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- PDB-8iuj: Cryo-EM structure of Euglena gracilis super-complex III2+IV2, com... -

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Basic information

Entry
Database: PDB / ID: 8iuj
TitleCryo-EM structure of Euglena gracilis super-complex III2+IV2, composite
Components
  • (Cytochrome c oxidase subunit ...) x 2
  • (Ubiquinol-cytochrome- ...) x 2
  • COX4
  • COX5b-2
  • COX5c
  • COX6a
  • COX6b-1
  • COX7a
  • COX7c
  • COXEG1
  • COXEG10
  • COXEG3
  • COXEG4
  • COXEG5
  • COXEG6
  • COXEG7
  • COXEG8
  • COXEG9
  • Cytochrome b
  • Cytochrome c1, heme protein
  • MPP-beta
  • Putative NADH dehydrogenase subunit 6
  • UQCR10
  • UQCR9
  • UQCRB
  • UQCRFS1
  • UQCRH
  • UQCRQ
KeywordsELECTRON TRANSPORT / Electron transport chain / supercomplex / membrane protein / Euglena gracilis
Function / homology
Function and homology information


cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / cytochrome-c oxidase activity / respirasome / respiratory electron transport chain / mitochondrial inner membrane / electron transfer activity / copper ion binding ...cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / cytochrome-c oxidase activity / respirasome / respiratory electron transport chain / mitochondrial inner membrane / electron transfer activity / copper ion binding / heme binding / mitochondrion / membrane / metal ion binding
Similarity search - Function
Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD ...Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Di-haem cytochrome, transmembrane / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c-like domain superfamily / Cupredoxin
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / Chem-S12 ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / Chem-S12 / Cytochrome b / Cytochrome c1, heme protein / Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial / Ubiquinol-cytochrome-C reductase complex subunit IX, mitochondrial / Cytochrome c oxidase subunit 1 / Putative NADH dehydrogenase subunit 6 / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesEuglena gracilis (euglena)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsWu, M.C. / Tian, H.T. / He, Z.X. / Hu, Y.Q. / Zhou, L.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentZJU100 Young Professor China
CitationJournal: Nat Commun / Year: 2024
Title: Euglena's atypical respiratory chain adapts to the discoidal cristae and flexible metabolism.
Authors: Zhaoxiang He / Mengchen Wu / Hongtao Tian / Liangdong Wang / Yiqi Hu / Fangzhu Han / Jiancang Zhou / Yong Wang / Long Zhou /
Abstract: Euglena gracilis, a model organism of the eukaryotic supergroup Discoba harbouring also clinically important parasitic species, possesses diverse metabolic strategies and an atypical electron ...Euglena gracilis, a model organism of the eukaryotic supergroup Discoba harbouring also clinically important parasitic species, possesses diverse metabolic strategies and an atypical electron transport chain. While structures of the electron transport chain complexes and supercomplexes of most other eukaryotic clades have been reported, no similar structure is currently available for Discoba, limiting the understandings of its core metabolism and leaving a gap in the evolutionary tree of eukaryotic bioenergetics. Here, we report high-resolution cryo-EM structures of Euglena's respirasome I + III + IV and supercomplex III + IV. A previously unreported fatty acid synthesis domain locates on the tip of complex I's peripheral arm, providing a clear picture of its atypical subunit composition identified previously. Individual complexes are re-arranged in the respirasome to adapt to the non-uniform membrane curvature of the discoidal cristae. Furthermore, Euglena's conformationally rigid complex I is deactivated by restricting ubiquinone's access to its substrate tunnel. Our findings provide structural insights for therapeutic developments against euglenozoan parasite infections.
History
DepositionMar 24, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
QA: MPP-beta
QC: Cytochrome b
QD: Cytochrome c1, heme protein
QH: UQCRQ
QJ: UQCR10
QK: Ubiquinol-cytochrome-C reductase complex subunit IX, mitochondrial
Qa: MPP-beta
Qc: Cytochrome b
Qd: Cytochrome c1, heme protein
Qh: UQCRQ
Qj: UQCR10
Qk: Ubiquinol-cytochrome-C reductase complex subunit IX, mitochondrial
4a: COXEG1
4c: COXEG3
4e: COXEG5
4h: COXEG8
4j: COXEG10
5c: COX5c
6a: COX6a
6b: COX6b-1
7c: COX7c
c1: Cytochrome c oxidase subunit 1
c2: Cytochrome c oxidase subunit 2
c3: Putative NADH dehydrogenase subunit 6
dc: COX4
4A: COXEG1
4C: COXEG3
4E: COXEG5
4H: COXEG8
4J: COXEG10
5C: COX5c
6B: COX6b-1
7C: COX7c
C1: Cytochrome c oxidase subunit 1
C2: Cytochrome c oxidase subunit 2
C3: Putative NADH dehydrogenase subunit 6
DC: COX4
6A: COX6a
QE: UQCRFS1
Qe: UQCRFS1
QF: UQCRH
QG: UQCRB
QI: UQCR9
Qb: Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial
Qf: UQCRH
Qg: UQCRB
Qi: UQCR9
QB: Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial
5B: COX5b-2
4D: COXEG4
4F: COXEG6
4G: COXEG7
4I: COXEG9
7a: COX7a
4d: COXEG4
4f: COXEG6
4g: COXEG7
4i: COXEG9
5b: COX5b-2
7A: COX7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,508,540135
Polymers1,450,28760
Non-polymers58,25375
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 26 types, 52 molecules QAQaQCQcQDQdQHQhQJQj4a4A4c4C4e4E4h4H4j4J5c5C6a6A6b6B7c7Cc3C3...

#1: Protein MPP-beta


Mass: 53520.293 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#2: Protein Cytochrome b /


Mass: 42476.266 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
References: UniProt: A0A0S2YRT7
#3: Protein Cytochrome c1, heme protein / / Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol- ...Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol-cytochrome-c reductase complex cytochrome c1 subunit / Cytochrome c-1


Mass: 27889.436 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
References: UniProt: P20114, quinol-cytochrome-c reductase
#4: Protein UQCRQ


Mass: 10079.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#5: Protein UQCR10


Mass: 17577.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#7: Protein COXEG1


Mass: 27278.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#8: Protein COXEG3


Mass: 16394.043 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#9: Protein COXEG5


Mass: 19464.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#10: Protein COXEG8


Mass: 24495.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#11: Protein COXEG10


Mass: 10043.338 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#12: Protein COX5c


Mass: 23788.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#13: Protein COX6a


Mass: 13079.197 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#14: Protein COX6b-1


Mass: 32995.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#15: Protein COX7c


Mass: 19897.588 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#18: Protein Putative NADH dehydrogenase subunit 6 /


Mass: 19414.947 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
References: UniProt: Q9XN18
#19: Protein COX4


Mass: 20427.480 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#20: Protein UQCRFS1


Mass: 27825.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#21: Protein UQCRH


Mass: 8207.571 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#22: Protein UQCRB /


Mass: 27404.115 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#23: Protein UQCR9


Mass: 6939.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#25: Protein COX5b-2 /


Mass: 19736.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#26: Protein COXEG4


Mass: 19359.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#27: Protein COXEG6


Mass: 8728.172 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#28: Protein COXEG7


Mass: 35651.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#29: Protein COXEG9


Mass: 31754.857 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
#30: Protein COX7a


Mass: 20078.975 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.

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Ubiquinol-cytochrome- ... , 2 types, 4 molecules QKQkQbQB

#6: Protein Ubiquinol-cytochrome-C reductase complex subunit IX, mitochondrial / Coenzyme Q – cytochrome c reductase


Mass: 11300.364 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
References: UniProt: P43266
#24: Protein Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial


Mass: 51132.660 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
References: UniProt: P43265

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Cytochrome c oxidase subunit ... , 2 types, 4 molecules c1C1c2C2

#16: Protein Cytochrome c oxidase subunit 1 /


Mass: 55759.504 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
References: UniProt: Q34463, cytochrome-c oxidase
#17: Protein Cytochrome c oxidase subunit 2 /


Mass: 22443.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
Plasmid details: Shanghai Guangyu Biological Technology Co., Ltd.
References: UniProt: Q9XN19

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Non-polymers , 12 types, 75 molecules

#31: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#33: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#34: Chemical...
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#35: Chemical ChemComp-PX2 / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE


Mass: 535.671 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H52O8P
#36: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#37: Chemical
ChemComp-HEA / HEME-A / Heme A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#38: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#39: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#40: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#41: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#42: Chemical ChemComp-S12 / O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine / 1-oleoyl-2-hydroxy-sn-glycero-3-phospho-L-serine


Type: L-peptide linking / Mass: 523.597 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46NO9P

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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

Component
IDNameTypeEntity IDParent-IDSource
1Euglena gracilis supercomplex III2+IV2COMPLEX#1-#300NATURAL
2Euglena gracilis supercomplex III2+IV2COMPLEX#1-#301NATURAL
Molecular weightValue: 1.4 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Euglena gracilis (euglena)3039
32Euglena gracilis (euglena)3039
Buffer solutionpH: 7.4
Details: SEC buffer (30 mM Tris pH 7.4, 100 mM NaCl, 0.002% PMSF, 0.1% GDN (w/v), 1mM EDTA)
Buffer component
IDConc.NameFormulaBuffer-ID
130 mMTrimethylsilylTris1
2100 mMSodium chlorideNaClSodium chloride1
30.002 %Phenylmethylsulfonyl fluoridePMSFPMSF1
40.1 %Glyco-diosgeninGDN1
51 mMEthylene diamine tetraacetic acidEDTAEthylenediaminetetraacetic acid1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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 FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 7.8 sec. / Electron dose: 51.5 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9807
Image scansWidth: 4096 / Height: 4096

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM software
IDNameVersionCategory
1crYOLO1.6.0particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7PHENIX1.20.1model fitting
8Coot0.9.6model fitting
10cryoSPARCv.3.3.2initial Euler assignment
11cryoSPARCv.3.3.2final Euler assignment
12cryoSPARCv.3.3.2classification
13cryoSPARCv.3.3.23D reconstruction
14PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3232325
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135598 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 419.11 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005103392
ELECTRON MICROSCOPYf_angle_d0.5445140111
ELECTRON MICROSCOPYf_chiral_restr0.041915016
ELECTRON MICROSCOPYf_plane_restr0.004117490
ELECTRON MICROSCOPYf_dihedral_angle_d11.495738831

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