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- PDB-6ywv: The structure of the Atp25 bound assembly intermediate of the mit... -

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Basic information

Entry
Database: PDB / ID: 6ywv
TitleThe structure of the Atp25 bound assembly intermediate of the mitoribosome from Neurospora crassa
Components
  • (50S ribosomal protein ...) x 5
  • (50S ribosomal subunit ...) x 2
  • (54S ribosomal protein ...) x 2
  • (60S ribosomal protein ...) x 8
  • (Mitochondrial ...) x 8
  • (Uncharacterized ...) x 11
  • 23 S rRNA
  • ATPase synthesis protein 25, mitochondrial
  • Aconitate hydratase
  • KOW domain-containing protein
  • RNase III domain-containing protein
  • Ribosomal protein
  • Ribosomal protein L13
KeywordsTRANSLATION / Neurospora crassa / translating Mitoribosomes / tRNA / mRNA / mL108
Function / homology
Function and homology information


mitochondrial gene expression / DNA strand exchange activity / ribonuclease III activity / : / mitochondrial large ribosomal subunit / mRNA stabilization / mitochondrial translation / RNA processing / single-stranded DNA binding / double-stranded RNA binding ...mitochondrial gene expression / DNA strand exchange activity / ribonuclease III activity / : / mitochondrial large ribosomal subunit / mRNA stabilization / mitochondrial translation / RNA processing / single-stranded DNA binding / double-stranded RNA binding / large ribosomal subunit / transferase activity / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / mitochondrial inner membrane / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / mitochondrion / RNA binding / metal ion binding
Similarity search - Function
ATPase synthesis protein 25, mitochondrial / 54S ribosomal protein L44, mitochondrial / : / Large ribosomal subunit protein uL24m / Ribosomal protein L31, mitochondrial / Ribosomal protein L20, mitochondrial / Mitochondrial homologous recombination protein 1 / 54S ribosomal protein L25 / 54S ribosomal protein L15, mitochondrial / MRPL25 domain ...ATPase synthesis protein 25, mitochondrial / 54S ribosomal protein L44, mitochondrial / : / Large ribosomal subunit protein uL24m / Ribosomal protein L31, mitochondrial / Ribosomal protein L20, mitochondrial / Mitochondrial homologous recombination protein 1 / 54S ribosomal protein L25 / 54S ribosomal protein L15, mitochondrial / MRPL25 domain / 54S ribosomal protein L28, mitochondrial / 54S ribosomal protein L3, double-stranded RNA binding domain / Mitochondrial ribosomal protein subunit L20 / Transcriptional regulation of mitochondrial recombination / Mitochondrial ribosomal protein mL59 / Mitochondrial ribosomal protein L31 / 54S ribosomal protein L36, yeast / : / Ribosomal protein L31p, N-terminal / Ribonuclease-III-like / Ribosomal silencing factor during starvation / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Ribosomal protein L53, mitochondrial / 39S ribosomal protein L53/MRP-L53 / Ribosomal protein L37, mitochondrial / Mitochondrial ribosomal protein L37 / : / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L50, mitochondria / Ribosomal subunit 39S / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L27/L41, mitochondrial / : / Mitochondrial ribosomal protein L27 / 39S ribosomal protein L46, mitochondrial / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein, eukaryotic / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / PEBP-like superfamily / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double-stranded RNA-binding domain / NUDIX domain / : / NUDIX hydrolase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / NUDIX hydrolase-like domain superfamily / Ribosomal protein L11, bacterial-type / Nucleotidyltransferase superfamily / Ribosomal protein L10-like domain superfamily / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L17 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L6, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L14P, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / : / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L32p / Ribosomal protein L17
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SPERMINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / Large ribosomal subunit protein uL16m / Large ribosomal subunit protein bL32m ...: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SPERMINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / Large ribosomal subunit protein uL16m / Large ribosomal subunit protein bL32m / Large ribosomal subunit protein uL5m / Large ribosomal subunit protein mL58 / Large ribosomal subunit protein bL27m / Large ribosomal subunit protein bL31m / Large ribosomal subunit protein bL34m / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein uL3m / Large ribosomal subunit protein uL30m / Large ribosomal subunit protein uL11m / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein mL38 / Large ribosomal subunit protein mL67 / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein uL6m / Large ribosomal subunit protein mL57 / Large ribosomal subunit protein mL46 / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein bL36m / Large ribosomal subunit protein mL49 / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein mL41 / Large ribosomal subunit protein mL50 / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein uL23m / Large ribosomal subunit protein mL44 / ATPase synthesis protein 25, mitochondrial / Large ribosomal subunit protein uL15m / Large ribosomal subunit protein uL14m / Large ribosomal subunit protein uL13m / Large ribosomal subunit protein bL28m / Large ribosomal subunit protein uL2m / Large ribosomal subunit protein mL54 / Large ribosomal subunit protein mL59 / Large ribosomal subunit protein bL21m / Large ribosomal subunit protein mL53 / Large ribosomal subunit protein mL60 / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL4m
Similarity search - Component
Biological speciesNeurospora crassa OR74A (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsAmunts, A. / Itoh, Y. / Naschberger, A.
Funding support Sweden, European Union, 4items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107 Sweden
European Research Council (ERC)(ERC-2018-StG-805230European Union
Knut and Alice Wallenberg Foundation2018.0080 Sweden
European Molecular Biology Organization (EMBO)H2020-MSCA-IF-2017European Union
CitationJournal: Nat Commun / Year: 2020
Title: Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi.
Authors: Yuzuru Itoh / Andreas Naschberger / Narges Mortezaei / Johannes M Herrmann / Alexey Amunts /
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 ...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) 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.
History
DepositionApr 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: 23 S rRNA
B: 60S ribosomal protein L2
C: 60S ribosomal protein L3
D: 60S ribosomal protein L4, variant
E: 50S ribosomal protein L5
F: 60S ribosomal protein L6
f: Uncharacterized protein
g: 60S ribosomal protein L19
H: Ribosomal protein L13
I: 50S ribosomal protein L14
J: 50S ribosomal subunit protein L15
K: 60S ribosomal protein L16
L: 50S ribosomal protein L17
M: Mitochondrial ribosomal protein
N: Aconitate hydratase
O: Mitochondrial large ribosomal subunit
P: Mitochondrial ribosomal protein subunit L23
Q: KOW domain-containing protein
R: Uncharacterized protein
S: 50S ribosomal protein L24
T: 54S ribosomal protein L4, mitochondrial
U: 50S ribosomal protein L30
V: Uncharacterized protein
W: Mitochondrial ribosomal protein subunit L32
X: Uncharacterized protein
Y: Uncharacterized protein
0: Ribosomal protein
1: Mitochondrial large ribosomal subunit YmL35
2: Uncharacterized protein
3: Uncharacterized protein
4: Mitochondrial ribosomal protein L43
5: 60S ribosomal protein L3
6: 50S ribosomal subunit L30
7: Uncharacterized protein
8: Uncharacterized protein
h: Mitochondrial ribosomal protein L44
i: Uncharacterized protein
9: RNase III domain-containing protein
a: 60S ribosomal protein L20
b: Mitochondrial 60S ribosomal protein L25
c: 54S ribosomal protein L31, mitochondrial
d: Uncharacterized protein
n: ATPase synthesis protein 25, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,356,131214
Polymers2,350,73543
Non-polymers5,396171
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area372920 Å2
ΔGint-3864 kcal/mol
Surface area597340 Å2
MethodPISA

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain 23 S rRNA


Mass: 1114857.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus)

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60S ribosomal protein ... , 8 types, 8 molecules BCDFgK5a

#2: Protein 60S ribosomal protein L2


Mass: 42260.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SCX7
#3: Protein 60S ribosomal protein L3


Mass: 41262.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K8T6
#4: Protein 60S ribosomal protein L4, variant


Mass: 36402.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: V5IMN1
#6: Protein 60S ribosomal protein L6


Mass: 28629.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RZF0
#8: Protein 60S ribosomal protein L19


Mass: 16629.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RX40
#12: Protein 60S ribosomal protein L16


Mass: 27443.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: F5HIJ5
#32: Protein 60S ribosomal protein L3


Mass: 48106.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SA88
#39: Protein 60S ribosomal protein L20


Mass: 25439.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K6U7

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50S ribosomal protein ... , 5 types, 5 molecules EILSU

#5: Protein 50S ribosomal protein L5


Mass: 39170.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K6P0
#10: Protein 50S ribosomal protein L14


Mass: 14135.630 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SBJ8
#13: Protein 50S ribosomal protein L17


Mass: 22181.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K8C8
#20: Protein 50S ribosomal protein L24


Mass: 31501.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SC44
#22: Protein 50S ribosomal protein L30


Mass: 18196.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K8Y7

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Uncharacterized ... , 11 types, 11 molecules fRVXY2378id

#7: Protein Uncharacterized protein


Mass: 37363.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RZ62
#19: Protein Uncharacterized protein


Mass: 49549.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K730
#23: Protein Uncharacterized protein


Mass: 23766.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K7L7
#25: Protein Uncharacterized protein


Mass: 7027.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: V5IM60
#26: Protein Uncharacterized protein


Mass: 14853.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K7P9
#29: Protein Uncharacterized protein


Mass: 41496.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: A0A0B0DWX0
#30: Protein Uncharacterized protein


Mass: 11796.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S5W0
#34: Protein Uncharacterized protein


Mass: 18180.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S518
#35: Protein Uncharacterized protein


Mass: 49748.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S711
#37: Protein Uncharacterized protein


Mass: 23179.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SCZ3
#42: Protein Uncharacterized protein


Mass: 32516.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RYM5

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Protein , 6 types, 6 molecules HNQ09n

#9: Protein Ribosomal protein L13


Mass: 20334.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SBV6
#15: Protein Aconitate hydratase


Mass: 23953.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SGE5
#18: Protein KOW domain-containing protein


Mass: 45460.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RXU7
#27: Protein Ribosomal protein


Mass: 13960.405 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S4E7
#38: Protein RNase III domain-containing protein


Mass: 29625.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S1R6
#43: Protein ATPase synthesis protein 25, mitochondrial


Mass: 77985.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SAC2

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50S ribosomal subunit ... , 2 types, 2 molecules J6

#11: Protein 50S ribosomal subunit protein L15


Mass: 33951.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SB98
#33: Protein 50S ribosomal subunit L30


Mass: 41322.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S1Z3

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Mitochondrial ... , 8 types, 8 molecules MOPW14hb

#14: Protein Mitochondrial ribosomal protein


Mass: 28235.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RYW8
#16: Protein Mitochondrial large ribosomal subunit


Mass: 41565.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S5N0
#17: Protein Mitochondrial ribosomal protein subunit L23


Mass: 26005.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SA60
#24: Protein Mitochondrial ribosomal protein subunit L32


Mass: 14114.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K4P1
#28: Protein Mitochondrial large ribosomal subunit YmL35


Mass: 50749.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RXV8
#31: Protein Mitochondrial ribosomal protein L43


Mass: 15126.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S300
#36: Protein Mitochondrial ribosomal protein L44


Mass: 11128.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SGH0
#40: Protein Mitochondrial 60S ribosomal protein L25


Mass: 18745.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SEK9

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54S ribosomal protein ... , 2 types, 2 molecules Tc

#21: Protein 54S ribosomal protein L4, mitochondrial


Mass: 29645.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S910
#41: Protein 54S ribosomal protein L31, mitochondrial


Mass: 13131.485 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: U9W8F2

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Non-polymers , 5 types, 171 molecules

#44: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 144 / Source method: obtained synthetically / Formula: Mg
#45: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#46: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#47: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: K
#48: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Assembly intermediate of the mitoribosome of Neurospora crassa
Type: RIBOSOME / Entity ID: #1-#43 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Neurospora crassa OR74A (fungus)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid-KOHHEPES-KOH1
215 mMPotassium chlorideKCl1
315 mMMagnesium acetateMg(C2H3O2)21
40.05 %n-Dodecyl B-D-maltosideDDM1
50.0075 %1,3-bis(sn-3-phosphatidyl)-sn-glycerolCardiolipin1
62 mMDithiothreitolDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 130000 X / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 35 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 3172
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 20 / Used frames/image: 1-20

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Processing

Software
NameVersionClassification
phenix.real_space_refinedev_3742refinement
PHENIXdev_3742refinement
EM software
IDNameCategory
2EPUimage acquisition
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24142 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 21.45 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002124129
ELECTRON MICROSCOPYf_angle_d0.4008179961
ELECTRON MICROSCOPYf_chiral_restr0.030721919
ELECTRON MICROSCOPYf_plane_restr0.002513620
ELECTRON MICROSCOPYf_dihedral_angle_d21.026555122

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