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- EMDB-10430: Mouse RNF213 mutant R4753K modeling the Moyamoya-disease-related ... -

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Basic information

Entry
Database: EMDB / ID: EMD-10430
TitleMouse RNF213 mutant R4753K modeling the Moyamoya-disease-related Human variant R4810K
Map dataComposite map assembled from 4 focused refinements
Sample
  • Complex: full length mouse RNF213 with the R4753K mutation
    • Protein or peptide: RNF213,E3 ubiquitin-protein ligase RNF213,E3 ubiquitin-protein ligase RNF213
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
Function / homology
Function and homology information


lipid ubiquitination / lipid droplet formation / negative regulation of non-canonical Wnt signaling pathway / xenophagy / Antigen processing: Ubiquitination & Proteasome degradation / Transferases; Acyltransferases; Aminoacyltransferases / sprouting angiogenesis / immune system process / protein K63-linked ubiquitination / regulation of lipid metabolic process ...lipid ubiquitination / lipid droplet formation / negative regulation of non-canonical Wnt signaling pathway / xenophagy / Antigen processing: Ubiquitination & Proteasome degradation / Transferases; Acyltransferases; Aminoacyltransferases / sprouting angiogenesis / immune system process / protein K63-linked ubiquitination / regulation of lipid metabolic process / protein autoubiquitination / lipid droplet / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / angiogenesis / protein ubiquitination / defense response to bacterium / nucleolus / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase RNF213 / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. ...E3 ubiquitin-protein ligase RNF213 / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF213
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsAhel J / Meinhart A / Haselbach D / Clausen T
Funding support Austria, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)AdG 694978 Austria
CitationJournal: Elife / Year: 2020
Title: Moyamoya disease factor RNF213 is a giant E3 ligase with a dynein-like core and a distinct ubiquitin-transfer mechanism.
Authors: Juraj Ahel / Anita Lehner / Antonia Vogel / Alexander Schleiffer / Anton Meinhart / David Haselbach / Tim Clausen /
Abstract: RNF213 is the major susceptibility factor for Moyamoya disease, a progressive cerebrovascular disorder that often leads to brain stroke in adults and children. Characterization of disease-associated ...RNF213 is the major susceptibility factor for Moyamoya disease, a progressive cerebrovascular disorder that often leads to brain stroke in adults and children. Characterization of disease-associated mutations has been complicated by the enormous size of RNF213. Here, we present the cryo-EM structure of mouse RNF213. The structure reveals the intricate fold of the 584 kDa protein, comprising an N-terminal stalk, a dynein-like core with six ATPase units, and a multidomain E3 module. Collaboration with UbcH7, a cysteine-reactive E2, points to an unexplored ubiquitin-transfer mechanism that proceeds in a RING-independent manner. Moreover, we show that pathologic MMD mutations cluster in the composite E3 domain, likely interfering with substrate ubiquitination. In conclusion, the structure of RNF213 uncovers a distinct type of an E3 enzyme, highlighting the growing mechanistic diversity in ubiquitination cascades. Our results also provide the molecular framework for investigating the emerging role of RNF213 in lipid metabolism, hypoxia, and angiogenesis.
History
DepositionOct 31, 2019-
Header (metadata) releaseJul 1, 2020-
Map releaseJul 1, 2020-
UpdateJan 13, 2021-
Current statusJan 13, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6tay
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10430.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map assembled from 4 focused refinements
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.019 / Movie #1: 0.019
Minimum - Maximum-0.004337043 - 0.14622968
Average (Standard dev.)0.0005997717 (±0.002782871)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 366.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z366.080366.080366.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.0040.1460.001

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Supplemental data

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Additional map: None

Fileemd_10430_additional_1.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: focused refinement on the second half of the AAA-region

Fileemd_10430_additional_2.map
Annotationfocused refinement on the second half of the AAA-region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: None

Fileemd_10430_additional_3.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: focused refinement on the N-terminus

Fileemd_10430_additional_4.map
Annotationfocused refinement on the N-terminus
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : full length mouse RNF213 with the R4753K mutation

EntireName: full length mouse RNF213 with the R4753K mutation
Components
  • Complex: full length mouse RNF213 with the R4753K mutation
    • Protein or peptide: RNF213,E3 ubiquitin-protein ligase RNF213,E3 ubiquitin-protein ligase RNF213
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: full length mouse RNF213 with the R4753K mutation

SupramoleculeName: full length mouse RNF213 with the R4753K mutation / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant strain: BTI-Tn-5B1-4 / Recombinant plasmid: EMBacY
Molecular weightExperimental: 580 KDa

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Macromolecule #1: RNF213,E3 ubiquitin-protein ligase RNF213,E3 ubiquitin-protein li...

MacromoleculeName: RNF213,E3 ubiquitin-protein ligase RNF213,E3 ubiquitin-protein ligase RNF213
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 527.650312 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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)KLTLGLSIL FMVEAAEFTV PKKDLDSLCY LLIPSAGSPE ALHSDLSPVL RIRQRWRIYL TNLCLR CID ERCDRWLGIL PLLHTCMQKS PPKKNSKSQP EDTWAGLEGI SFSEFRDKAP TRSQPLQFMQ SKMALLRVDE YLFRSWL SV VPLESLSSYL ENSIDYLSDV PVRVLDCLQG ISYRLPGLRK ISNQNMKKDV ENVFKMLMHL VDIYQHRIFG ENLLQIYL T ECLTLHETVC NITANHQFFE IPALSAELIC KLLELSPPGH TDEGLPEKSY EDLVTSTLQE ALATTRNWLR SLFKSRMLS ISSAYVRLTY SEEMAVWRRL VEIGFPEKHG WKGSLLGDME GRLKQEPPRL QISFFCSSQC RDGGLHDSVS RSFEKCVIEA VSSACQSQT SVLEGLSCQD LQKFGTLLSA VITKSWPVHN GEPVFDVDEI FKYLLKWPDV RQLFELCGTN EKIIDNITEE G RQLMATAE SVFQKVAGEL ENGTIVVGQL ELILEHQSQF LDIWNLNRRR LPSQEKACDV RSLLKRRRDD LLFLKQEKRY VE SLLRQLG RVKHLVQVDF GNIEIIHSQD LSNKKLNEAV IKLPNSSSYK RETHYCLSPD IREMASKLDS LKDSHIFQDF WQE TAESLN TLDKDPRELK VSLPEVLEYL YNPCYDNFYT LYENLKSGKI TFAEVDAIFK DFVDKYDELK NDLKFMCTMN PQDQ KGWIS ERVGQIKEYH TLHQAVSSAK VILQVRRALG VTGDFSVLNP LLNFADSFED FGNEKLDQIS PQFIKAKQLL QDISE PRQR CLEELARQTE LVAWLHKALE DINELKVFVD LASISAGEND IDVDRVACFH DAVQGYASLL YKMDERTNFS DFMNHL QEL WRALDNDQHL PDKLKDSARN LEWLKTVKES HGSVELSSLS LATAINSRGV YVIEAPKDGQ KISPDTVLRL LLPDGHG YP EALRTYSTEE LKELLNKLML MSGKKDHNSN TEVEKFSEVF SNMQRLVHVF IKLHCAGNML FRTWTAKVYC CPDGGIFM N FGLELLSQLT EKGDVIQLLG ALCRQMEDFL DNWKTVVAQK RAEHFYLNFY TAEQLVYLSS ELRKPRPSEA ALMMLSFIK GKCTVQDLVQ ATSACESKAD RYCLREVMKK LPQQLLSEPS LMGKLQVIMM QSLVYMSAFL PHCLDLDALG RCLAHLATMG GTPVERPLP KGLQAGQPNL ILCGHSEVLP AALAIYMQAP RQPLPTFDEV LLCTPATTIE EVELLLRRCL TSGSQGHKVY S LLFADQLS YEVGCQAEEF FQSLCTRAHR EDYQLVILCD AAREHCYIPS TFSQYKVPLV PQAPLPNIQA YLQSHYQVPK RL LSAATVF RDGLCVGIVT SERAGVGKSL YVNTLHTKLK AKLRDETVPL KIIRLTEPHL DENQVLSALL PFLKEKYQKM PVI FHIDIS TSVQTGIPIF LFKLLILQYL MDINGKIWRR SPGHLYLVEI PQGLSVQPKR SSKLNARAPL FKFLDLFPKV TCRP PKEVI DMELTPERSH TDPAMDPVEF CSEAFQRPYQ YLKRFHQQQN LDTFQYEKGS VEGSPEECLQ HFLIYCGLIN PSWSE LRNF AWFLNCQLKD CEASIFCKSA FTGDTLRGFK NFVVTFMILM ARDFATPTLH TSDQSPGRQS VTIGEVVEED LAPFSL RKR WESEPHPYVF FNGDHMTMTF IGFHLETNNN GYVDAINPSN GKVIKKDVMT KELFDGLRLQ RVPFNIDFDN LPRYEKL ER LCLALGIEWP IDPDETYELT TDNMLKILAI EMRFRCGIPV IIMGETGCGK TRLIKFLSDL KRGSVEAETM KLVKVHGG T TPSMIYSKVK EAERTAFSNK AQHKLDTILF FDEANTTEAV SCIKEILCDR TVDGEHLHED SGLHIIAACN PYRKHSQEM ILRLESAGLG YRVSAEETAD RLGSIPLRQL VYRVHALPPS LIPLVWDFGQ LNDSAEKLYI QQIVQRLVDS VSVNPSETCV IADVLSASQ MFMRKRENEC GFVSLRDVER CVKVFRWFHD HSDMLLKELD KFLHESSDST HTFERDPVLW SLVMAIGVCY H ASLEEKAS YRTAIARCFP KPYNSSRAIL DEVTHVQDLF LRGAPIRTNI ARNLALKENV FMMVICIELK IPLFLVGKPG SS KSLAKII VADAMQGQAA FSELFRCLKQ VHLVSFQCSP HSTPQGIIST FKQCARFQQG KDLGQYVSVV VLDEVGLAED SPK MPLKTL HPLLEDGCIE DDPAPYKKVG FVGISNWALD PAKMNRGIFV SRGSPNEKEL IESAEGICSS DRLVQDKIRG YFAP FAKAY ETVCQKQDKE FFGLRDYYSL IKMVFAKAKA SKRGLSPQDI THAVLRNFSG KDNIQALSIF TASLPEARYK EEVST VELI KQNIYPGPQA SSRGLDGAES RYLLVLTRNY VALQILQQTF FEGQQPEIIF GSSFPQDQEY TQICRNINRV KICMET GKM VVLLNLQNLY ESLYDALNQY YVYLGGQKYV DLGLGTHRVK CRVHTAFRLI VIEEKDVVYK QFPVPLINRL EKHYLDM NT VLQPWQKSIV QELQQWAHEF ADVKADQFIA RHKYSPADVF IGYHSDACAS VVLQAVERQG CRDLTEELYR KVSEEARS I LLDCATPDAV VRLSGSSLGS FTAKQLSQEY YYAQQHNSFV DFLQAHLRMT HHECRAVFTE ITTFSRLLTG NDCDVLASE LRGLASKPVV LSLQQYDTEY SFLKDVRSWL TNPGKRKVLV IQADFDDGTR SAQLVASAKY TAINEINKTQ GTKDFVFVYF VTKLSRMGS GTSYVGFHGG LWRSVHIDDL RRSTIMASDV TKLQNVTISQ LFKPEDKPEQ EEMEIETSQS KELAEEQMEV E DSEEMKKA SDPRSCDCSQ FLDTTRLVQS CVQGAVGMLR DQNESCARNM RRVTILLDLL NEDNTRNASF LRESKMRLHV LL NKQEENQ VRSLKEWVTR EAANQDALQE AGTFRHTLWK RVQDVVTPIL ASMIAHIDRD GNLELLAQPD SPAWVQDLWM FIY SDIKFL NISLVLNNTR SNSEMSFILV QSHMNLLKDA YNAVPFSWRI RDYLEELWVQ AQYITDTEGL SKKFVEIFQK TPLG VFLAQ FPVAQQQKLL QSYLKDFLLL TMKVSSREEL MFLQMALWSC LRELQEASGT PDETYKFPLS LPWVHLAFQH FRTRL QNFS RILTIHPQVL SSLSQAAEKH SLAGCEMTLD AFAAMACAEM LKGDLLKPSP KAWLQLVKNL STPLELVCSE GYLCDS GSM TRSVIQEVRA LWNRIFSIAL FVEHVLLGTE SHIPELSPLV TTYVSLLDKC LEEDSNLKTC RPFVAVMTTL CDCKDKA SK KFSRFGIQPC FICHGDAQDP VCLPCDHVYC LRCIQTWLIP GQMMCPYCLT DLPDKFSPTV SQDHRKAIEK HAQFRHMC N SFFVDLVSTM CFKDNTPPEK SVIDTLLSLL FVQKELLRDA SQKHREHTKS LSPFDDVVDQ TPVIRSVLLK LLLKYSFHE VKDYIQNYLT QLEKKAFLTE DKTELYLLFI SCLEDSVHQK TSAGCRNLEQ VLREEGHFLR TYSPGLQGQE PVRIASVEYL QEVARVRLC LDLAADFLSE LQEGSELAED KRRFLKHVEE FCTRVNNDWH RVYLVRKLSS QRGMEFVQSF SKQGHPCQWV F PRKVIAQQ KDHVSLMDRY LVHGNEYKAV RDATAKAVLE CKTLDIGNAL MACRSPKPQQ TAYLLLALYT EVAALYRSPN GS LHPEAKQ LEAVNKFIKE SKILSDPNIR CFARSLVDNT LPLLKIRSAN SILKGTVTEM AVHVATILLC GHNQILKPLR NLA FYPVNM ANAFLPTMPE DLLVHARTWR GLENVTWYTC PRGHPCSVGE CGRPMQESTC LDCGLPVGGL NHTPHEGFSA IRNN EDRTQ TGHVLGSPQS SGVAEVSDRG QSPVVFILTR LLTHLAMLVG ATHNPQALTV IIKPWVQDPQ GFLQQHIQRD LEQLT KMLG RSADETIHVV HLILSSLLRV QSHGVLNFNA ELSTKGCRNN WEKHFETLLL RELKHLDKNL PAINALISQD ERISSN PVT KIIYGDPATF LPHLPQKSII HCSKIWSCRR KITVEYLQHI VEQKNGKETV PVLWHFLQKE AELRLVKFLP EILALQR DL VKQFQNVSRV EYSSIKGFIH SHSSDGLRKL LHDRITIFLS TWNALRRSLE TNGEIKLPKD YCCSDLDLDA EFEVILPR R QGLGLCGTAL VSYLISLHNN MVYTVQKFSN EDNSYSVDIS EVADLHVISY EVERDLNPLI LSNCQYQVQQ GGETSQEFD LEKIQRQISS RFLQGKPRLT LKGIPTLVYR RDWNYEHLFM DIKNKMAQSS LPNLAISTIS GQLQSYSDAC EALSIIEITL GFLSTAGGD PGMDLNVYIE EVLRMCDQTA QVLKAFSRCQ LRHIIALWQF LSAHKSEQRL RLNKELFREI DVQYKEELST Q HQRLLGTF LNEAGLDAFL LELHEMIVLK LKGPRAANSF NPNWSLKDTL VSYMETKDSD ILSEVESQFP EEILMSSCIS VW KIAATRK WDRQSRGGGH HHHHHHHHH

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / 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

Concentration0.4 mg/mL
BufferpH: 7.2
Component:
ConcentrationNameFormula
20.0 mMHEPES
200.0 mMpotassium chlorideKCl
0.25 mMTECEP
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.01 kPa
Details: SCD 005 Sputter Coater (BAL-TEC) grid sitting on a metallic mesh during glow discharge
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP
Details: blot for 1.5 seconds using using Whatman Filter Paper Grade 1.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Name: GIF Bioquantum
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 6561 / Average exposure time: 10.0 sec. / Average electron dose: 47.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 10 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 374000

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6tay:
Mouse RNF213 mutant R4753K modeling the Moyamoya-disease-related Human variant R4810K

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