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- PDB-9qo0: Pre-activated 9-subunit COP9 signalosome and neddylated SCF (Skp1... -

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Entry
Database: PDB / ID: 9qo0
TitlePre-activated 9-subunit COP9 signalosome and neddylated SCF (Skp1-Skp2-Cks1) complex structure
Components
  • (COP9 signalosome complex subunit ...) x 9
  • (S-phase kinase-associated protein ...) x 2
  • Cullin-1
  • Cyclin-dependent kinases regulatory subunit 1
  • E3 ubiquitin-protein ligase RBX1
  • NEDD8
KeywordsLIGASE / E3 ligases / COP9 signalosome
Function / homology
Function and homology information


negative regulation of protein localization to nucleolus / negative regulation of protein neddylation / COP9 signalosome assembly / macrophage migration inhibitory factor binding / regulation of DNA damage response, signal transduction by p53 class mediator / regulation of IRE1-mediated unfolded protein response / Parkin-FBXW7-Cul1 ubiquitin ligase complex / exosomal secretion / GTPase inhibitor activity / deNEDDylase activity ...negative regulation of protein localization to nucleolus / negative regulation of protein neddylation / COP9 signalosome assembly / macrophage migration inhibitory factor binding / regulation of DNA damage response, signal transduction by p53 class mediator / regulation of IRE1-mediated unfolded protein response / Parkin-FBXW7-Cul1 ubiquitin ligase complex / exosomal secretion / GTPase inhibitor activity / deNEDDylase activity / activation of NF-kappaB-inducing kinase activity / synaptic assembly at neuromuscular junction / F-box domain binding / Aberrant regulation of mitotic exit in cancer due to RB1 defects / protein deneddylation / regulation of protein neddylation / eukaryotic translation initiation factor 3 complex / cellular response to camptothecin / negative regulation of beige fat cell differentiation / PcG protein complex / COP9 signalosome / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / deubiquitinase activity / negative regulation of mitophagy / positive regulation of keratinocyte differentiation / cullin-RING ubiquitin ligase complex / regulation of xenophagy / maintenance of protein location in nucleus / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / Cul7-RING ubiquitin ligase complex / cyclin-dependent protein serine/threonine kinase activator activity / regulation of cell cycle process / neural crest cell differentiation / RNA polymerase II transcription initiation surveillance / positive regulation of protein autoubiquitination / protein neddylation / Hydrolases; Acting on peptide bonds (peptidases) / regulation of JNK cascade / ubiquitin ligase activator activity / regulation of BMP signaling pathway / NEDD8 ligase activity / regulation of mitophagy / negative regulation of response to oxidative stress / regulation of centrosome duplication / RHOBTB1 GTPase cycle / protein K27-linked ubiquitination / VCB complex / Cul5-RING ubiquitin ligase complex / metal-dependent deubiquitinase activity / ubiquitin-ubiquitin ligase activity / regulation of TOR signaling / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / negative regulation of DNA-templated DNA replication / intercellular bridge / Cul3-RING ubiquitin ligase complex / regulation of mitotic cytokinesis / regulation of DNA damage checkpoint / negative regulation of type I interferon production / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / regulation of cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / regulation of stem cell population maintenance / Cul4B-RING E3 ubiquitin ligase complex / TGF-beta receptor signaling activates SMADs / ubiquitin ligase complex scaffold activity / negative regulation of adipose tissue development / regulation of proteolysis / regulation of cellular response to stress / limb development / regulation of postsynapse assembly / response to light stimulus / cyclin-dependent protein kinase holoenzyme complex / protein monoubiquitination / anatomical structure morphogenesis / JNK cascade / cullin family protein binding / centrosome duplication / regulation of DNA-templated DNA replication initiation / protein K63-linked ubiquitination / cilium assembly / positive regulation of double-strand break repair via homologous recombination / ubiquitin-like ligase-substrate adaptor activity / intrinsic apoptotic signaling pathway / ribosome-associated ubiquitin-dependent protein catabolic process / signal transduction in response to DNA damage / negative regulation of insulin receptor signaling pathway / Nuclear events stimulated by ALK signaling in cancer / protein K48-linked ubiquitination / regulation of cellular response to insulin stimulus / translation initiation factor activity / positive regulation of TORC1 signaling / transcription-coupled nucleotide-excision repair
Similarity search - Function
COP9 signalosome complex, subunit 9, metazoa / Myeloma-overexpressed-like / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / COP9 signalosome complex subunit 7, helix I / : ...COP9 signalosome complex, subunit 9, metazoa / Myeloma-overexpressed-like / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / COP9 signalosome complex subunit 7, helix I / : / COP9 signalosome complex subunit 7a helix I domain / COP9 signalosome complex subunit 3-like, C-terminal helix / CSN7 helical bundle subdomain / COP9 signalosome, subunit CSN8 / COP9 signalosome complex subunit 4, helix turn helix domain / : / CSN4/RPN5/eIF3a helix turn helix domain / COP9 signalosome complex subunit 3, N-terminal helical repeats / COP9 signalosome subunit 6 / : / : / COP9 signalosome complex subunit 1, C-terminal helix / COP9 signalosome complex subunit 2, C-terminal helix / Cop9 signalosome subunit 5 C-terminal domain / Cop9 signalosome subunit 5 C-terminal domain / Nedd8-like ubiquitin / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin alpha solenoid domain / : / : / : / PSMD12/CSN4, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome subunit RPN7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / PCI/PINT associated module / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / : / PCI domain / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Proteasome component (PCI) domain / PCI domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Tetratricopeptide-like helical domain superfamily / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Cyclin-dependent kinases regulatory subunit 1 / COP9 signalosome complex subunit 2 / E3 ubiquitin-protein ligase RBX1 / S-phase kinase-associated protein 1 / COP9 signalosome complex subunit 1 / S-phase kinase-associated protein 2 / Cullin-1 / Ubiquitin-like protein NEDD8 / COP9 signalosome complex subunit 6 ...INOSITOL HEXAKISPHOSPHATE / Cyclin-dependent kinases regulatory subunit 1 / COP9 signalosome complex subunit 2 / E3 ubiquitin-protein ligase RBX1 / S-phase kinase-associated protein 1 / COP9 signalosome complex subunit 1 / S-phase kinase-associated protein 2 / Cullin-1 / Ubiquitin-like protein NEDD8 / COP9 signalosome complex subunit 6 / COP9 signalosome complex subunit 9 / COP9 signalosome complex subunit 5 / COP9 signalosome complex subunit 8 / COP9 signalosome complex subunit 4 / COP9 signalosome complex subunit 7b / COP9 signalosome complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsDing, S. / Clapperton, J.A. / Maeots, M.E. / Shaaban, M. / Enchev, R.I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick InstituteCC2059 United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis of CSN-mediated SCF deneddylation.
Authors: Shan Ding / Julie A Clapperton / Märt-Erik Mäeots / Simone Kunzelmann / Mohammed Shaaban / Radoslav I Enchev /
Abstract: Cullin-RING ligases (CRLs) are the largest family of E3 ligases, with ubiquitination activity dynamically regulated by neddylation and deneddylation by the COP9 signalosome (CSN). CSN-mediated ...Cullin-RING ligases (CRLs) are the largest family of E3 ligases, with ubiquitination activity dynamically regulated by neddylation and deneddylation by the COP9 signalosome (CSN). CSN-mediated deneddylation not only deactivates CRLs but also enables substrate receptor exchange. Although CSN is a promising drug target, the structural basis underlying its catalytic mechanism remains unclear. Here, we use cryo-electron microscopy (cryo-EM) to uncover distinct functional states of CSN-CRL (SCF) complexes, capturing key intermediates of the deneddylation cycle. We visualise an autoinhibited docking state and a catalytic intermediate in which CSN5 Ins-1 loop, RBX1 RING and neddylated Cullin WHB domains are repositioned for isopeptide cleavage. We further resolve four dissociation intermediates that define the stepwise release of CSN from its product, with RBX1 RING stabilising key interactions. Additionally, our structures locate CSNAP within a CSN3-CSN8 groove. Together, our study provides a mechanistic model for CSN function and informs the rational design of CSN-targeted therapeutics.
History
DepositionMar 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: COP9 signalosome complex subunit 4
G: COP9 signalosome complex subunit 7b
K: NEDD8
N: Cyclin-dependent kinases regulatory subunit 1
P: COP9 signalosome complex subunit 9
A: COP9 signalosome complex subunit 1
B: COP9 signalosome complex subunit 2
C: COP9 signalosome complex subunit 3
E: COP9 signalosome complex subunit 5
F: COP9 signalosome complex subunit 6
H: COP9 signalosome complex subunit 8
I: Cullin-1
J: E3 ubiquitin-protein ligase RBX1
L: S-phase kinase-associated protein 1
M: S-phase kinase-associated protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)522,15719
Polymers521,30015
Non-polymers8564
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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COP9 signalosome complex subunit ... , 9 types, 9 molecules DGPABCEFH

#1: Protein COP9 signalosome complex subunit 4 / SGN4 / Signalosome subunit 4 / JAB1-containing signalosome subunit 4


Mass: 46322.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS4, CSN4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BT78
#2: Protein COP9 signalosome complex subunit 7b / SGN7b / Signalosome subunit 7b / JAB1-containing signalosome subunit 7b


Mass: 29656.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS7B, CSN7B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9H9Q2
#5: Protein COP9 signalosome complex subunit 9 / CSN acidic protein / CSNAP / Myeloma-overexpressed gene 2 protein


Mass: 6213.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS9, MYEOV2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WXC6
#6: Protein COP9 signalosome complex subunit 1 / Signalosome subunit 1 / G protein pathway suppressor 1 / GPS-1 / JAB1-containing signalosome ...Signalosome subunit 1 / G protein pathway suppressor 1 / GPS-1 / JAB1-containing signalosome subunit 1 / Protein MFH


Mass: 55606.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPS1, COPS1, CSN1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13098
#7: Protein COP9 signalosome complex subunit 2 / Signalosome subunit 2 / Alien homolog / JAB1-containing signalosome subunit 2 / Thyroid receptor- ...Signalosome subunit 2 / Alien homolog / JAB1-containing signalosome subunit 2 / Thyroid receptor-interacting protein 15 / TRIP-15


Mass: 51664.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS2, CSN2, TRIP15 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P61201
#8: Protein COP9 signalosome complex subunit 3 / SGN3 / Signalosome subunit 3 / JAB1-containing signalosome subunit 3


Mass: 47924.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS3, CSN3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UNS2
#9: Protein COP9 signalosome complex subunit 5 / SGN5 / Signalosome subunit 5 / Jun activation domain-binding protein 1


Mass: 37621.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS5, CSN5, JAB1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q92905, Hydrolases; Acting on peptide bonds (peptidases)
#10: Protein COP9 signalosome complex subunit 6 / Signalosome subunit 6 / JAB1-containing signalosome subunit 6 / MOV34 homolog / Vpr-interacting protein / hVIP


Mass: 36203.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS6, CSN6, HVIP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7L5N1
#11: Protein COP9 signalosome complex subunit 8 / Signalosome subunit 8 / COP9 homolog / hCOP9 / JAB1-containing signalosome subunit 8


Mass: 23245.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COPS8, CSN8 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q99627

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Protein , 4 types, 4 molecules KNIJ

#3: Protein NEDD8 / Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / ...Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / Ubiquitin-like protein Nedd8


Mass: 8573.978 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15843
#4: Protein Cyclin-dependent kinases regulatory subunit 1 / CKS-1


Mass: 9679.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CKS1B, CKS1, PNAS-143, PNAS-16 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61024
#12: Protein Cullin-1 / CUL-1


Mass: 89800.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13616
#13: Protein E3 ubiquitin-protein ligase RBX1 / E3 ubiquitin-protein transferase RBX1 / Protein ZYP / RING finger protein 75 / RING-box protein 1 / ...E3 ubiquitin-protein transferase RBX1 / Protein ZYP / RING finger protein 75 / RING-box protein 1 / Rbx1 / Regulator of cullins 1 / ROC1


Mass: 12289.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBX1, RNF75, ROC1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P62877, RING-type E3 ubiquitin transferase, cullin-RING-type E3 NEDD8 transferase

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S-phase kinase-associated protein ... , 2 types, 2 molecules LM

#14: Protein S-phase kinase-associated protein 1 / Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti ...Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti protein II / OCP-II / RNA polymerase II elongation factor-like protein / SIII / Transcription elongation factor B polypeptide 1-like / p19skp1


Mass: 18679.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63208
#15: Protein S-phase kinase-associated protein 2 / Cyclin-A/CDK2-associated protein p45 / F-box protein Skp2 / F-box/LRR-repeat protein 1 / p45skp2


Mass: 47817.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP2, FBXL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13309

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Non-polymers , 2 types, 4 molecules

#16: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY
Has protein modificationY

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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
1Pre-active conformation structure of 9-subunit COP9 signalosome and neddylated SCF (Skp1-Skp2-Cks1) complexCOMPLEX#1-#150RECOMBINANT
2COP9 signalosomeCOMPLEX#1-#2, #5-#111RECOMBINANT
3Neddylated SCF (Skp1-Skp2-Cks1) complexCOMPLEX#3-#4, #12-#151RECOMBINANT
4Neddylated Cullin-1/Rbx1 complexCOMPLEX#3, #12-#133RECOMBINANT
5Skp1-Skp2-Cks1COMPLEX#4, #14-#153RECOMBINANT
6Cullin-1/Rbx1COMPLEX#12-#134RECOMBINANT
7Nedd8COMPLEX#34RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
54Homo sapiens (human)9606
65Homo sapiens (human)9606
76Homo sapiens (human)9606
87Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spodoptera frugiperda (fall armyworm)7108
32Spodoptera frugiperda (fall armyworm)7108
43Spodoptera frugiperda (fall armyworm)7108
54Spodoptera frugiperda (fall armyworm)7108
65Escherichia coli BL21(DE3) (bacteria)469008
76Spodoptera frugiperda (fall armyworm)7108
87Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 7.5 / Details: 15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 47 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameCategory
1crYOLOparticle selection
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 400018 / Symmetry type: POINT
RefinementHighest resolution: 3.26 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00329873
ELECTRON MICROSCOPYf_angle_d0.5640432
ELECTRON MICROSCOPYf_dihedral_angle_d6.2344080
ELECTRON MICROSCOPYf_chiral_restr0.0364665
ELECTRON MICROSCOPYf_plane_restr0.0045136

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