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- EMDB-9362: Structure of human mitochondrial translation initiation factor 3 ... -

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Entry
Database: EMDB / ID: 9362
TitleStructure of human mitochondrial translation initiation factor 3 bound to the small ribosomal subunit -Class I
Map dataStructure of human mitochondrial translation initiation factor 3 bound to the small ribosomal subunit
SampleStructure of human mitochondrial translation initiation factor 3 bound to the small ribosomal subunit
  • nucleic-acidNucleic acid
  • (28S ribosomal protein ...) x 26
  • DAP3 protein
  • Coiled-coil-helix-coiled-coil-helix domain containing 1
  • Pentatricopeptide repeat domain-containing protein 3, mitochondrial
  • Aurora kinase A interacting protein 1
  • Translation initiation factor IF-3, mitochondrial
Function / homologyCoiled-coil-helix-coiled-coil-helix domain-containing protein 1 / Ribosomal protein S9, conserved site / Ribosomal protein S6 superfamily / MRPS27/PTCD2 / Mitochondrial 28S ribosomal protein S27 / Mitochondrial 28S ribosomal protein S34 / Ribosomal protein S10 domain / P-loop containing nucleoside triphosphate hydrolase / Mitochondrial 28S ribosomal protein S31 / 28S ribosomal protein S24, mitochondrial ...Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / Ribosomal protein S9, conserved site / Ribosomal protein S6 superfamily / MRPS27/PTCD2 / Mitochondrial 28S ribosomal protein S27 / Mitochondrial 28S ribosomal protein S34 / Ribosomal protein S10 domain / P-loop containing nucleoside triphosphate hydrolase / Mitochondrial 28S ribosomal protein S31 / 28S ribosomal protein S24, mitochondrial / 28S ribosomal protein S26 / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S23/S25, mitochondrial / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S5 domain 2-type fold / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Translation initiation factor 3, C-terminal / Translation initiation factor 3, N-terminal / Ribosomal protein S23/Rsm25, mitochondrial / Ribosomal protein S28, mitochondrial / Ribosomal protein S22, mitochondrial / Ribosomal protein S23/S29, mitochondrial / Ribosomal protein S24/S35, mitochondrial, conserved domain / 28S ribosomal protein S27, mitochondrial / Ribosomal protein S18, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein S5 domain 2-type fold, subgroup / Thioredoxin-like superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / CHCH domain / Translation initiation factor IF-3, N-terminal domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S6 / Ribosomal protein S21 / Ribosomal protein S18 / Ribosomal protein S16 / Translation initiation factor IF-3, C-terminal domain / Ribosomal protein S11 / Ribosomal protein S9/S16 / Ribosomal protein S17 / Ribosomal protein S10p/S20e / Ribosomal protein S2 / Ribosomal protein S7 domain superfamily / Ribosomal protein S15 / Ribosomal protein S14p/S29e / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / 28S ribosomal protein S10, mitochondrial / 28S ribosomal protein S18b, mitochondrial / 28S ribosomal protein S25, mitochondrial / Ribosomal protein S24/S35, mitochondrial / 28S ribosomal protein S17, mitochondrial / Ribosomal protein S21 superfamily / Pentatricopeptide repeat domain-containing protein 3 / Ribosomal protein S11 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S27/S33, mitochondrial / Mitochondrial ribosomal subunit S27 / Mitochondrial 28S ribosomal protein S34 / Mitochondrial ribosomal subunit protein / Mitochondrial ribosomal death-associated protein 3 / Mitochondrial 28S ribosomal protein S22 / Mitochondrial ribosomal protein MRP-S35 / Mitochondrial ribosomal protein S23 / PPR repeat family / Pentatricopeptide repeat domain / Mitochondrial ribosome subunit S26 / Mitochondrial ribosome subunit S24 / Mitochondrial 28S ribosomal protein S31 / Ribosomal protein S11 signature. / Ribosomal protein S5/S7 / Ribosomal protein S12 signature. / Ribosomal protein S18 signature. / Ribosomal protein S9 signature. / Ribosomal protein S5 signature. / Ribosomal protein S2 signature 1. / S5 double stranded RNA-binding domain profile. / Pentatricopeptide (PPR) repeat profile. / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / Domain of unknown function DUF1713 / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein S17/S11 / Ribosomal protein S16 / Nucleic acid-binding, OB-fold / Tetratricopeptide-like helical domain superfamily / CHCH / Cysteine alpha-hairpin motif superfamily / S15/NS1, RNA-binding / Ribosomal protein S29, mitochondrial / Ribosomal protein/NADH dehydrogenase domain
Function and homology information
SourceHomo sapiens (human) / Bovine (cattle) / Human (human)
Methodsingle particle reconstruction / cryo EM / 3.48 Å resolution
AuthorsSharma M / Koripella R / Agrawal R
CitationJournal: iScience / Year: 2019
Title: Structure of Human Mitochondrial Translation Initiation Factor 3 Bound to the Small Ribosomal Subunit.
Authors: Ravi K Koripella / Manjuli R Sharma / Md Emdadul Haque / Paul Risteff / Linda L Spremulli / Rajendra K Agrawal
Abstract: The human mitochondrial translational initiation factor 3 (IF3) carries mitochondrial-specific amino acid extensions at both its N and C termini (N- and C-terminal extensions [NTE and CTE, ...The human mitochondrial translational initiation factor 3 (IF3) carries mitochondrial-specific amino acid extensions at both its N and C termini (N- and C-terminal extensions [NTE and CTE, respectively]), when compared with its eubacterial counterpart. Here we present 3.3- to 3.5-Å-resolution cryoelectron microscopic structures of the mammalian 28S mitoribosomal subunit in complex with human IF3. Unique contacts observed between the 28S subunit and N-terminal domain of IF3 explain its unusually high affinity for the 28S subunit, whereas the position of the mito-specific NTE suggests NTE's role in binding of initiator tRNA to the 28S subunit. The location of the C-terminal domain (CTD) clarifies its anti-association activity, whereas the orientation of the mito-specific CTE provides a mechanistic explanation for its role in destabilizing initiator tRNA in the absence of mRNA. Furthermore, our structure hints at a possible role of the CTD in recruiting leaderless mRNAs for translation initiation. Our findings highlight unique features of IF3 in mitochondrial translation initiation.
Validation ReportPDB-ID: 6nf8

SummaryFull reportAbout validation report
DateDeposition: Dec 19, 2018 / Header (metadata) release: Feb 27, 2019 / Map release: Feb 27, 2019 / Last update: Feb 27, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6nf8
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9362.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.07 Å/pix.
= 428. Å
400 pix
1.07 Å/pix.
= 428. Å
400 pix
1.07 Å/pix.
= 428. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour Level:0.15 (by author), 0.25 (movie #1):
Minimum - Maximum-1.2054142 - 2.2557297
Average (Standard dev.)-0.0012940647 (0.06735699)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin0.00.00.0
Limit399.0399.0399.0
Spacing400400400
CellA=B=C: 428.00003 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z428.000428.000428.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ364364364
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-1.2052.256-0.001

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Supplemental data

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Sample components

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Entire Structure of human mitochondrial translation initiation factor 3 ...

EntireName: Structure of human mitochondrial translation initiation factor 3 bound to the small ribosomal subunit
Details: Structure of human mitochondrial translation initiation factor 3 bound to the small ribosomal subunit
Number of components: 33

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Component #1: protein, Structure of human mitochondrial translation initiation ...

ProteinName: Structure of human mitochondrial translation initiation factor 3 bound to the small ribosomal subunit
Details: Structure of human mitochondrial translation initiation factor 3 bound to the small ribosomal subunit
Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #2: nucleic-acid, 28S ribosomal RNA, mitochondria

Nucleic-acidName: 28S ribosomal RNA, mitochondria / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CAUAGGUUUG GUCCCAGCCU UCCUGUUAAC UCUUAAUAAA CUUACACAUG CAAGCAUCUA CACCCCAGUG AGAAUGCCCU CUAGGUUAUU AAAACUAAGA GGAGCUGGCA UCAAGCACAC ACCCUGUAGC UCACGACGCC UUGCUUAACC ACACCCCACG GGAAACAGCA GUGACAAAAA UUAAGCCAUA AACGAAAGUU UGACUAAGUU AUAUUAAUUA GGGUUGGUAA AUCUCGUGCC AGCCACCGCG GUCAUACGAU UAACCCAAGC UAACAGGAGU ACGGCGUAAA ACGUGUUAAA GCACCAUACC AAAUAGGGUU AAAUUCUAAC UAAGCUGUAA AAAGCCAUGA UUAAAAUAAA AAUAAAUGAC GAAAGUGACC CUACAAUAGC CGACGCACUA UAGCUAAGAC CCAAACUGGG AUUAGAUACC CCACUAUGCU UAGCCCUAAA CACAGAUAAU UACAUAAACA AAAUUAUUCG CCAGAGUACU ACUAGCAACA GCUUAAAACU CAAAGGACUU GGCGGUGCUU UAUAUCCUUC UAGAGGAGCC UGUUCUAUAA UCGAUAAACC CCGAUAAACC UCACCAAUUC UUGCUAAUAC AGUCUAUAUA CCGCCAUCUU CAGCAAACCC UAAAAAGGAA AAAAAGUAAG CGUAAUUAUG AUACAUAAAA ACGUUAGGUC AAGGUGUAAC CUAUGAAAUG GGAAGAAAUG GGCUACAUUC UCUACACCAA GAGAAUCAAG CACGAAAGUU AUUAUGAAAC CAAUAACCAA AGGAGGAUUU AGCAGUAAAC UAAGAAUAGA GUGCUUAGUU GAAUUAGGCC AUGAAGCACG CACACACCGC CCGUCACCCU CCUCAAAUAG AUUCAGUGCA UCUAACCCUA UUUAAACGCA CUAGCUACAU GAGAGGAGAC AAGUCGUAAC AAGGUAAGCA UACUGGAAAG UGUGCUUGGA UAAAU
MassTheoretical: 306.932719 kDa
SourceSpecies: Bovine (cattle)

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Component #3: protein, 28S ribosomal protein S24, mitochondrial

ProteinName: 28S ribosomal protein S24, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.111455 kDa
SourceSpecies: Bovine (cattle)

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Component #4: protein, 28S ribosomal protein S5, mitochondrial

ProteinName: 28S ribosomal protein S5, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.956941 kDa
SourceSpecies: Bovine (cattle)

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Component #5: protein, 28S ribosomal protein S12, mitochondrial

ProteinName: 28S ribosomal protein S12, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.479285 kDa
SourceSpecies: Bovine (cattle)

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Component #6: protein, 28S ribosomal protein S16, mitochondrial

ProteinName: 28S ribosomal protein S16, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.157631 kDa
SourceSpecies: Bovine (cattle)

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Component #7: protein, 28S ribosomal protein S17, mitochondrial

ProteinName: 28S ribosomal protein S17, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.497051 kDa
SourceSpecies: Bovine (cattle)

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Component #8: protein, 28S ribosomal protein S22, mitochondrial

ProteinName: 28S ribosomal protein S22, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.720562 kDa
SourceSpecies: Bovine (cattle)

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Component #9: protein, 28S ribosomal protein S25, mitochondrial

ProteinName: 28S ribosomal protein S25, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.085312 kDa
SourceSpecies: Bovine (cattle)

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Component #10: protein, 28S ribosomal protein S26, mitochondrial

ProteinName: 28S ribosomal protein S26, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.815941 kDa
SourceSpecies: Bovine (cattle)

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Component #11: protein, 28S ribosomal protein S27, mitochondrial

ProteinName: 28S ribosomal protein S27, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.017867 kDa
SourceSpecies: Bovine (cattle)

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Component #12: protein, 28S ribosomal protein S34, mitochondrial

ProteinName: 28S ribosomal protein S34, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.880799 kDa
SourceSpecies: Bovine (cattle)

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Component #13: protein, 28S ribosomal protein S18b, mitochondrial

ProteinName: 28S ribosomal protein S18b, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.217355 kDa
SourceSpecies: Bovine (cattle)

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Component #14: protein, 28S ribosomal protein S7, mitochondrial

ProteinName: 28S ribosomal protein S7, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.17901 kDa
SourceSpecies: Bovine (cattle)

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Component #15: protein, 28S ribosomal protein S9, mitochondrial

ProteinName: 28S ribosomal protein S9, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.302754 kDa
SourceSpecies: Bovine (cattle)

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Component #16: protein, 28S ribosomal protein S10, mitochondrial

ProteinName: 28S ribosomal protein S10, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.069605 kDa
SourceSpecies: Bovine (cattle)

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Component #17: protein, 28S ribosomal protein S14, mitochondrial

ProteinName: 28S ribosomal protein S14, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.073671 kDa
SourceSpecies: Bovine (cattle)

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Component #18: protein, DAP3 protein

ProteinName: DAP3 protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.505719 kDa
SourceSpecies: Bovine (cattle)

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Component #19: protein, 28S ribosomal protein S31, mitochondrial

ProteinName: 28S ribosomal protein S31, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.740461 kDa
SourceSpecies: Bovine (cattle)

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Component #20: protein, 28S ribosomal protein S33, mitochondrial

ProteinName: 28S ribosomal protein S33, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.480582 kDa
SourceSpecies: Bovine (cattle)

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Component #21: protein, 28S ribosomal protein S35, mitochondrial

ProteinName: 28S ribosomal protein S35, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.129746 kDa
SourceSpecies: Bovine (cattle)

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Component #22: protein, Coiled-coil-helix-coiled-coil-helix domain containing 1

ProteinName: Coiled-coil-helix-coiled-coil-helix domain containing 1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.581974 kDa
SourceSpecies: Bovine (cattle)

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Component #23: protein, Pentatricopeptide repeat domain-containing protein 3, mi...

ProteinName: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 60.587832 kDa
SourceSpecies: Bovine (cattle)

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Component #24: protein, 28S ribosomal protein S2, mitochondrial

ProteinName: 28S ribosomal protein S2, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.775492 kDa
SourceSpecies: Bovine (cattle)

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Component #25: protein, 28S ribosomal protein S6, mitochondrial

ProteinName: 28S ribosomal protein S6, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.171551 kDa
SourceSpecies: Bovine (cattle)

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Component #26: protein, 28S ribosomal protein S11, mitochondrial

ProteinName: 28S ribosomal protein S11, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.869008 kDa
SourceSpecies: Bovine (cattle)

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Component #27: protein, 28S ribosomal protein S15, mitochondrial

ProteinName: 28S ribosomal protein S15, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.245316 kDa
SourceSpecies: Bovine (cattle)

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Component #28: protein, 28S ribosomal protein S18c, mitochondrial

ProteinName: 28S ribosomal protein S18c, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.240283 kDa
SourceSpecies: Bovine (cattle)

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Component #29: protein, 28S ribosomal protein S21, mitochondrial

ProteinName: 28S ribosomal protein S21, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.697583 kDa
SourceSpecies: Bovine (cattle)

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Component #30: protein, 28S ribosomal protein S23, mitochondrial

ProteinName: 28S ribosomal protein S23, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.625533 kDa
SourceSpecies: Bovine (cattle)

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Component #31: protein, 28S ribosomal protein S28, mitochondrial

ProteinName: 28S ribosomal protein S28, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.077977 kDa
SourceSpecies: Bovine (cattle)

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Component #32: protein, Aurora kinase A interacting protein 1

ProteinName: Aurora kinase A interacting protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.968365 kDa
SourceSpecies: Bovine (cattle)

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Component #33: protein, Translation initiation factor IF-3, mitochondrial

ProteinName: Translation initiation factor IF-3, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.21316 kDa
SourceSpecies: Human (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.6
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Electron dose: 7 e/Å2 / Illumination mode: OTHER
LensImaging mode: OTHER
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 99178
3D reconstructionAlgorithm: FOURIER SPACE / Software: cryoSPARC / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Input PDB model: 3JD5
Overall bvalue: 97
Output model

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