6RW4

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 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 ...

    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

    Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden. joanna.rorbach@ki.se.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S2, mitochondrialB296Homo sapiensMutation(s): 0 
Gene Names: MRPS2CGI-91
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S24, mitochondrialC167Homo sapiensMutation(s): 0 
Gene Names: MRPS24HSPC335
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S5, mitochondrialD430Homo sapiensMutation(s): 0 
Gene Names: MRPS5
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S6, mitochondrialE125Homo sapiensMutation(s): 0 
Gene Names: MRPS6C21orf101RPMS6
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S7, mitochondrialF242Homo sapiensMutation(s): 0 
Gene Names: MRPS7
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S9, mitochondrialG396Homo sapiensMutation(s): 0 
Gene Names: MRPS9RPMS9
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S10, mitochondrialH201Homo sapiensMutation(s): 0 
Gene Names: MRPS10MSTP040
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S11, mitochondrialI194Homo sapiensMutation(s): 0 
Gene Names: MRPS11RPMS11HCC2
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S12, mitochondrialJ138Homo sapiensMutation(s): 0 
Gene Names: MRPS12RPMS12RPSM12
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S14, mitochondrialK128Homo sapiensMutation(s): 0 
Gene Names: MRPS14
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S15, mitochondrialL257Homo sapiensMutation(s): 0 
Gene Names: MRPS15RPMS15DC37
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrialM137Homo sapiensMutation(s): 0 
Gene Names: MRPS16RPMS16CGI-132
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S17, mitochondrialN130Homo sapiensMutation(s): 0 
Gene Names: MRPS17RPMS17HSPC011
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrialO258Homo sapiensMutation(s): 0 
Gene Names: MRPS18BC6orf14HSPC183PTD017
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S18c, mitochondrialP142Homo sapiensMutation(s): 0 
Gene Names: MRPS18CCGI-134
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S21, mitochondrialQ86Homo sapiensMutation(s): 1 
Gene Names: MRPS21RPMS21MDS016
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S22, mitochondrialR360Homo sapiensMutation(s): 0 
Gene Names: MRPS22C3orf5RPMS22GK002
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S23, mitochondrialS190Homo sapiensMutation(s): 0 
Gene Names: MRPS23CGI-138HSPC329
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S25, mitochondrialT173Homo sapiensMutation(s): 0 
Gene Names: MRPS25RPMS25
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S26, mitochondrialU205Homo sapiensMutation(s): 0 
Gene Names: MRPS26C20orf193RPMS13
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S27, mitochondrialV414Homo sapiensMutation(s): 0 
Gene Names: MRPS27KIAA0264
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S28, mitochondrialW187Homo sapiensMutation(s): 0 
Gene Names: MRPS28MRPS35HSPC007
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S29, mitochondrialX398Homo sapiensMutation(s): 0 
Gene Names: DAP3MRPS29
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S31, mitochondrialY395Homo sapiensMutation(s): 0 
Gene Names: MRPS31IMOGN38
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S33, mitochondrialZ106Homo sapiensMutation(s): 0 
Gene Names: MRPS33CGI-139PTD003
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S34, mitochondrialAA [auth 0]218Homo sapiensMutation(s): 0 
Gene Names: MRPS34
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S35, mitochondrialBA [auth 1]323Homo sapiensMutation(s): 0 
Gene Names: MRPS35MRPS28HDCMD11PMDS023PSEC0213
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1CA [auth 2]117Homo sapiensMutation(s): 0 
Gene Names: CHCHD1C10orf34MRPS37
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Aurora kinase A-interacting proteinDA [auth 3]199Homo sapiensMutation(s): 0 
Gene Names: AURKAIP1AIPAKIPMRPS38
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain-containing protein 3, mitochondrialEA [auth 4]689Homo sapiensMutation(s): 0 
Gene Names: PTCD3MRPS39TRG15
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor IF-3, mitochondrialFA [auth 8]285Homo sapiensMutation(s): 2 
Gene Names: MTIF3DC38
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Entity ID: 1
MoleculeChainsLengthOrganismImage
12S mitochondrial rRNAA955Homo sapiens
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Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

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GA [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
SRY (Subject of Investigation/LOI)
Query on SRY

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

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LD [auth X]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
ATP (Subject of Investigation/LOI)
Query on ATP

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JD [auth X]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
SPM (Subject of Investigation/LOI)
Query on SPM

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HA [auth A]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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

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GD [auth O]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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AD [auth A] , BD [auth A] , CD [auth A] , DD [auth A] , ED [auth A] , OC [auth A] , PC [auth A] , QC [auth A] , 
AD [auth A],  BD [auth A],  CD [auth A],  DD [auth A],  ED [auth A],  OC [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
 Ligand Interaction
MG
Query on MG

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AB [auth A] , AC [auth A] , BB [auth A] , BC [auth A] , CB [auth A] , CC [auth A] , DB [auth A] , DC [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],  FD [auth B],  GB [auth A],  GC [auth A],  HB [auth A],  HC [auth A],  IB [auth A],  IC [auth A],  JA [auth A],  JB [auth A],  JC [auth A],  KA [auth A],  KB [auth A],  KC [auth A],  KD [auth X],  LA [auth A],  LB [auth A],  LC [auth A],  MA [auth A],  MB [auth A],  MC [auth A],  MD [auth 3],  NA [auth A],  NB [auth A],  NC [auth A],  OA [auth A],  OB [auth A],  PA [auth A],  PB [auth A],  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
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AYA
Query on AYA
QL-PEPTIDE LINKINGC5 H9 N O3ALA
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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