6YW5

The structure of the small subunit of the mitoribosome from Neurospora crassa

  • Classification: TRANSLATION
  • Organism(s): Neurospora crassa OR74A
  • Mutation(s): No 

  • Deposited: 2020-04-29 Released: 2020-11-11 
  • Deposition Author(s): Amunts, A., Itoh, Y., Naschberger, A.
  • Funding Organization(s): Swedish Research Council, European Research Council (ERC), Knut and Alice Wallenberg Foundation, European Molecular Biology Organization (EMBO)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 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

Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi.

Itoh, Y.Naschberger, A.Mortezaei, N.Herrmann, J.M.Amunts, A.

(2020) Nat Commun 11: 5187-5187

  • DOI: https://doi.org/10.1038/s41467-020-18830-w
  • Primary Citation of Related Structures:  
    6YW5, 6YWE, 6YWS, 6YWV, 6YWX, 6YWY

  • PubMed Abstract: 

    Mitoribosomes are specialized protein synthesis machineries in mitochondria. However, how mRNA binds to its dedicated channel, and tRNA moves as the mitoribosomal subunit rotate with respect to each other is not understood. We report models of the translating fungal mitoribosome with mRNA, tRNA and nascent polypeptide, as well as an assembly intermediate. Nicotinamide adenine dinucleotide (NAD) is found in the central protuberance of the large subunit, and the ATPase inhibitory factor 1 (IF 1 ) in the small subunit. The models of the active mitoribosome explain how mRNA binds through a dedicated protein platform on the small subunit, tRNA is translocated with the help of the protein mL108, bridging it with L1 stalk on the large subunit, and nascent polypeptide paths through a newly shaped exit tunnel involving a series of structural rearrangements. An assembly intermediate is modeled with the maturation factor Atp25, providing insight into the biogenesis of the mitoribosomal large subunit and translation regulation.


  • Organizational Affiliation

    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
uS2mA [auth AA]470Neurospora crassa OR74AMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mito ribosomal protein S2B [auth BB]428Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S5, mitochondrialC [auth CC]508Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mito ribosomal protein S4D [auth DD]453Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S5E [auth EE]477Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Mito ribosomal protein S6F [auth FF]117Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_S7 domain-containing proteinG [auth GG]309Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8H [auth HH]161Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
uS9mI [auth II]315Neurospora crassa OR74AMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S10, mitochondrialJ [auth JJ]268Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein subunit S18K [auth KK]376Neurospora crassa OR74AMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial 30S ribosomal protein S12L [auth LL]174Neurospora crassa OR74AMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13M [auth MM]119Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial 40S ribosomal protein MRP2N [auth NN]113Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S15O [auth OO]320Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q1K5G1 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S16, mitochondrialP [auth PP]107Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial 37S ribosomal protein S17Q [auth QQ]165Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Mito ribosomal protein S18R [auth RR]256Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q1K8E0 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S19S [auth SS]91Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q1K8V2 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Mito ribosomal protein S21T [auth TT]236Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q7SAJ1 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S25, mitochondrialU [auth UU]253Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
mS26V [auth VV]316Neurospora crassa OR74AMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
mS27W [auth WW]396Neurospora crassa OR74AMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein DAP3X [auth XX]469Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
mS33Y [auth YY]108Neurospora crassa OR74AMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S24, mitochondrialZ [auth ZZ]382Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein mrp10, mitochondrialAA [auth 11]90Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
DUF1713 domain-containing proteinBA [auth 22]344Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
IGR domain-containing proteinCA [auth 33]236Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Fe superoxide dismutaseDA [auth 44],
EA [auth 55]
310Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
mS42FA [auth 66]348Neurospora crassa OR74AMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
mS46GA [auth 77]414Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
3-hydroxyisobutyryl-CoA hydrolase, mitochondrialHA [auth 88]508Neurospora crassa OR74AMutation(s): 0 
EC: 3.1.2.4
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
mS47IA [auth 00],
JA [auth 99]
95Neurospora crassa OR74AMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
IF1LA [auth V]219Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains LengthOrganismImage
16S rRNAKA [auth aa]1,864Neurospora crassa OR74A
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
PA [auth XX]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
K
Query on K

Download Ideal Coordinates CCD File 
AF [auth aa]
BF [auth aa]
IE [auth aa]
JE [auth aa]
KE [auth aa]
AF [auth aa],
BF [auth aa],
IE [auth aa],
JE [auth aa],
KE [auth aa],
LE [auth aa],
ME [auth aa],
NE [auth aa],
OE [auth aa],
PE [auth aa],
QE [auth aa],
RE [auth aa],
SA [auth 77],
SE [auth aa],
TA [auth 88],
TE [auth aa],
UE [auth aa],
VE [auth aa],
WE [auth aa],
XE [auth aa],
YE [auth aa],
ZE [auth aa]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth aa]
AC [auth aa]
AD [auth aa]
AE [auth aa]
BB [auth aa]
AB [auth aa],
AC [auth aa],
AD [auth aa],
AE [auth aa],
BB [auth aa],
BC [auth aa],
BD [auth aa],
BE [auth aa],
CB [auth aa],
CC [auth aa],
CD [auth aa],
CE [auth aa],
DB [auth aa],
DC [auth aa],
DD [auth aa],
DE [auth aa],
EB [auth aa],
EC [auth aa],
ED [auth aa],
EE [auth aa],
FB [auth aa],
FC [auth aa],
FD [auth aa],
FE [auth aa],
GB [auth aa],
GC [auth aa],
GD [auth aa],
GE [auth aa],
HB [auth aa],
HC [auth aa],
HD [auth aa],
HE [auth aa],
IB [auth aa],
IC [auth aa],
ID [auth aa],
JB [auth aa],
JC [auth aa],
JD [auth aa],
KB [auth aa],
KC [auth aa],
KD [auth aa],
LB [auth aa],
LC [auth aa],
LD [auth aa],
MA [auth BB],
MB [auth aa],
MC [auth aa],
MD [auth aa],
NA [auth KK],
NB [auth aa],
NC [auth aa],
ND [auth aa],
OA [auth QQ],
OB [auth aa],
OC [auth aa],
OD [auth aa],
PB [auth aa],
PC [auth aa],
PD [auth aa],
QA [auth XX],
QB [auth aa],
QC [auth aa],
QD [auth aa],
RA [auth YY],
RB [auth aa],
RC [auth aa],
RD [auth aa],
SB [auth aa],
SC [auth aa],
SD [auth aa],
TB [auth aa],
TC [auth aa],
TD [auth aa],
UA [auth 00],
UB [auth aa],
UC [auth aa],
UD [auth aa],
VA [auth aa],
VB [auth aa],
VC [auth aa],
VD [auth aa],
WA [auth aa],
WB [auth aa],
WC [auth aa],
WD [auth aa],
XA [auth aa],
XB [auth aa],
XC [auth aa],
XD [auth aa],
YA [auth aa],
YB [auth aa],
YC [auth aa],
YD [auth aa],
ZA [auth aa],
ZB [auth aa],
ZC [auth aa],
ZD [auth aa]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSwedenNT_2015-04107
European Research Council (ERC)European Union(ERC-2018-StG-805230
Knut and Alice Wallenberg FoundationSweden2018.0080
European Molecular Biology Organization (EMBO)European UnionH2020-MSCA-IF-2017

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Database references, Structure summary