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- EMDB-12931: Mouse RNF213:UBE2L3 transthiolation intermediate, chemically stab... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-12931
TitleMouse RNF213:UBE2L3 transthiolation intermediate, chemically stabilized
Map datafull reconstructed density
Sample
  • Complex: RNF213-ABP(UBE2L3-Ub)
    • Complex: RNF213-ABP(UBE2L3-Ub)
      • Protein or peptide: E3 ubiquitin-protein ligase RNF213
    • Complex: RNF213-ABP(UBE2L3-Ub)
      • Protein or peptide: Ubiquitin-conjugating enzyme E2 L3
  • 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 / cell cycle phase transition / ubiquitin-protein transferase activator activity / xenophagy / Antigen processing: Ubiquitination & Proteasome degradation / protein K11-linked ubiquitination / Transferases; Acyltransferases; Aminoacyltransferases / cellular response to glucocorticoid stimulus ...lipid ubiquitination / lipid droplet formation / negative regulation of non-canonical Wnt signaling pathway / cell cycle phase transition / ubiquitin-protein transferase activator activity / xenophagy / Antigen processing: Ubiquitination & Proteasome degradation / protein K11-linked ubiquitination / Transferases; Acyltransferases; Aminoacyltransferases / cellular response to glucocorticoid stimulus / positive regulation of ubiquitin-protein transferase activity / sprouting angiogenesis / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / cellular response to steroid hormone stimulus / immune system process / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / regulation of lipid metabolic process / protein autoubiquitination / ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / lipid droplet / positive regulation of protein ubiquitination / Regulation of TNFR1 signaling / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein modification process / RING-type E3 ubiquitin transferase / Regulation of necroptotic cell death / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / ubiquitin-dependent protein catabolic process / angiogenesis / cell population proliferation / transcription coactivator activity / protein ubiquitination / defense response to bacterium / ubiquitin protein ligase binding / nucleolus / regulation of DNA-templated transcription / enzyme binding / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / 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) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 ...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) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / 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 / Ubiquitin-conjugating enzyme E2 L3
Similarity search - Component
Biological speciesMus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsAhel J / Clausen T
Funding support Austria, United Kingdom, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)694978 Austria
Austrian Research Promotion Agency852936 Austria
Medical Research Council (MRC, United Kingdom)MC_UU_12016/8 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/ P003982/1 United Kingdom
CitationJournal: To Be Published
Title: E3 ubiquitin ligase RNF213 employs a non-canonical zinc finger active site and is allosterically regulated by ATP
Authors: Ahel J / Fletcher AJ / Grabarczyk D / Roitinger E / Deszcz L / Lehner A / Virdee S / Clausen T
History
DepositionMay 11, 2021-
Header (metadata) releaseJun 1, 2022-
Map releaseJun 1, 2022-
UpdateJun 1, 2022-
Current statusJun 1, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_12931.png

Downloads & links

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Map

FileDownload / File: emd_12931.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull reconstructed density
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 352 pix.
= 377.344 Å		1.07 Å/pix.
x 352 pix.
= 377.344 Å		1.07 Å/pix.
x 352 pix.
= 377.344 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.011237639 - 0.031208439
Average (Standard dev.)4.4628632e-05 (±0.0011445131)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 377.344 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_12931_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: unfiltered half map 2 of the full reconstructed density

Fileemd_12931_half_map_1.map
Annotationunfiltered half map 2 of the full reconstructed density
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: unfiltered half map 1 of the full reconstructed density

Fileemd_12931_half_map_2.map
Annotationunfiltered half map 1 of the full reconstructed density
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RNF213-ABP(UBE2L3-Ub)

EntireName: RNF213-ABP(UBE2L3-Ub)
Components
  • Complex: RNF213-ABP(UBE2L3-Ub)
    • Complex: RNF213-ABP(UBE2L3-Ub)
      • Protein or peptide: E3 ubiquitin-protein ligase RNF213
    • Complex: RNF213-ABP(UBE2L3-Ub)
      • Protein or peptide: Ubiquitin-conjugating enzyme E2 L3
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: RNF213-ABP(UBE2L3-Ub)

SupramoleculeName: RNF213-ABP(UBE2L3-Ub) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: chemically stabilized complex between mouse RNF213 and a modified human UBE2L3 ABP (activity based probe), coupled to modified human ubiquitin
Molecular weightTheoretical: 580 KDa

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Supramolecule #2: RNF213-ABP(UBE2L3-Ub)

SupramoleculeName: RNF213-ABP(UBE2L3-Ub) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: E3 ubiquitin-protein ligase RNF213
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Supramolecule #3: RNF213-ABP(UBE2L3-Ub)

SupramoleculeName: RNF213-ABP(UBE2L3-Ub) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: Ubiquitin-conjugating enzyme E2 L3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: E3 ubiquitin-protein ligase RNF213

MacromoleculeName: 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: 586.5455 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MECPQCGHVS SEKAPKFCSE CGQKLPSAAT VQGDLKNDNT LVVSSTPEGK TEQGAVLREE EVLLSSTDPG KELEKPEESD SNASWTTQM SKKEKRRRKR QGTISSSEAP SSGLWSLDMP PSPGSHNSAL PQNQAQQGGA ASQPGHPLDT ENMPMEDGFV H TEGSGSPL ...String:
MECPQCGHVS SEKAPKFCSE CGQKLPSAAT VQGDLKNDNT LVVSSTPEGK TEQGAVLREE EVLLSSTDPG KELEKPEESD SNASWTTQM SKKEKRRRKR QGTISSSEAP SSGLWSLDMP PSPGSHNSAL PQNQAQQGGA ASQPGHPLDT ENMPMEDGFV H TEGSGSPL QGQAAERTDA QSNLAPSDLA EVKDLNTSKP SVDKGLPLDG GPALSAFKGH PKMTDASQKA PLPESKGETS GQ EKKVPPI DAAASPVKTA GKETGEDVRK PKPSPVSPVA SKHGDQEAEL KGKLATPVRK SNEGGNTQPE DQRKPGEGRN FAA AVKTQQ AAAPQQAAAP EPTSAFNPRD TVTVYFHAIV SRHFGFNPEE HKVYVRGGEG LGQKGWTDAC EMYCTQDLHD LGSL VEGKM DIPRQSLDKP IPYKYVIHRG GSSKDTVEYE FIYEQAQKKG EHVNRCLRVV STSLGNGDWH QYDDIICMRS TGFFQ QAKN RILDSTRKEL LKGKKQAAVV MLDRIFSVLQ PWSDINLQSF MTQFLQFYSV VREPMIHDGR ARKWTSLQYE EKEVWT NLW EHVKKQMAPF LEGKSGESLP ADCPVRSKLT LGLSILFMVE AAEFTVPKKD LDSLCYLLIP SAGSPEALHS DLSPVLR IR QRWRIYLTNL CLRCIDERCD RWLGILPLLH TCMQKSPPKK NSKSQPEDTW AGLEGISFSE FRDKAPTRSQ PLQFMQSK M ALLRVDEYLF RSWLSVVPLE SLSSYLENSI DYLSDVPVRV LDCLQGISYR LPGLRKISNQ NMKKDVENVF KMLMHLVDI YQHRIFGENL LQIYLTECLT LHETVCNITA NHQFFEIPAL SAELICKLLE LSPPGHTDEG LPEKSYEDLV TSTLQEALAT TRNWLRSLF KSRMLSISSA YVRLTYSEEM AVWRRLVEIG FPEKHGWKGS LLGDMEGRLK QEPPRLQISF FCSSQCRDGG L HDSVSRSF EKCVIEAVSS ACQSQTSVLE GLSCQDLQKF GTLLSAVITK SWPVHNGEPV FDVDEIFKYL LKWPDVRQLF EL CGTNEKI IDNITEEGRQ LMATAESVFQ KVAGELENGT IVVGQLELIL EHQSQFLDIW NLNRRRLPSQ EKACDVRSLL KRR RDDLLF LKQEKRYVES LLRQLGRVKH LVQVDFGNIE IIHSQDLSNK KLNEAVIKLP NSSSYKRETH YCLSPDIREM ASKL DSLKD SHIFQDFWQE TAESLNTLDK DPRELKVSLP EVLEYLYNPC YDNFYTLYEN LKSGKITFAE VDAIFKDFVD KYDEL KNDL KFMCTMNPQD QKGWISERVG QIKEYHTLHQ AVSSAKVILQ VRRALGVTGD FSVLNPLLNF ADSFEDFGNE KLDQIS PQF IKAKQLLQDI SEPRQRCLEE LARQTELVAW LHKALEDINE LKVFVDLASI SAGENDIDVD RVACFHDAVQ GYASLLY KM DERTNFSDFM NHLQELWRAL DNDQHLPDKL KDSARNLEWL KTVKESHGSV ELSSLSLATA INSRGVYVIE APKDGQKI S PDTVLRLLLP DGHGYPEALR TYSTEELKEL LNKLMLMSGK KDHNSNTEVE KFSEVFSNMQ RLVHVFIKLH CAGNMLFRT WTAKVYCCPD GGIFMNFGLE LLSQLTEKGD VIQLLGALCR QMEDFLDNWK TVVAQKRAEH FYLNFYTAEQ LVYLSSELRK PRPSEAALM MLSFIKGKCT VQDLVQATSA CESKADRYCL REVMKKLPQQ LLSEPSLMGK LQVIMMQSLV YMSAFLPHCL D LDALGRCL AHLATMGGTP VERPLPKGLQ AGQPNLILCG HSEVLPAALA IYMQAPRQPL PTFDEVLLCT PATTIEEVEL LL RRCLTSG SQGHKVYSLL FADQLSYEVG CQAEEFFQSL CTRAHREDYQ LVILCDAARE HCYIPSTFSQ YKVPLVPQAP LPN IQAYLQ SHYQVPKRLL SAATVFRDGL CVGIVTSERA GVGKSLYVNT LHTKLKAKLR DETVPLKIIR LTEPHLDENQ VLSA LLPFL KEKYQKMPVI FHIDISTSVQ TGIPIFLFKL LILQYLMDIN GKIWRRSPGH LYLVEIPQGL SVQPKRSSKL NARAP LFKF LDLFPKVTCR PPKEVIDMEL TPERSHTDPA MDPVEFCSEA FQRPYQYLKR FHQQQNLDTF QYEKGSVEGS PEECLQ HFL IYCGLINPSW SELRNFAWFL NCQLKDCEAS IFCKSAFTGD TLRGFKNFVV TFMILMARDF ATPTLHTSDQ SPGRQSV TI GEVVEEDLAP FSLRKRWESE PHPYVFFNGD HMTMTFIGFH LETNNNGYVD AINPSNGKVI KKDVMTKELF DGLRLQRV P FNIDFDNLPR YEKLERLCLA LGIEWPIDPD ETYELTTDNM LKILAIEMRF RCGIPVIIMG ETGCGKTRLI KFLSDLKRG SVEAETMKLV KVHGGTTPSM IYSKVKEAER TAFSNKAQHK LDTILFFDEA NTTEAVSCIK EILCDRTVDG EHLHEDSGLH IIAACNPYR KHSQEMILRL ESAGLGYRVS AEETADRLGS IPLRQLVYRV HALPPSLIPL VWDFGQLNDS AEKLYIQQIV Q RLVDSVSV NPSETCVIAD VLSASQMFMR KRENECGFVS LRDVERCVKV FRWFHDHSDM LLKELDKFLH ESSDSTHTFE RD PVLWSLV MAIGVCYHAS LEEKASYRTA IARCFPKPYN SSRAILDEVT HVQDLFLRGA PIRTNIARNL ALKENVFMMV ICI ELKIPL FLVGKPGSSK SLAKIIVADA MQGQAAFSEL FRCLKQVHLV SFQCSPHSTP QGIISTFKQC ARFQQGKDLG QYVS VVVLD EVGLAEDSPK MPLKTLHPLL EDGCIEDDPA PYKKVGFVGI SNWALDPAKM NRGIFVSRGS PNEKELIESA EGICS SDRL VQDKIRGYFA PFAKAYETVC QKQDKEFFGL RDYYSLIKMV FAKAKASKRG LSPQDITHAV LRNFSGKDNI QALSIF TAS LPEARYKEEV STVELIKQNI YPGPQASSRG LDGAESRYLL VLTRNYVALQ ILQQTFFEGQ QPEIIFGSSF PQDQEYT QI CRNINRVKIC METGKMVVLL NLQNLYESLY DALNQYYVYL GGQKYVDLGL GTHRVKCRVH TAFRLIVIEE KDVVYKQF P VPLINRLEKH YLDMNTVLQP WQKSIVQELQ QWAHEFADVK ADQFIARHKY SPADVFIGYH SDACASVVLQ AVERQGCRD LTEELYRKVS EEARSILLDC ATPDAVVRLS GSSLGSFTAK QLSQEYYYAQ QHNSFVDFLQ AHLRMTHHEC RAVFTEITTF SRLLTGNDC DVLASELRGL ASKPVVLSLQ QYDTEYSFLK DVRSWLTNPG KRKVLVIQAD FDDGTRSAQL VASAKYTAIN E INKTQGTK DFVFVYFVTK LSRMGSGTSY VGFHGGLWRS VHIDDLRRST IMASDVTKLQ NVTISQLFKP EDKPEQEEME IE TSQSKEL AEEQMEVEDS EEMKKASDPR SCDCSQFLDT TRLVQSCVQG AVGMLRDQNE SCARNMRRVT ILLDLLNEDN TRN ASFLRE SKMRLHVLLN KQEENQVRSL KEWVTREAAN QDALQEAGTF RHTLWKRVQD VVTPILASMI AHIDRDGNLE LLAQ PDSPA WVQDLWMFIY SDIKFLNISL VLNNTRSNSE MSFILVQSHM NLLKDAYNAV PFSWRIRDYL EELWVQAQYI TDTEG LSKK FVEIFQKTPL GVFLAQFPVA QQQKLLQSYL KDFLLLTMKV SSREELMFLQ MALWSCLREL QEASGTPDET YKFPLS LPW VHLAFQHFRT RLQNFSRILT IHPQVLSSLS QAAEKHSLAG CEMTLDAFAA MACAEMLKGD LLKPSPKAWL QLVKNLS TP LELVCSEGYL CDSGSMTRSV IQEVRALWNR IFSIALFVEH VLLGTESHIP ELSPLVTTYV SLLDKCLEED SNLKTCRP F VAVMTTLCDC KDKASKKFSR FGIQPCFICH GDAQDPVCLP CDHVYCLRCI QTWLIPGQMM CPYCLTDLPD KFSPTVSQD HRKAIEKHAQ FRHMCNSFFV DLVSTMCFKD NTPPEKSVID TLLSLLFVQK ELLRDASQKH REHTKSLSPF DDVVDQTPVI RSVLLKLLL KYSFHEVKDY IQNYLTQLEK KAFLTEDKTE LYLLFISCLE DSVHQKTSAG CRNLEQVLRE EGHFLRTYSP G LQGQEPVR IASVEYLQEV ARVRLCLDLA ADFLSELQEG SELAEDKRRF LKHVEEFCTR VNNDWHRVYL VRKLSSQRGM EF VQSFSKQ GHPCQWVFPR KVIAQQKDHV SLMDRYLVHG NEYKAVRDAT AKAVLECKTL DIGNALMACR SPKPQQTAYL LLA LYTEVA ALYRSPNGSL HPEAKQLEAV NKFIKESKIL SDPNIRCFAR SLVDNTLPLL KIRSANSILK GTVTEMAVHV ATIL LCGHN QILKPLRNLA FYPVNMANAF LPTMPEDLLV HARTWRGLEN VTWYTCPRGH PCSVGECGRP MQESTCLDCG LPVGG LNHT PHEGFSAIRN NEDRTQTGHV LGSPQSSGVA EVSDRGQSPV VFILTRLLTH LAMLVGATHN PQALTVIIKP WVQDPQ GFL QQHIQRDLEQ LTKMLGRSAD ETIHVVHLIL SSLLRVQSHG VLNFNAELST KGCRNNWEKH FETLLLRELK HLDKNLP AI NALISQDERI SSNPVTKIIY GDPATFLPHL PQKSIIHCSK IWSCRRKITV EYLQHIVEQK NGKETVPVLW HFLQKEAE L RLVKFLPEIL ALQRDLVKQF QNVSRVEYSS IRGFIHSHSS DGLRKLLHDR ITIFLSTWNA LRRSLETNGE IKLPKDYCC SDLDLDAEFE VILPRRQGLG LCGTALVSYL ISLHNNMVYT VQKFSNEDNS YSVDISEVAD LHVISYEVER DLNPLILSNC QYQVQQGGE TSQEFDLEKI QRQISSRFLQ GKPRLTLKGI PTLVYRRDWN YEHLFMDIKN KMAQSSLPNL AISTISGQLQ S YSDACEAL SIIEITLGFL STAGGDPGMD LNVYIEEVLR MCDQTAQVLK AFSRCQLRHI IALWQFLSAH KSEQRLRLNK EL FREIDVQ YKEELSTQHQ RLLGTFLNEA GLDAFLLELH EMIVLKLKGP RAANSFNPNW SLKDTLVSYM ETKDSDILSE VES QFPEEI LMSSCISVWK IAATRKWDRQ SRGGGHHHHH HHHHH

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Macromolecule #2: Ubiquitin-conjugating enzyme E2 L3

MacromoleculeName: Ubiquitin-conjugating enzyme E2 L3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.197908 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GWSHPQFEKP GSMAASRRLM KELEEIRKSG MKNFRNIQVD EANLLTWQGL IVPDNPPYDK GAFRIEINFP AEYPFKPPKI TFKTKIYHP NIDEKGQVCL PVISAENWKP ATKTDQVIQS LIALVNDPQP EHPLRADLAE EYSKDRKKFS KNAEEFTKKY G EKRPVD

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / 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 #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / 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

BufferpH: 7.2
Component:
ConcentrationFormula
200.0 mMKCl
25.0 mMHEPES
0.25 mMTCEP
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Instrument: LEICA PLUNGER

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Electron microscopy

MicroscopeTFS 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: -2.5 µm / Nominal defocus min: -0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4591 / Average exposure time: 3.92 sec. / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: EMDB MAP
EMDB ID:

10429

Initial angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 2 / Avg.num./class: 100000
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 98000
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6tax

chain_id: A

4q5e

chain_id: C
Output model

PDB-7oik:
Mouse RNF213:UBE2L3 transthiolation intermediate, chemically stabilized

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