8QRN

mt-SSU in GTPBP8 knock-out cells, state 4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

GTPBP8 plays a role in mitoribosome formation in human mitochondria.

Cipullo, M.Valentin Gese, G.Gopalakrishna, S.Krueger, A.Lobo, V.Pirozhkova, M.A.Marks, J.Palenikova, P.Shiriaev, D.Liu, Y.Misic, J.Cai, Y.Nguyen, M.D.Abdelbagi, A.Li, X.Minczuk, M.Hafner, M.Benhalevy, D.Sarshad, A.A.Atanassov, I.Hallberg, B.M.Rorbach, J.

(2024) Nat Commun 15: 5664-5664

  • DOI: https://doi.org/10.1038/s41467-024-50011-x
  • Primary Citation of Related Structures:  
    8QRK, 8QRL, 8QRM, 8QRN, 8QU1, 8QU5

  • PubMed Abstract: 

    Mitochondrial gene expression relies on mitoribosomes to translate mitochondrial mRNAs. The biogenesis of mitoribosomes is an intricate process involving multiple assembly factors. Among these factors, GTP-binding proteins (GTPBPs) play important roles. In bacterial systems, numerous GTPBPs are required for ribosome subunit maturation, with EngB being a GTPBP involved in the ribosomal large subunit assembly. In this study, we focus on exploring the function of GTPBP8, the human homolog of EngB. We find that ablation of GTPBP8 leads to the inhibition of mitochondrial translation, resulting in significant impairment of oxidative phosphorylation. Structural analysis of mitoribosomes from GTPBP8 knock-out cells shows the accumulation of mitoribosomal large subunit assembly intermediates that are incapable of forming functional monosomes. Furthermore, fPAR-CLIP analysis reveals that GTPBP8 is an RNA-binding protein that interacts specifically with the mitochondrial ribosome large subunit 16 S rRNA. Our study highlights the role of GTPBP8 as a component of the mitochondrial gene expression machinery involved in mitochondrial large subunit maturation.


  • Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17165, Sweden.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S2, mitochondrial296Homo sapiensMutation(s): 0 
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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: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor IF-2, mitochondrialGA [auth 7]691Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000085760 
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Entity ID: 1
MoleculeChains LengthOrganismImage
12S mitochondrial rRNA955Homo sapiens
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Entity ID: 32
MoleculeChains LengthOrganismImage
fMet-tRNAMetFA [auth 5]71Homo sapiens
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Entity ID: 34
MoleculeChains LengthOrganismImage
mRNAHA [auth 6]3Homo sapiens
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

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

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KA [auth A]STREPTOMYCIN
C21 H39 N7 O12
UCSJYZPVAKXKNQ-HZYVHMACSA-N
GTP
Query on GTP

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ND [auth 7]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GNP
Query on GNP

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

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

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JA [auth A]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
FME
Query on FME

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MD [auth 5]N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
FES
Query on FES

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

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FD [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]
NC [auth A]
AD [auth A],
BD [auth A],
CD [auth A],
DD [auth A],
NC [auth A],
OC [auth A],
PC [auth A],
PD [auth 7],
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],
ED [auth B],
FB [auth A],
FC [auth A],
GB [auth A],
GC [auth A],
HB [auth A],
HC [auth A],
IB [auth A],
IC [auth A],
ID [auth X],
JB [auth A],
JC [auth A],
KB [auth A],
KC [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth 3],
MA [auth A],
MB [auth A],
MC [auth A],
NA [auth A],
NB [auth A],
OA [auth A],
OB [auth A],
OD [auth 7],
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
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: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2024-07-17
    Changes: Database references