7OF5

Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 and GTPBP5 (dataset2).


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of GTPase-mediated mitochondrial ribosome biogenesis and recycling.

Hillen, H.S.Lavdovskaia, E.Nadler, F.Hanitsch, E.Linden, A.Bohnsack, K.E.Urlaub, H.Richter-Dennerlein, R.

(2021) Nat Commun 12: 3672-3672

  • DOI: https://doi.org/10.1038/s41467-021-23702-y
  • Primary Citation of Related Structures:  
    7OF0, 7OF2, 7OF3, 7OF4, 7OF5, 7OF6, 7OF7

  • PubMed Abstract: 

    Ribosome biogenesis requires auxiliary factors to promote folding and assembly of ribosomal proteins and RNA. Particularly, maturation of the peptidyl transferase center (PTC) is mediated by conserved GTPases, but the molecular basis is poorly understood. Here, we define the mechanism of GTPase-driven maturation of the human mitochondrial large ribosomal subunit (mtLSU) using endogenous complex purification, in vitro reconstitution and cryo-EM. Structures of transient native mtLSU assembly intermediates that accumulate in GTPBP6-deficient cells reveal how the biogenesis factors GTPBP5, MTERF4 and NSUN4 facilitate PTC folding. Addition of recombinant GTPBP6 reconstitutes late mtLSU biogenesis in vitro and shows that GTPBP6 triggers a molecular switch and progression to a near-mature PTC state. Additionally, cryo-EM analysis of GTPBP6-treated mature mitochondrial ribosomes reveals the structural basis for the dual-role of GTPBP6 in ribosome biogenesis and recycling. Together, these results provide a framework for understanding step-wise PTC folding as a critical conserved quality control checkpoint.


  • Organizational Affiliation

    Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany. hauke.hillen@med.uni-goettingen.de.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L32, mitochondrialA [auth 0]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106591 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L33, mitochondrialB [auth 1]65Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000243147 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L34, mitochondrialC [auth 2]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130312 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L35, mitochondrialD [auth 3]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132313 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L36, mitochondrialE [auth 4]103Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171421 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L37, mitochondrialF [auth 5]423Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116221 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L38, mitochondrialG [auth 6]380Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204316 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L39, mitochondrialH [auth 7]338Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000154719 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L40, mitochondrialI [auth 8]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185608 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L41, mitochondrialJ [auth 9]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182154 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
5-methylcytosine rRNA methyltransferase NSUN4M [auth C]384Homo sapiensMutation(s): 0 
EC: 2.1.1
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GTEx:  ENSG00000117481 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialN [auth D]305Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112651 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L3, mitochondrialO [auth E]348Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114686 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrialP [auth F]311Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105364 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription termination factor 4, mitochondrialQ [auth G]381Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122085 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialR [auth H]267Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143436 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L10, mitochondrialS [auth I]261Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159111 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L11, mitochondrialT [auth J]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174547 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L13, mitochondrialU [auth K]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172172 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L14, mitochondrialV [auth L]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000180992 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L15, mitochondrialW [auth M]296Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137547 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L16, mitochondrialX [auth N]251Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166902 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L17, mitochondrialY [auth O]175Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000158042 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L18, mitochondrialZ [auth P]180Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112110 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L19, mitochondrialAA [auth Q]292Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115364 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L20, mitochondrialBA [auth R]149Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000242485 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L21, mitochondrialCA [auth S]205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197345 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L22, mitochondrialDA [auth T]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000082515 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L23, mitochondrialEA [auth U]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000214026 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L24, mitochondrialFA [auth V]216Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143314 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L27, mitochondrialGA [auth W]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108826 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L28, mitochondrialHA [auth X]256Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086504 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L47, mitochondrialIA [auth Y]250Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136522 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L30, mitochondrialJA [auth Z]161Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185414 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L42, mitochondrialKA [auth a]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198015 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L43, mitochondrialLA [auth b]215Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000055950 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L44, mitochondrialMA [auth c]332Homo sapiensMutation(s): 0 
EC: 3.1.26
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GTEx:  ENSG00000135900 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L45, mitochondrialNA [auth d]306Homo sapiensMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L46, mitochondrialOA [auth e]279Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000259494 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrialPA [auth f]212Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175581 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L49, mitochondrialQA [auth g]166Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149792 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L50, mitochondrialRA [auth h]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136897 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L51, mitochondrialSA [auth i]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000111639 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L52, mitochondrialTA [auth j]123Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172590 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L53, mitochondrialUA [auth k]112Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204822 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L55, mitochondrialVA [auth m]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162910 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein 63, mitochondrialWA [auth o]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173141 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase ICT1, mitochondrialXA [auth p]206Homo sapiensMutation(s): 0 
EC: 3.1.1.29
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Find proteins for Q14197 (Homo sapiens)
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GTEx:  ENSG00000167862 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Growth arrest and DNA damage-inducible proteins-interacting protein 1YA [auth q]222Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000179271 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S18a, mitochondrialZA [auth r]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096080 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialAB [auth s]439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112996 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial assembly of ribosomal large subunit protein 1BB [auth u]234Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156928 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
MIEF1 upstream open reading frame proteinCB [auth v]70Homo sapiensMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialDB [auth w]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000004779 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosome-associated GTPase 2EB [auth x]406Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101181 
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Entity ID: 11
MoleculeChains LengthOrganismImage
16S ribosomal RNAK [auth A]1,559Homo sapiens
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Entity ID: 12
MoleculeChains LengthOrganismImage
Mitochondrial tRNAValL [auth B]69Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
XD [auth A],
YD [auth A]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BE [auth r],
FB [auth 0],
GB [auth 4]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth A]
AD [auth A]
AE [auth g]
BC [auth A]
BD [auth A]
AC [auth A],
AD [auth A],
AE [auth g],
BC [auth A],
BD [auth A],
CC [auth A],
CD [auth A],
DC [auth A],
DD [auth A],
EC [auth A],
ED [auth A],
FC [auth A],
FD [auth A],
GC [auth A],
GD [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
XB [auth A],
XC [auth A],
YB [auth A],
YC [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyRI 2715/1-1
German Research Foundation (DFG)GermanyEXC 2067/1-390729940
German Research Foundation (DFG)GermanyFOR2848
German Research Foundation (DFG)GermanySFB860
German Research Foundation (DFG)GermanySFB1160

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references
  • Version 1.2: 2021-06-30
    Changes: Database references
  • Version 1.3: 2024-07-10
    Changes: Data collection, Database references, Refinement description