6YWV

The structure of the Atp25 bound assembly intermediate of the mitoribosome from Neurospora crassa

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

  • Deposited: 2020-04-30 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: 3.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2383Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q7SCX7 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3384Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q1K8T6 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4, variant325Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5352Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6255Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinG [auth f]347Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19H [auth g]158Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q7RX40 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L13I [auth H]183Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q7SBV6 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14J [auth I]131Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal subunit protein L15K [auth J]312Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q7SB98 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16L [auth K]249Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17M [auth L]193Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q1K8C8 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal proteinN [auth M]258Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q7RYW8 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Aconitate hydrataseO [auth N]217Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q7SGE5 (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
Mitochondrial large ribosomal subunitP [auth O]364Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q7S5N0 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein subunit L23Q [auth P]228Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q7SA60 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
KOW domain-containing proteinR [auth Q]396Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q7RXU7 (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
Uncharacterized proteinS [auth R]447Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q1K730 (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
50S ribosomal protein L24T [auth S]274Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q7SC44 (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
54S ribosomal protein L4, mitochondrialU [auth T]263Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q7S910 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30V [auth U]161Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q1K8Y7 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinW [auth V]219Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q1K7L7 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein subunit L32X [auth W]129Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinY [auth X]59Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinZ [auth Y]140Neurospora crassa OR74AMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal proteinAA [auth 0]124Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial large ribosomal subunit YmL35BA [auth 1]449Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinCA [auth 2]370Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for A0A0B0DWX0 (Neurospora crassa)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinDA [auth 3]103Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L43EA [auth 4]138Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3FA [auth 5]439Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal subunit L30GA [auth 6]368Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinHA [auth 7]165Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q7S518 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinIA [auth 8]443Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q7S711 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L44JA [auth h]98Neurospora crassa OR74AMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinKA [auth i]218Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q7SCZ3 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
RNase III domain-containing proteinLA [auth 9]267Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q7S1R6 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20MA [auth a]225Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q1K6U7 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial 60S ribosomal protein L25NA [auth b]162Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q7SEK9 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
Explore Q7SEK9 
Go to UniProtKB:  Q7SEK9
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UniProt GroupQ7SEK9
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
54S ribosomal protein L31, mitochondrialOA [auth c]110Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for U9W8F2 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
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UniProt GroupU9W8F2
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinPA [auth d]292Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q7RYM5 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
Explore Q7RYM5 
Go to UniProtKB:  Q7RYM5
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase synthesis protein 25, mitochondrialQA [auth n]699Neurospora crassa OR74AMutation(s): 0 
UniProt
Find proteins for Q7SAC2 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
Explore Q7SAC2 
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Entity ID: 1
MoleculeChains LengthOrganismImage
23 S rRNA3,464Neurospora crassa OR74A
Sequence Annotations
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
TE [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
SPM
Query on SPM

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EG [auth A]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
DH [auth W],
EH [auth 0]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
AH [auth A]
BH [auth A]
FG [auth A]
GG [auth A]
HG [auth A]
AH [auth A],
BH [auth A],
FG [auth A],
GG [auth A],
HG [auth A],
IG [auth A],
JG [auth A],
KG [auth A],
LG [auth A],
MG [auth A],
NG [auth A],
OG [auth A],
PG [auth A],
QG [auth A],
RG [auth A],
SG [auth A],
TG [auth A],
UG [auth A],
VG [auth A],
WG [auth A],
XG [auth A],
YG [auth A],
ZG [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AG [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth A],
CH [auth K],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
DG [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FH [auth c],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TF [auth A],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 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