6RW5

Structure of human mitochondrial 28S ribosome in complex with mitochondrial IF2 and IF3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Distinct pre-initiation steps in human mitochondrial translation.

Khawaja, A.Itoh, Y.Remes, C.Spahr, H.Yukhnovets, O.Hofig, H.Amunts, A.Rorbach, J.

(2020) Nat Commun 11: 2932-2932

  • DOI: https://doi.org/10.1038/s41467-020-16503-2
  • Primary Citation of Related Structures:  
    6RW4, 6RW5

  • PubMed Abstract: 

    Translation initiation in human mitochondria relies upon specialized mitoribosomes and initiation factors, mtIF2 and mtIF3, which have diverged from their bacterial counterparts. Here we report two distinct mitochondrial pre-initiation assembly steps involving those factors. Single-particle cryo-EM revealed that in the first step, interactions between mitochondria-specific protein mS37 and mtIF3 keep the small mitoribosomal subunit in a conformation favorable for a subsequent accommodation of mtIF2 in the second step. Combination with fluorescence cross-correlation spectroscopy analyses suggests that mtIF3 promotes complex assembly without mRNA or initiator tRNA binding, where exclusion is achieved by the N-terminal and C-terminal domains of mtIF3. Finally, the association of large mitoribosomal subunit is required for initiator tRNA and leaderless mRNA recruitment to form a stable initiation complex. These data reveal fundamental aspects of mammalian protein synthesis that are specific to mitochondria.


  • Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65, Solna, Sweden.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S2, mitochondrial296Homo sapiensMutation(s): 0 
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PHAROS:  Q9Y399
GTEx:  ENSG00000122140 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S24, mitochondrial167Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000062582 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S5, mitochondrial430Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144029 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S6, mitochondrial125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000243927 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S7, mitochondrial242Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125445 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S9, mitochondrial396Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000135972 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S10, mitochondrial201Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000048544 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S11, mitochondrial194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000181991 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S12, mitochondrial138Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000128626 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S14, mitochondrial128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000120333 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S15, mitochondrial257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116898 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrial137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182180 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S17, mitochondrial130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000239789 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrial258Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204568 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18c, mitochondrial142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163319 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S21, mitochondrial86Homo sapiensMutation(s): 1 
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GTEx:  ENSG00000266472 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S22, mitochondrial360Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175110 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S23, mitochondrial190Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000181610 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S25, mitochondrial173Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131368 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S26, mitochondrial205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125901 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S27, mitochondrial414Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000113048 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S28, mitochondrial187Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147586 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S29, mitochondrial398Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132676 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S31, mitochondrial395Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000102738 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S33, mitochondrial106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000090263 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S34, mitochondrialAA [auth 0]218Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000074071 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S35, mitochondrialBA [auth 1]323Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000061794 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1CA [auth 2]117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172586 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinase A-interacting proteinDA [auth 3]199Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175756 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain-containing protein 3, mitochondrialEA [auth 4]689Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132300 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor IF-2, mitochondrialFA [auth 7]699Homo sapiensMutation(s): 0 
Gene Names: MTIF2
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GTEx:  ENSG00000085760 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor IF-3, mitochondrialGA [auth 8]285Homo sapiensMutation(s): 2 
Gene Names: MTIF3DC38
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GTEx:  ENSG00000122033 
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Entity ID: 1
MoleculeChains LengthOrganismImage
12S mitochondrial rRNA955Homo sapiens
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Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

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HA [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
SRY
Query on SRY

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JA [auth A]STREPTOMYCIN
C21 H39 N7 O12
UCSJYZPVAKXKNQ-HZYVHMACSA-N
GNP (Subject of Investigation/LOI)
Query on GNP

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MD [auth X],
OD [auth 7]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
ATP
Query on ATP

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KD [auth X]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SPM
Query on SPM

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IA [auth A]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
FES
Query on FES

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ID [auth P],
JD [auth T]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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HD [auth O]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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AD [auth A]
BD [auth A]
CD [auth A]
DD [auth A]
ED [auth A]
AD [auth A],
BD [auth A],
CD [auth A],
DD [auth A],
ED [auth A],
FD [auth A],
PC [auth A],
QC [auth A],
RC [auth A],
SC [auth A],
TC [auth A],
UC [auth A],
VC [auth A],
WC [auth A],
XC [auth A],
YC [auth A],
ZC [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth A]
AC [auth A]
BB [auth A]
BC [auth A]
CB [auth A]
AB [auth A],
AC [auth A],
BB [auth A],
BC [auth A],
CB [auth A],
CC [auth A],
DB [auth A],
DC [auth A],
EB [auth A],
EC [auth A],
FB [auth A],
FC [auth A],
GB [auth A],
GC [auth A],
GD [auth B],
HB [auth A],
HC [auth A],
IB [auth A],
IC [auth A],
JB [auth A],
JC [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth X],
MA [auth A],
MB [auth A],
MC [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth 3],
OA [auth A],
OB [auth A],
OC [auth A],
PA [auth A],
PB [auth A],
PD [auth 7],
QA [auth A],
QB [auth A],
RA [auth A],
RB [auth A],
SA [auth A],
SB [auth A],
TA [auth A],
TB [auth A],
UA [auth A],
UB [auth A],
VA [auth A],
VB [auth A],
WA [auth A],
WB [auth A],
XA [auth A],
XB [auth A],
YA [auth A],
YB [auth A],
ZA [auth A],
ZB [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
AYA
Query on AYA
Q
L-PEPTIDE LINKINGC5 H9 N O3ALA
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.2
MODEL REFINEMENTPHENIX1.15rc2-3428

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-07-01
    Changes: Database references
  • Version 1.2: 2024-04-24
    Changes: Data collection, Database references, Refinement description