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- PDB-6nf8: Structure of human mitochondrial translation initiation factor 3 ... -

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Entry
Database: PDB / ID: 6nf8
TitleStructure of human mitochondrial translation initiation factor 3 bound to the small ribosomal subunit -Class I
Components
  • (28S ribosomal protein ...) x 26
  • 28S ribosomal RNA, mitochondria
  • Aurora kinase A interacting protein 1
  • Coiled-coil-helix-coiled-coil-helix domain containing 1
  • DAP3 protein
  • Pentatricopeptide repeat domain-containing protein 3, mitochondrial
  • Translation initiation factor IF-3, mitochondrial
KeywordsRIBOSOMAL PROTEIN / Mitochondrial translation Initiation Factor 3
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
Specimen sourceBos taurus (cattle)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.48 Å resolution
AuthorsSharma, M. / Koripella, R. / Agrawal, R.
Funding supportUnited States , 2 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human DevelopmentR01 GM61576United States
National Institutes of Health/National Institute of General Medical SciencesR01 GM 32734United States
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 Report
SummaryFull reportAbout validation report
DateDeposition: Dec 19, 2018 / Release: Feb 27, 2019

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Assembly

Deposited unit
A: 28S ribosomal RNA, mitochondria
C: 28S ribosomal protein S24, mitochondrial
E: 28S ribosomal protein S5, mitochondrial
L: 28S ribosomal protein S12, mitochondrial
P: 28S ribosomal protein S16, mitochondrial
Q: 28S ribosomal protein S17, mitochondrial
a: 28S ribosomal protein S22, mitochondrial
c: 28S ribosomal protein S25, mitochondrial
d: 28S ribosomal protein S26, mitochondrial
e: 28S ribosomal protein S27, mitochondrial
j: 28S ribosomal protein S34, mitochondrial
p: 28S ribosomal protein S18b, mitochondrial
G: 28S ribosomal protein S7, mitochondrial
I: 28S ribosomal protein S9, mitochondrial
J: 28S ribosomal protein S10, mitochondrial
N: 28S ribosomal protein S14, mitochondrial
g: DAP3 protein
h: 28S ribosomal protein S31, mitochondrial
i: 28S ribosomal protein S33, mitochondrial
k: 28S ribosomal protein S35, mitochondrial
m: Coiled-coil-helix-coiled-coil-helix domain containing 1
o: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
B: 28S ribosomal protein S2, mitochondrial
F: 28S ribosomal protein S6, mitochondrial
K: 28S ribosomal protein S11, mitochondrial
O: 28S ribosomal protein S15, mitochondrial
R: 28S ribosomal protein S18c, mitochondrial
U: 28S ribosomal protein S21, mitochondrial
b: 28S ribosomal protein S23, mitochondrial
f: 28S ribosomal protein S28, mitochondrial
n: Aurora kinase A interacting protein 1
z: Translation initiation factor IF-3, mitochondrial


Theoretical massNumber of molelcules
Total (without water)1,143,40932
Polyers1,143,40932
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)189510
ΔGint (kcal/M)-1219
Surface area (Å2)386140

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain 28S ribosomal RNA, mitochondria /


Mass: 306932.719 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)

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28S ribosomal protein ... , 26 types, 26 molecules CELPQacdejpGIJNhikBFKORUbf

#2: Protein/peptide 28S ribosomal protein S24, mitochondrial / Ribosome / S24mt


Mass: 19111.455 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2M2T7
#3: Protein/peptide 28S ribosomal protein S5, mitochondrial / Ribosome / S5mt


Mass: 47956.941 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2KID9
#4: Protein/peptide 28S ribosomal protein S12, mitochondrial / Ribosome / S12mt


Mass: 15479.285 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q29RU1
#5: Protein/peptide 28S ribosomal protein S16, mitochondrial / Ribosome / S16mt


Mass: 15157.631 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P82915
#6: Protein/peptide 28S ribosomal protein S17, mitochondrial / Ribosome / S17mt


Mass: 14497.051 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P82916
#7: Protein/peptide 28S ribosomal protein S22, mitochondrial / Ribosome / S22mt


Mass: 40720.562 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P82649
#8: Protein/peptide 28S ribosomal protein S25, mitochondrial / Ribosome / S25mt


Mass: 20085.312 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P82669
#9: Protein/peptide 28S ribosomal protein S26, mitochondrial / Ribosome / S26mt


Mass: 23815.941 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3SZ86
#10: Protein/peptide 28S ribosomal protein S27, mitochondrial / Ribosome / S27mt / Mitochondrial ribosomal protein S27


Mass: 48017.867 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q32PI8
#11: Protein/peptide 28S ribosomal protein S34, mitochondrial / Ribosome / S34mt


Mass: 25880.799 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P82929
#12: Protein/peptide 28S ribosomal protein S18b, mitochondrial / Ribosome / S18mt-b / 28S ribosomal protein S18-2 / mitochondrial / MRP-S18-2


Mass: 29217.355 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P82918
#13: Protein/peptide 28S ribosomal protein S7, mitochondrial / Ribosome / S7mt


Mass: 28179.010 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3T040
#14: Protein/peptide 28S ribosomal protein S9, mitochondrial / Ribosome / S9mt


Mass: 45302.754 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q58DQ5
#15: Protein/peptide 28S ribosomal protein S10, mitochondrial / Ribosome / S10mt


Mass: 23069.605 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P82670
#16: Protein/peptide 28S ribosomal protein S14, mitochondrial / Ribosome / S14mt


Mass: 15073.671 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B860
#18: Protein/peptide 28S ribosomal protein S31, mitochondrial / Ribosome / S31mt


Mass: 43740.461 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P82925
#19: Protein/peptide 28S ribosomal protein S33, mitochondrial / Ribosome / S33mt


Mass: 12480.582 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P82926
#20: Protein/peptide 28S ribosomal protein S35, mitochondrial / Ribosome / S35mt / 28S ribosomal protein S28 / mitochondrial / S28mt


Mass: 37129.746 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2YDF6
#23: Protein/peptide 28S ribosomal protein S2, mitochondrial / Ribosome / S2mt


Mass: 31775.492 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P82923
#24: Protein/peptide 28S ribosomal protein S6, mitochondrial / Ribosome / S6mt


Mass: 14171.551 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P82931
#25: Protein/peptide 28S ribosomal protein S11, mitochondrial / Ribosome / S11mt


Mass: 20869.008 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P82911
#26: Protein/peptide 28S ribosomal protein S15, mitochondrial / Ribosome / S15mt


Mass: 29245.316 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P82913
#27: Protein/peptide 28S ribosomal protein S18c, mitochondrial / Ribosome / S18mt-c / 28S ribosomal protein S18-1 / mitochondrial / MRP-S18-1


Mass: 16240.283 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P82917
#28: Protein/peptide 28S ribosomal protein S21, mitochondrial / Ribosome / S21mt


Mass: 10697.583 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P82920
#29: Protein/peptide 28S ribosomal protein S23, mitochondrial / Ribosome / S23mt


Mass: 21625.533 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2NL27
#30: Protein/peptide 28S ribosomal protein S28, mitochondrial / Ribosome / S28mt


Mass: 21077.977 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P82928

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Protein/peptide , 5 types, 5 molecules gmonz

#17: Protein/peptide DAP3 protein


Mass: 40505.719 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: A6QQP1
#21: Protein/peptide Coiled-coil-helix-coiled-coil-helix domain containing 1


Mass: 13581.974 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2HJE8
#22: Protein/peptide Pentatricopeptide repeat domain-containing protein 3, mitochondrial / 28S ribosomal protein S39 / mitochondrial / MRP-S39


Mass: 60587.832 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2KI62
#31: Protein/peptide Aurora kinase A interacting protein 1


Mass: 22968.365 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q0VCJ1
#32: Protein/peptide Translation initiation factor IF-3, mitochondrial / IF3mt


Mass: 28213.160 Da / Num. of mol.: 1 / Fragment: residues 32-278 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H2K0

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Structure of human mitochondrial translation initiation factor 3 bound to the small ribosomal subunit
Type: RIBOSOME
Details: Structure of human mitochondrial translation initiation factor 3 bound to the small ribosomal subunit
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32
Source: NATURAL
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
219606Homo sapiens (human)
119913Bos taurus (cattle)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
7Cootmodel fitting
9PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 99178 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingOverall b value: 97 / Ref protocol: OTHER
Atomic model buildingPDB-ID: 3JD5

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