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- EMDB-18216: Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylate... -

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Basic information

Entry
Database: EMDB / ID: EMD-18216
TitleStructure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused cullin dimer
Map dataDeepEMhancer map
Sample
  • Complex: Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused cullin dimer
    • Protein or peptide: Cullin-9
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: NEDD8
    • Protein or peptide: Unknown
  • Ligand: ZINC ION
KeywordsCullin-RING RBR E3 Ligase / LIGASE
Function / homology
Function and homology information


cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of proteolysis / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / protein neddylation ...cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of proteolysis / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / protein neddylation / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / negative regulation of response to oxidative stress / ubiquitin-ubiquitin ligase activity / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / regulation of mitotic nuclear division / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of type I interferon production / Cul3-RING ubiquitin ligase complex / Prolactin receptor signaling / TGF-beta receptor signaling activates SMADs / protein monoubiquitination / cullin family protein binding / anatomical structure morphogenesis / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / positive regulation of TORC1 signaling / post-translational protein modification / regulation of cellular response to insulin stimulus / Regulation of BACH1 activity / T cell activation / Degradation of DVL / cellular response to amino acid stimulus / Iron uptake and transport / Recognition of DNA damage by PCNA-containing replication complex / Degradation of GLI1 by the proteasome / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / DNA Damage Recognition in GG-NER / protein modification process / RING-type E3 ubiquitin transferase / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / microtubule cytoskeleton organization / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / Interleukin-1 signaling / Dual incision in TC-NER / modification-dependent protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / Orc1 removal from chromatin / protein polyubiquitination / Regulation of RAS by GAPs / positive regulation of protein catabolic process / Regulation of RUNX2 expression and activity / protein tag activity / cellular response to UV / UCH proteinases / MAPK cascade / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / protein localization / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Cargo recognition for clathrin-mediated endocytosis / Neddylation / ubiquitin-dependent protein catabolic process / spermatogenesis / positive regulation of canonical NF-kappaB signal transduction / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / molecular adaptor activity / protein ubiquitination / DNA repair / DNA damage response / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / proteolysis / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
: / : / : / CPH domain / Mouse development and cellular proliferation protein Cullin-7 / IBR domain, a half RING-finger domain / Nedd8-like ubiquitin / IBR domain / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) ...: / : / : / CPH domain / Mouse development and cellular proliferation protein Cullin-7 / IBR domain, a half RING-finger domain / Nedd8-like ubiquitin / IBR domain / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin, conserved site / Cullin family signature. / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Galactose-binding-like domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Armadillo-like helical / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Armadillo-type fold / Ribosomal protein L2, domain 2 / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / NEDD8 / Cullin-9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsHopf LVM / Horn-Ghetko D / Schulman BA
Funding supportEuropean Union, Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)789016European Union
Max Planck Society Germany
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Noncanonical assembly, neddylation and chimeric cullin-RING/RBR ubiquitylation by the 1.8 MDa CUL9 E3 ligase complex.
Authors: Daniel Horn-Ghetko / Linus V M Hopf / Ishita Tripathi-Giesgen / Jiale Du / Sebastian Kostrhon / D Tung Vu / Viola Beier / Barbara Steigenberger / J Rajan Prabu / Luca Stier / Elias M Bruss / ...Authors: Daniel Horn-Ghetko / Linus V M Hopf / Ishita Tripathi-Giesgen / Jiale Du / Sebastian Kostrhon / D Tung Vu / Viola Beier / Barbara Steigenberger / J Rajan Prabu / Luca Stier / Elias M Bruss / Matthias Mann / Yue Xiong / Brenda A Schulman /
Abstract: Ubiquitin ligation is typically executed by hallmark E3 catalytic domains. Two such domains, 'cullin-RING' and 'RBR', are individually found in several hundred human E3 ligases, and collaborate with ...Ubiquitin ligation is typically executed by hallmark E3 catalytic domains. Two such domains, 'cullin-RING' and 'RBR', are individually found in several hundred human E3 ligases, and collaborate with E2 enzymes to catalyze ubiquitylation. However, the vertebrate-specific CUL9 complex with RBX1 (also called ROC1), of interest due to its tumor suppressive interaction with TP53, uniquely encompasses both cullin-RING and RBR domains. Here, cryo-EM, biochemistry and cellular assays elucidate a 1.8-MDa hexameric human CUL9-RBX1 assembly. Within one dimeric subcomplex, an E2-bound RBR domain is activated by neddylation of its own cullin domain and positioning from the adjacent CUL9-RBX1 in trans. Our data show CUL9 as unique among RBX1-bound cullins in dependence on the metazoan-specific UBE2F neddylation enzyme, while the RBR domain protects it from deneddylation. Substrates are recruited to various upstream domains, while ubiquitylation relies on both CUL9's neddylated cullin and RBR domains achieving self-assembled and chimeric cullin-RING/RBR E3 ligase activity.
History
DepositionAug 16, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18216.png

Downloads & links

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Map

FileDownload / File: emd_18216.map.gz / Format: CCP4 / Size: 488.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 504 pix.
= 429.005 Å		0.85 Å/pix.
x 504 pix.
= 429.005 Å		0.85 Å/pix.
x 504 pix.
= 429.005 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.063
Minimum - Maximum-0.0017793869 - 2.094444
Average (Standard dev.)0.0010601684 (±0.022821931)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions504504504
Spacing504504504
CellA=B=C: 429.0048 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18216_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Additional map: postprocess map

Fileemd_18216_additional_1.map
Annotationpostprocess map
Projections & Slices
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Half map: #2

Fileemd_18216_half_map_1.map
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Histogram

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Half map: #1

Fileemd_18216_half_map_2.map
Projections & Slices
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Sample components

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Entire : Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylate...

EntireName: Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused cullin dimer
Components
  • Complex: Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused cullin dimer
    • Protein or peptide: Cullin-9
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: NEDD8
    • Protein or peptide: Unknown
  • Ligand: ZINC ION

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Supramolecule #1: Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylate...

SupramoleculeName: Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused cullin dimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / Details: Structure of dimeric subunit
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cullin-9

MacromoleculeName: Cullin-9 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 281.686062 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPMVGERHAG DLMVPLGPRL QAYPEELIRQ RPGHDGHPEY LIRWSVLKCG EVGKVGVEEG KAEHILMWLS APEVYANCPG LLGERALSK GLQHEPAGVS GSFPRDPGGL DEVAMGEMEA DVQALVRRAA RQLAESGTPS LTAAVLHTIH VLSAYASIGP L TGVFRETG ...String:
GPMVGERHAG DLMVPLGPRL QAYPEELIRQ RPGHDGHPEY LIRWSVLKCG EVGKVGVEEG KAEHILMWLS APEVYANCPG LLGERALSK GLQHEPAGVS GSFPRDPGGL DEVAMGEMEA DVQALVRRAA RQLAESGTPS LTAAVLHTIH VLSAYASIGP L TGVFRETG ALDLLMHMLC NPEPQIRRSA GKMLQALAAH DAGSRAHVLL SLSQQDGIEQ HMDFDSRYTL LELFAETTSS EE HCMAFEG IHLPQIPGKL LFSLVKRYLC VTSLLDQLNS SPELGAGDQS SPCATREKSR GQRELEFSMA VGNLISELVR SMG WARNLS EQGMSPPRPT RSIFQPYISG PSLLLPTIVT TPRRQGWVFR QRSEFSSRSG YGEYVQQTLQ PGMRVRMLDD YEEI SAGDE GEFRQSNNGI PPVQVFWQST GRTYWVHWHM LEILGPEEAT EDKASAAVEK GAGATVLGTA FPSWDWNPMD GLYPL PYLQ PEPQKNERVG YLTQAEWWEL LFFIKKLDLC EQQPIFQNLW KNLDETLGEK ALGEISVSVE MAESLLQVLS SRFEGS TLN DLLNSQIYTK YGLLSNEPSS SSTSRNHSCT PDPEEESKSE ASFSEEETES LKAKAEAPKT EAEPTKTRTE TPMAQSD SQ LFNQLLVTEG MTLPTEMKEA ASEMARALRG PGPRSSLDQH VAAVVATVQI SSLDTNLQLS GLSALSQAVE EVTERDHP L VRPDRSLREK LVKMLVELLT NQVGEKMVVV QALRLLYLLM TKHEWRPLFA REGGIYAVLV CMQEYKTSVL VQQAGLAAL KMLAVASSSE IPTFVTGRDS IHSLFDAQMT REIFASIDSA TRPGSESLLL TVPAAVILML NTEGCSSAAR NGLLLLNLLL CNHHTLGDQ IITQELRDTL FRHSGIAPRT EPMPTTRTIL MMLLNRYSEP PGSPERAALE TPIIQGQDGS PELLIRSLVG G PSAELLLD LERVLCREGS PGGAVRPLLK RLQQETQPFL LLLRTLDAPG PNKTLLLSVL RVITRLLDFP EAMVLPWHEV LE PCLNCLS GPSSDSEIVQ ELTCFLHRLA SMHKDYAVVL CCLGAKEILS KVLDKHSAQL LLGCELRDLV TECEKYAQLY SNL TSSILA GCIQMVLGQI EDHRRTHQPI NIPFFDVFLR HLCQGSSVEV KEDKCWEKVE VSSNPHRASK LTDHNPKTYW ESNG STGSH YITLHMHRGV LVRQLTLLVA SEDSSYMPAR VVVFGGDSTS CIGTELNTVN VMPSASRVIL LENLNRFWPI IQIRI KRCQ QGGIDTRVRG VEVLGPKPTF WPLFREQLCR RTCLFYTIRA QAWSRDIAED HRRLLQLCPR LNRVLRHEQN FADRFL PDD EAAQALGKTC WEALVSPLVQ NITSPDAEGV SALGWLLDQY LEQRETSRNP LSRAASFASR VRRLCHLLVH VEPPPGP SP EPSTRPFSKN SKGRDRSPAP SPVLPSSSLR NITQCWLSVV QEQVSRFLAA AWRAPDFVPR YCKLYEHLQR AGSELFGP R AAFMLALRSG FSGALLQQSF LTAAHMSEQF ARYIDQQIQG GLIGGAPGVE MLGQLQRHLE PIMVLSGLEL ATTFEHFYQ HYMADRLLSF GSSWLEGAVL EQIGLCFPNR LPQLMLQSLS TSEELQRQFH LFQLQRLDKL FLEQEDEEEK RLEEEEEEEE EEEAEKELF IEDPSPAISI LVLSPRCWPV SPLCYLYHPR KCLPTEFCDA LDRFSSFYSQ SQNHPVLDMG PHRRLQWTWL G RAELQFGK QILHVSTVQM WLLLKFNQTE EVSVETLLKD SDLSPELLLQ ALVPLTSGNG PLTLHEGQDF PHGGVLRLHE PG PQRSGEA LWLIPPQAYL NVEKDEGRTL EQKRNLLSCL LVRILKAHGE KGLHIDQLVC LVLEAWQKGP NPPGTLGHTV AGG VACTST DVLSCILHLL GQGYVKRRDD RPQILMYAAP EPMGPCRGQA DVPFCGSQSE TSKPSPEAVA TLASLQLPAG RTMS PQEVE GLMKQTVRQV QETLNLEPDV AQHLLAHSHW GAEQLLQSYS EDPEPLLLAA GLCVHQAQAV PVRPDHCPVC VSPLG CDDD LPSLCCMHYC CKSCWNEYLT TRIEQNLVLN CTCPIADCPA QPTGAFIRAI VSSPEVISKY EKALLRGYVE SCSNLT WCT NPQGCDRILC RQGLGCGTTC SKCGWASCFN CSFPEAHYPA SCGHMSQWVD DGGYYDGMSV EAQSKHLAKL ISKRCPS CQ APIEKNEGCL HMTCAKCNHG FCWRCLKSWK PNHKDYYNCS AMVSKAARQE KRFQDYNERC TFHHQAREFA VNLRNRVS A IHEVPPPRSF TFLNDACQGL EQARKVLAYA CVYSFYSQDA EYMDVVEQQT ENLELHTNAL QILLEETLLR CRDLASSLR LLRADCLSTG MELLRRIQER LLAILQHSAQ DFRVGLQSPS VEAWEAKGPN MPGSQPQASS GPEAEEEEED DEDDVPEWQQ DEFDEELDN DSFSYDESEN LDQETFFFGD EEEDEDEAYD

UniProtKB: Cullin-9

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Macromolecule #2: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.289977 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

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Macromolecule #3: NEDD8

MacromoleculeName: NEDD8 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.086562 KDa
SequenceString:
MLIKVKTLTG KEIEIDIEPT DKVERIKERV EEKEGIPPQQ QRLIYSGKQM NDEKTAADYK ILGGSVLHLV LALRGGGGLR Q

UniProtKB: NEDD8

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Macromolecule #4: Unknown

MacromoleculeName: Unknown / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.868854 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 10 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71928
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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