ribosomal subunit protein mS33 / 28S ribosomal protein S33 / mitochondrial / MRP-S33 / S33mt


Mass: 11952.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y291

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Protein , 2 types, 2 molecules 27

#3: Protein Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S37 / mitochondrial / MRP-S37 / Mitochondrial small ribosomal subunit protein ...28S ribosomal protein S37 / mitochondrial / MRP-S37 / Mitochondrial small ribosomal subunit protein mS37 / Nuclear protein C2360


Mass: 13498.819 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96BP2
#8: Protein Translation initiation factor IF-2, mitochondrial / IF-2(Mt) / IF-2Mt / IF2(mt)


Mass: 63169.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46199

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RNA chain , 3 types, 3 molecules 56A

#6: RNA chain RNA (71-MER)


Mass: 22664.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 1896813686
#7: RNA chain mRNA (5'-R(P*AP*UP*GP*U)-3')


Mass: 1241.786 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#9: RNA chain 12S mitochondrial RNA


Mass: 306547.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1858621102

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28S ribosomal protein ... , 11 types, 11 molecules CDEFJKOPQSY

#11: Protein 28S ribosomal protein S24, mitochondrial / S24mt / Mitochondrial small ribosomal subunit protein uS3m / bMRP-47 / bMRP47


Mass: 15333.757 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EL2
#12: Protein 28S ribosomal protein S5, mitochondrial / S5mt / Mitochondrial small ribosomal subunit protein uS5m


Mass: 38919.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82675
#13: Protein 28S ribosomal protein S6, mitochondrial / S6mt / Mitochondrial small ribosomal subunit protein bS6m


Mass: 13861.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82932
#14: Protein 28S ribosomal protein S7, mitochondrial / S7mt / Mitochondrial small ribosomal subunit protein uS7m / bMRP-27a / bMRP27a


Mass: 24569.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2R9
#18: Protein 28S ribosomal protein S12, mitochondrial / S12mt / MT-RPS12 / Mitochondrial small ribosomal subunit protein uS12m


Mass: 12013.163 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15235
#19: Protein 28S ribosomal protein S14, mitochondrial / S14mt / Mitochondrial small ribosomal subunit protein uS14m


Mass: 12282.349 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60783
#23: Protein 28S ribosomal protein S18b, mitochondrial


Mass: 22573.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#24: Protein 28S ribosomal protein S18c, mitochondrial


Mass: 11188.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#25: Protein 28S ribosomal protein S21, mitochondrial / S21mt / Mitochondrial small ribosomal subunit protein bS21m


Mass: 10764.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82921
#27: Protein 28S ribosomal protein S23, mitochondrial


Mass: 15702.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#33: Protein 28S ribosomal protein S27, mitochondrial


Mass: 17631.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Non-polymers , 8 types, 1497 molecules

#35: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 72 / Source method: obtained synthetically / Formula: Mg
#36: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: K
#37: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#38: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#39: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#40: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#41: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#42: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1399 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: Human mitochondrial 28S PIC with tRNA and mtIF2 / Type: RIBOSOME / Entity ID: #1-#34 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
12cryoSPARC4.73D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107666 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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  • 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

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