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

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Entry
Database: PDB / ID: 6neq
TitleStructure of human mitochondrial translation initiation factor 3 bound to the small ribosomal subunit-Class-II
Components
  • (28S ribosomal protein ...) x 26
  • 28S ribosomal RNA, mitochondrial
  • 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 / Human mitochondrial translation Initiation Factor 3
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial translational initiation / peptide biosynthetic process / mitochondrial ribosome binding / translation factor activity, RNA binding / mitochondrial ribosome assembly / Mitochondrial translation initiation / positive regulation of mitochondrial translation / mitochondrial ribosome ...Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial translational initiation / peptide biosynthetic process / mitochondrial ribosome binding / translation factor activity, RNA binding / mitochondrial ribosome assembly / Mitochondrial translation initiation / positive regulation of mitochondrial translation / mitochondrial ribosome / mitochondrial small ribosomal subunit / ribosome disassembly / mitochondrial translation / Mitochondrial protein degradation / ribosomal small subunit binding / translation initiation factor activity / kinase activity / regulation of translation / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / tRNA binding / cell population proliferation / mitochondrial inner membrane / rRNA binding / ribosome / structural constituent of ribosome / translation / protein domain specific binding / ribonucleoprotein complex / mRNA binding / apoptotic process / nucleolus / mitochondrion / RNA binding / nucleoplasm
Similarity search - Function
Helix Hairpins - #1480 / Translation initiation factor 3 / Translation initiation factor 3, N-terminal / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Translation initiation factor IF-3, N-terminal domain / S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S26 ...Helix Hairpins - #1480 / Translation initiation factor 3 / Translation initiation factor 3, N-terminal / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Translation initiation factor IF-3, N-terminal domain / S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / Cysteine alpha-hairpin motif superfamily / 28S ribosomal protein S27, mitochondrial / MRPS27/PTCD2 / Mitochondrial 28S ribosomal protein S27 / Ribosomal protein S22, mitochondrial / Ribosomal protein S23, mitochondrial / Ribosomal protein S23/S25, mitochondrial / Mitochondrial 28S ribosomal protein S31 / : / Mitochondrial 28S ribosomal protein S22 / Mitochondrial ribosomal protein S23 / Mitochondrial 28S ribosomal protein S31 / Ribosomal protein S29, mitochondrial / Ribosomal protein S28, mitochondrial / Mitochondrial 28S ribosomal protein S34 / 28S ribosomal protein S10, mitochondrial / Mitochondrial ribosomal protein MRP-S35 / Mitochondrial 28S ribosomal protein S34 / 28S ribosomal protein S24, mitochondrial / Pentatricopeptide repeat domain-containing protein 3 / 28S ribosomal protein S17, mitochondrial / 28S ribosomal protein S18b, mitochondrial / : / : / Mitochondrial ribosome subunit S24 / Small ribosomal subunit protein uS5m, N-terminal / Small ribosomal subunit protein mS39, PPR / 28S ribosomal protein S25, mitochondrial / Ribosomal protein S6/Translation elongation factor EF1B / Pentatricopeptide repeat domain / Ribosomal protein S11/S14 / 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. / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Pentatricopeptide repeat / 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 / Ribosomal protein S21 / Nucleic acid-binding proteins / Ribosomal protein S21 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / 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 S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Ribosomal protein S2 signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / 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, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Nucleotidyltransferase; domain 5 / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S10p/S20e
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein mS29 / Small ribosomal subunit protein mS22 / Small ribosomal subunit protein mS25 / Small ribosomal subunit protein uS10m / Small ribosomal subunit protein uS11m / Small ribosomal subunit protein uS15m / Small ribosomal subunit protein bS16m ...RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein mS29 / Small ribosomal subunit protein mS22 / Small ribosomal subunit protein mS25 / Small ribosomal subunit protein uS10m / Small ribosomal subunit protein uS11m / Small ribosomal subunit protein uS15m / Small ribosomal subunit protein bS16m / Small ribosomal subunit protein uS17m / Small ribosomal subunit protein bS18m / Small ribosomal subunit protein mS40 / Small ribosomal subunit protein bS21m / Small ribosomal subunit protein uS2m / Small ribosomal subunit protein mS31 / Small ribosomal subunit protein mS33 / Small ribosomal subunit protein bS1m / Small ribosomal subunit protein mS34 / Small ribosomal subunit protein bS6m / Small ribosomal subunit protein mS38 / Small ribosomal subunit protein uS12m / Coiled-coil-helix-coiled-coil-helix domain containing 1 / Small ribosomal subunit protein mS39 / Small ribosomal subunit protein uS5m / Small ribosomal subunit protein uS3m / Small ribosomal subunit protein mS23 / Small ribosomal subunit protein mS35 / Small ribosomal subunit protein mS27 / Small ribosomal subunit protein mS26 / Small ribosomal subunit protein uS7m / Small ribosomal subunit protein uS9m / Small ribosomal subunit protein uS14m / Translation initiation factor IF-3, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsSharma, M. / Koripella, R. / Agrawal, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01 GM61576 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM 32734 United 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.
History
DepositionDec 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Assembly

Deposited unit
A: 28S ribosomal RNA, mitochondrial
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
Polymers1,143,40932
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area187130 Å2
ΔGint-1207 kcal/mol
Surface area385160 Å2

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain 28S ribosomal RNA, mitochondrial


Mass: 306932.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)

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

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


Mass: 19111.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q2M2T7
#3: Protein 28S ribosomal protein S5, mitochondrial / S5mt


Mass: 47956.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q2KID9
#4: Protein 28S ribosomal protein S12, mitochondrial / S12mt


Mass: 15479.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q29RU1
#5: Protein 28S ribosomal protein S16, mitochondrial / S16mt


Mass: 15157.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P82915
#6: Protein 28S ribosomal protein S17, mitochondrial / S17mt


Mass: 14497.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P82916
#7: Protein 28S ribosomal protein S22, mitochondrial / S22mt


Mass: 40720.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P82649
#8: Protein 28S ribosomal protein S25, mitochondrial / S25mt


Mass: 20085.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P82669
#9: Protein 28S ribosomal protein S26, mitochondrial / S26mt


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


Mass: 48017.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: MRPS27 / Production host: Bos taurus (domestic cattle) / References: UniProt: Q32PI8
#11: Protein 28S ribosomal protein S34, mitochondrial / S34mt


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


Mass: 29217.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P82918
#13: Protein 28S ribosomal protein S7, mitochondrial / S7mt


Mass: 28179.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q3T040
#14: Protein 28S ribosomal protein S9, mitochondrial / S9mt


Mass: 45302.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q58DQ5
#15: Protein 28S ribosomal protein S10, mitochondrial / S10mt


Mass: 23069.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P82670
#16: Protein 28S ribosomal protein S14, mitochondrial / S14mt


Mass: 15073.671 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q6B860
#18: Protein 28S ribosomal protein S31, mitochondrial / S31mt


Mass: 43740.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P82925
#19: Protein 28S ribosomal protein S33, mitochondrial / S33mt


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


Mass: 37129.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q2YDF6
#23: Protein 28S ribosomal protein S2, mitochondrial / S2mt


Mass: 31775.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P82923
#24: Protein 28S ribosomal protein S6, mitochondrial / S6mt


Mass: 14171.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P82931
#25: Protein 28S ribosomal protein S11, mitochondrial / S11mt


Mass: 20869.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P82911
#26: Protein 28S ribosomal protein S15, mitochondrial / S15mt


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


Mass: 16240.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P82917
#28: Protein 28S ribosomal protein S21, mitochondrial / S21mt


Mass: 10697.583 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P82920
#29: Protein 28S ribosomal protein S23, mitochondrial / S23mt


Mass: 21625.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q2NL27
#30: Protein 28S ribosomal protein S28, mitochondrial / S28mt


Mass: 21077.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P82928

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Protein , 5 types, 5 molecules gmonz

#17: Protein DAP3 protein


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


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


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


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


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

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Details

Has protein modificationY

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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: 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: all / Source: NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
11Bos taurus (domestic cattle)9913
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
MicroscopyModel: 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: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 198355 / Symmetry type: POINT
Atomic model buildingB value: 97 / Protocol: OTHER
Atomic model buildingPDB-ID: 3JD5

3jd5


Accession code: 3JD5 / Source name: PDB / Type: experimental model

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