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- EMDB-50914: Structure of human RNF213 bound to the secreted effector IpaH2.5 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-50914
TitleStructure of human RNF213 bound to the secreted effector IpaH2.5 from Shigella flexneri
Map dataComposite cryoEM map of IpaH2.5-RNF213 complex, produced from a combination of locally refined sharpened maps
Sample
  • Complex: E3 ligase RNF213, bound to the secreted effector IpaH2.5 from Shigella flexneri
    • Protein or peptide: E3 ubiquitin-protein ligase IpaH2.5
    • Protein or peptide: E3 ubiquitin-protein ligase RNF213
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsRNF213 / IpaH2.5 / IpaH / E3 ligase / RING / LRR / NEL / secreted effector / Shigella / inhibitor / complex / AAA ATPase / ANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


lipid ubiquitination / negative regulation of non-canonical Wnt signaling pathway / lipid droplet formation / xenophagy / Suppression of apoptosis / Transferases; Acyltransferases; Aminoacyltransferases / sprouting angiogenesis / immune system process / regulation of lipid metabolic process / protein K63-linked ubiquitination ...lipid ubiquitination / negative regulation of non-canonical Wnt signaling pathway / lipid droplet formation / xenophagy / Suppression of apoptosis / Transferases; Acyltransferases; Aminoacyltransferases / sprouting angiogenesis / immune system process / regulation of lipid metabolic process / protein K63-linked ubiquitination / protein autoubiquitination / lipid droplet / RING-type E3 ubiquitin transferase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Signaling by ALK fusions and activated point mutants / Antigen processing: Ubiquitination & Proteasome degradation / toxin activity / ubiquitin-dependent protein catabolic process / angiogenesis / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / cohesin loader activity / ATP-dependent H3-H4 histone complex chaperone activity / DNA clamp loader activity / host cell cytoplasm / protein ubiquitination / defense response to bacterium / nucleolus / ATP hydrolysis activity / extracellular region / ATP binding / metal ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase RNF213 / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / Novel E3 ligase (NEL) domain profile. / Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / : ...E3 ubiquitin-protein ligase RNF213 / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / Novel E3 ligase (NEL) domain profile. / Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / : / Leucine-rich repeats, bacterial type / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Leucine-rich repeat profile. / Ring finger / Leucine-rich repeat / Leucine-rich repeat domain superfamily / 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 IpaH2.5 / E3 ubiquitin-protein ligase RNF213
Similarity search - Component
Biological speciesHomo sapiens (human) / Shigella flexneri 5a str. M90T (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsNaydenova K / Randow F
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)U105170648 United Kingdom
Wellcome Trust222503/Z/21/Z United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Shigella flexneri evades LPS ubiquitylation through IpaH1.4-mediated degradation of RNF213.
Authors: Katerina Naydenova / Keith B Boyle / Claudio Pathe / Prathyush Pothukuchi / Ana Crespillo-Casado / Felix Scharte / Pierre-Mehdi Hammoudi / Elsje G Otten / Neal M Alto / Felix Randow /
Abstract: Pathogens have evolved diverse strategies to counteract host immunity. Ubiquitylation of lipopolysaccharide (LPS) on cytosol-invading bacteria by the E3 ligase RNF213 creates 'eat me' signals for ...Pathogens have evolved diverse strategies to counteract host immunity. Ubiquitylation of lipopolysaccharide (LPS) on cytosol-invading bacteria by the E3 ligase RNF213 creates 'eat me' signals for antibacterial autophagy, but whether and how cytosol-adapted bacteria avoid LPS ubiquitylation remains poorly understood. Here, we show that the enterobacterium Shigella flexneri actively antagonizes LPS ubiquitylation through IpaH1.4, a secreted effector protein with ubiquitin E3 ligase activity. IpaH1.4 binds to RNF213, ubiquitylates it and targets it for proteasomal degradation, thus counteracting host-protective LPS ubiquitylation. To understand how IpaH1.4 recognizes RNF213, we determined the cryogenic electron microscopy structure of the IpaH1.4-RNF213 complex. The specificity of the interaction is achieved through the leucine-rich repeat of IpaH1.4, which binds the RING domain of RNF213 by hijacking the conserved RING interface required for binding to ubiquitin-charged E2 enzymes. IpaH1.4 also targets other E3 ligases involved in inflammation and immunity through binding to the E2-interacting face of their RING domains, including the E3 ligase LUBAC that is required for the synthesis of M1-linked ubiquitin chains on cytosol-invading bacteria downstream of RNF213. We conclude that IpaH1.4 has evolved to antagonize multiple antibacterial and proinflammatory host E3 ligases.
History
DepositionJul 7, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50914.png

Downloads & links

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Map

FileDownload / File: emd_50914.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite cryoEM map of IpaH2.5-RNF213 complex, produced from a combination of locally refined sharpened maps
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 400 pix.
= 495. Å		1.24 Å/pix.
x 400 pix.
= 495. Å		1.24 Å/pix.
x 400 pix.
= 495. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-0.000042727814 - 7.3913136
Average (Standard dev.)0.0059444876 (±0.08079945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 494.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : E3 ligase RNF213, bound to the secreted effector IpaH2.5 from Shi...

EntireName: E3 ligase RNF213, bound to the secreted effector IpaH2.5 from Shigella flexneri
Components
  • Complex: E3 ligase RNF213, bound to the secreted effector IpaH2.5 from Shigella flexneri
    • Protein or peptide: E3 ubiquitin-protein ligase IpaH2.5
    • Protein or peptide: E3 ubiquitin-protein ligase RNF213
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: E3 ligase RNF213, bound to the secreted effector IpaH2.5 from Shi...

SupramoleculeName: E3 ligase RNF213, bound to the secreted effector IpaH2.5 from Shigella flexneri
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: E3 ubiquitin-protein ligase IpaH2.5

MacromoleculeName: E3 ubiquitin-protein ligase IpaH2.5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Shigella flexneri 5a str. M90T (bacteria) / Strain: M90T (5a)
Molecular weightTheoretical: 63.651699 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MIKSTNIQVI GSGIMHQINN IHSLTLFSLP VSLSPSCNEY YLKVWSEWER NGTPGEQRNI AFNRLKICLQ NQEAELNLSE LDLKTLPDL PPQITTLEIR KNLLTHLPDL PPMLKVIHAQ FNQLESLPAL PETLEELNAG DNKIKELPFL PENLTHLRVH N NRLHILPL ...String:
MIKSTNIQVI GSGIMHQINN IHSLTLFSLP VSLSPSCNEY YLKVWSEWER NGTPGEQRNI AFNRLKICLQ NQEAELNLSE LDLKTLPDL PPQITTLEIR KNLLTHLPDL PPMLKVIHAQ FNQLESLPAL PETLEELNAG DNKIKELPFL PENLTHLRVH N NRLHILPL LPPELKLLVV SGNRLDSIPP FPDKLEGLAL ANNFIEQLPE LPFSMNRAVL MNNNLTTLPE SVLRLAQNAF VN VAGNPLS GHTMRTLQQI TTGPDYSGPQ IFFSMGNSAT ISAPEHSLAD AVTAWFPENK QSDVSQIWHA FEHEEHANTF SAF LDRLSD TVSARNTSGF REQVAAWLEK LSASAELRQQ SFAVAADATE SCEDRVALTW NNLRKTLLVH QASEGLFDND TGAL LSLGR EMFRLEILED IARDKVRTLH FVDEIEVYLA FQTMLAEKLQ LSTAVKEMRF YGVSGVTAND LRTAEAMVRS REENE FTDW FSLWGPWHAV LKRTEADRWA QAEEQKYEML ENEYSQRVAD RLKASGLSGD ADAEREAGAQ VMRETEQQIY RQLTDE VLA

UniProtKB: E3 ubiquitin-protein ligase IpaH2.5

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Macromolecule #2: E3 ubiquitin-protein ligase RNF213

MacromoleculeName: E3 ubiquitin-protein ligase RNF213 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 596.45025 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MASWSHPQFE KGSAGSAAGS GAGWSHPQFE KENLYFQAMS MECPSCQHVS KEETPKFCSQ CGERLPPAAP IADSENNNST MASASEGEM ECGQELKEEG GPCLFPGSDS WQENPEEPCS KASWTVQESK KKKRKKKKKG NKSASSELAS LPLSPASPCH L TLLSNPWP ...String:
MASWSHPQFE KGSAGSAAGS GAGWSHPQFE KENLYFQAMS MECPSCQHVS KEETPKFCSQ CGERLPPAAP IADSENNNST MASASEGEM ECGQELKEEG GPCLFPGSDS WQENPEEPCS KASWTVQESK KKKRKKKKKG NKSASSELAS LPLSPASPCH L TLLSNPWP QDTALPHSQA QQSGPTGQPS QPPGTATTPL EGDGLSAPTE VGDSPLQAQA LGEAGVATGS EAQSSPQFQD HT EGEDQDA SIPSGGRGLS QEGTGPPTSA GEGHSRTEDA AQELLLPESK GGSSEPGTEL QTTEQQAGAS ASMAVDAVAE PAN AVKGAG KEMKEKTQRM KQPPATTPPF KTHCQEAETK TKDEMAAAEE KVGKNEQGEP EDLKKPEGKN RSAAAVKNEK EQKN QEADV QEVKASTLSP GGGVTVFFHA IISLHFPFNP DLHKVFIRGG EEFGESKWDS NICELHYTRD LGHDRVLVEG IVCIS KKHL DKYIPYKYVI YNGESFEYEF IYKHQQKKGE YVNRCLFIKS SLLGSGDWHQ YYDIVYMKPH GRLQKVMNHI TDGPRK DLV KGKQIAAALM LDSTFSILQT WDTINLNSFF TQFEQFCFVL QQPMIYEGQA QLWTDLQYRE KEVKRYLWQH LKKHVVP LP DGKSTDFLPV DCPVRSKLKT GLIVLFVVEK IELLLEGSLD WLCHLLTSDA SSPDEFHRDL SHILGIPQSW RLYLVNLC Q RCMDTRTYTW LGALPVLHCC MELAPRHKDA WRQPEDTWAA LEGLSFSPFR EQMLDTSSLL QFMREKQHLL SIDEPLFRS WFSLLPLSHL VMYMENFIEH LGRFPAHILD CLSGIYYRLP GLEQVLNTQD VQDVQNVQNI LEMLLRLLDT YRDKIPEEAL SPSYLTVCL KLHEAICSST KLLKFYELPA LSAEIVCRMI RLLSLVDSAG QRDETGNNSV QTVFQGTLAA TKRWLREVFT K NMLTSSGA SFTYVKEIEV WRRLVEIQFP AEHGWKESLL GDMEWRLTKE EPLSQITAYC NSCWDTKGLE DSVAKTFEKC II EAVSSAC QSQTSILQGF SYSDLRKFGI VLSAVITKSW PRTADNFNDI LKHLLTLADV KHVFRLCGTD EKILANVTED AKR LIAVAD SVLTKVVGDL LSGTILVGQL ELIIKHKNQF LDIWQLREKS LSPQDEQCAV EEALDWRREE LLLLKKEKRC VDSL LKMCG NVKHLIQVDF GVLAVRHSQD LSSKRLNDTV TVRLSTSSNS QRATHYHLSS QVQEMAGKID LLRDSHIFQL FWREA AEPL SEPKEDQEAA ELLSEPEEES ERHILELEEV YDYLYQPSYR KFIKLHQDLK SGEVTLAEID VIFKDFVNKY TDLDSE LKI MCTVDHQDQR DWIKDRVEQI KEYHHLHQAV HAAKVILQVK ESLGLNGDFS VLNTLLNFTD NFDDFRRETL DQINQEL IQ AKKLLQDISE ARCKGLQALS LRKEFICWVR EALGGINELK VFVDLASISA GENDIDVDRV ACFHDAVQGY ASLLFKLD P SVDFSAFMKH LKKLWKALDK DQYLPRKLCD SARNLEWLKT VNESHGSVER SSLTLATAIN QRGIYVIQAP KGGQKISPD TVLHLILPES PGSHEESREY SLEEVKELLN KLMLMSGKKD RNNTEVERFS EVFCSVQRLS QAFIDLHSAG NMLFRTWIAM AYCSPKQGV SLQMDFGLDL VTELKEGGDV TELLAALCRQ MEHFLDSWKR FVTQKRMEHF YLNFYTAEQL VYLSTELRKQ P PSDAALTM LSFIKSNCTL RDVLRASVGC GSEAARYRMR RVMEELPLML LSEFSLVDKL RIIMEQSMRC LPAFLPDCLD LE TLGHCLA HLAGMGGSPV ERCLPRGLQV GQPNLVVCGH SEVLPAALAV YMQTPSQPLP TYDEVLLCTP ATTFEEVALL LRR CLTLGS LGHKVYSLLF ADQLSYEVAR QAEELFHNLC TQQHREDYQL VMVCDGDWEH CYLPSAFSQH KVFVTPQAPL EAIQ AYLAG HYRVPKQTLS AAAVFNDRLC VGIVASERAG VGKSLYVKRL HDKMKMQLNV KNVPLKTIRL IDPQVDESRV LGALL PFLD AQYQKVPVLF HLDVTSSVQT GIWVFLFKLL ILQYLMDING KMWLRNPCHL YIVEILERRT SVPSRSSSAL RTRVPQ FSF LDIFPKVTCR PPKEVIDMEL SALRSDTEPG MDLWEFCSET FQRPYQYLRR FNQNQDLDTF QYQEGSVEGT PEECLQH FL FHCGVINPSW SELRNFARFL NYQLRDCEAS LFCNPSFIGD TLRGFKKFVV TFMIFMARDF ATPSLHTSDQ SPGKHMVT M DGVREEDLAP FSLRKRWESE PHPYVFFNDD HTTMTFIGFH LQPNINGSVD AISHLTGKVI KRDVMTRDLY QGLLLQRVP FNVDFDKLPR HKKLERLCLT LGIPQATDPD KTYELTTDNM LKILAIEMRF RCGIPVIIMG ETGCGKTRLI KFLSDLRRGG TNADTIKLV KVHGGTTADM IYSRVREAEN VAFANKDQHQ LDTILFFDEA NTTEAISCIK EVLCDHMVDG QPLAEDSGLH I IAACNPYR KHSEEMICRL ESAGLGYRVS MEETADRLGS IPLRQLVYRV HALPPSLIPL VWDFGQLSDV AEKLYIQQIV QR LVESISL DENGTRVITE VLCASQGFMR KTEDECSFVS LRDVERCVKV FRWFHEHSAM LLAQLNAFLS KSSVSKNHTE RDP VLWSLM LAIGVCYHAS LEKKDSYRKA IARFFPKPYD DSRLLLDEIT RAQDLFLDGV PLRKTIAKNL ALKENVFMMV VCIE LKIPL FLVGKPGSSK SLAKTIVADA MQGPAAYSDL FRSLKQVHLV SFQCSPHSTP QGIISTFRQC ARFQQGKDLQ QYVSV VVLD EVGLAEDSPK MPLKTLHPLL EDGCIEDDPA PHKKVGFVGI SNWALDPAKM NRGIFVSRGS PNETELIESA KGICSS DIL VQDRVQGYFA SFAKAYETVC KRQDKEFFGL RDYYSLIKMV FAAAKASNRK PSPQDIAQAV LRNFSGKDDI QALDIFL AN LPEAKCSEEV SPMQLIKQNI FGPSQKVPGG EQEDAESRYL LVLTKNYVAL QILQQTFFEG DQQPEIIFGS GFPKDQEY T QLCRNINRVK ICMETGKMVL LLNLQNLYES LYDALNQYYV HLGGQKYVDL GLGTHRVKCR VHPNFRLIVI EEKDVVYKH FPIPLINRLE KHYLDINTVL EKWQKSIVEE LCAWVEKFIN VKAHHFQKRH KYSPSDVFIG YHSDACASVV LQVIERQGPR ALTEELHQK VSEEAKSILL NCATPDAVVR LSAYSLGGFA AEWLSQEYFH RQRHNSFADF LQAHLHTADL ERHAIFTEIT T FSRLLTSH DCEILESEVT GRAPKPTLLW LQQFDTEYSF LKEVRNCLTN TAKCKILIFQ TDFEDGIRSA QLIASAKYSV IN EINKIRE NEDRIFVYFI TKLSRVGRGT AYVGFHGGLW QSVHIDDLRR STLMVSDVTR LQHVTISQLF APGDLPELGL EHR AEDGHE EAMETEASTS GEVAEVAEEA METESSEKVG KETSELGGSD VSILDTTRLL RSCVQSAVGM LRDQNESCTR NMRR VVLLL GLLNEDDACH ASFLRVSKMR LSVFLKKQEE SQFHPLEWLA REACNQDALQ EAGTFRHTLW KRVQGAVTPL LASMI SFID RDGNLELLTR PDTPPWARDL WMFIFSDTML LNIPLVMNNE RHKGEMAYIV VQNHMNLSEN ASNNVPFSWK IKDYLE ELW VQAQYITDAE GLPKKFVDIF QQTPLGRFLA QLHGEPQQEL LQCYLKDFIL LTMRVSTEEE LKFLQMALWS CTRKLKA AS EAPEEEVSLP WVHLAYQRFR SRLQNFSRIL TIYPQVLHSL MEARWNHELA GCEMTLDAFA AMACTEMLTR NTLKPSPQ A WLQLVKNLSM PLELICSDEH MQGSGSLAQA VIREVRAQWS RIFSTALFVE HVLLGTESRV PELQGLVTEH VFLLDKCLR ENSDVKTHGP FEAVMRTLCE CKETASKTLS RFGIQPCSIC LGDAKDPVCL PCDHVHCLRC LRAWFASEQM ICPYCLTALP DEFSPAVSQ AHREAIEKHA RFRQMCNSFF VDLVSTICFK DNAPPEKEVI ESLLSLLFVQ KGRLRDAAQR HCEHTKSLSP F NDVVDKTP VIRSVILKLL LKYSFHDVKD YIQEYLTLLK KKAFITEDKT ELYMLFINCL EDSILEKTSA YSRNDELNHL EE EGRFLKA YSPASRGREP ANEASVEYLQ EVARIRLCLD RAADFLSEPE GGPEMAKEKQ CYLQQVKQFC IRVENDWHRV YLV RKLSSQ RGMEFVQGLS KPGRPHQWVF PKDVVKQQGL RQDHPGQMDR YLVYGDEYKA LRDAVAKAVL ECKPLGIKTA LKAC KTPQS QQSAYFLLTL FREVAILYRS HNASLHPTPE QCEAVSKFIG ECKILSPPDI SRFATSLVDN SVPLLRAGPS DSNLD GTVT EMAIHAAAVL LCGQNELLEP LKNLAFSPAT MAHAFLPTMP EDLLAQARRW KGLERVHWYT CPNGHPCSVG ECGRPM EQS ICIDCHAPIG GIDHKPRDGF HLVKDKADRT QTGHVLGNPQ RRDVVTCDRG LPPVVFLLIR LLTHLALLLG ASQSSQA LI NIIKPPVRDP KGFLQQHILK DLEQLAKMLG HSADETIGVV HLVLRRLLQE QHQLSSRRLL NFDTELSTKE MRNNWEKE I AAVISPELEH LDKTLPTMNN LISQDKRISS NPVAKIIYGD PVTFLPHLPR KSVVHCSKIW SCRKRITVEY LQHIVEQKN GKERVPILWH FLQKEAELRL VKFLPEILAL QRDLVKQFQN VQQVEYSSIR GFLSKHSSDG LRQLLHNRIT VFLSTWNKLR RSLETNGEI NLPKDYCSTD LDLDTEFEIL LPRRRGLGLC ATALVSYLIR LHNEIVYAVE KLSKENNSYS VDAAEVTELH V ISYEVERD LTPLILSNCQ YQVEEGRETV QEFDLEKIQR QIVSRFLQGK PRLSLKGIPT LVYRHDWNYE HLFMDIKNKM AQ DSLPSSV ISAISGQLQS YSDACEVLSV VEVTLGFLST AGGDPNMQLN VYTQDILQMG DQTIHVLKAL NRCQLKHTIA LWQ FLSAHK SEQLLRLHKE PFGEISSRYK ADLSPENAKL LSTFLNQTGL DAFLLELHEM IILKLKNPQT QTEERFRPQW SLRD TLVSY MQTKESEILP EMASQFPEEI LLASCVSVWK TAAVLKWNRE MR

UniProtKB: E3 ubiquitin-protein ligase RNF213

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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

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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: 3 / 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: 8
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 23344 / Average exposure time: 1.75 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.5 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 213053
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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