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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 / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation initiation / Mitochondrial ribosome-associated quality control / Mitochondrial translation termination / negative regulation of mitotic nuclear division / mitochondrial ribosome / ribosome disassembly ...mitochondrial translational initiation / translation factor activity, RNA binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation initiation / Mitochondrial ribosome-associated quality control / Mitochondrial translation termination / negative regulation of mitotic nuclear division / mitochondrial ribosome / ribosome disassembly / mitochondrial small ribosomal subunit / regulation of translational initiation / mitochondrial translation / positive regulation of proteolysis / apoptotic mitochondrial changes / ribosomal small subunit binding / 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 / intracellular membrane-bounded organelle / 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 / GTPase activity / mRNA binding / 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 / Ribosomal protein S21 superfamily / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / 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 S11 signature. / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S11 / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / 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 mS38 / 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: Shen, S. / Xu, Y. / Kober, D.L. / Wang, J.
History
DepositionMay 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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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