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- EMDB-15668: Cryo-EM structure of human BIRC6 - no substrate -

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Basic information

Entry
Database: EMDB / ID: EMD-15668
TitleCryo-EM structure of human BIRC6 - no substrate
Map data
Sample
  • Complex: Human BIRC6 homodimer
    • Protein or peptide: Baculoviral IAP repeat-containing protein 6
  • Ligand: ZINC ION
Function / homology
Function and homology information


spongiotrophoblast layer development / labyrinthine layer development / ALK mutants bind TKIs / Flemming body / microtubule organizing center / cysteine-type endopeptidase inhibitor activity / ubiquitin conjugating enzyme activity / Signaling by ALK fusions and activated point mutants / regulation of cytokinesis / negative regulation of extrinsic apoptotic signaling pathway ...spongiotrophoblast layer development / labyrinthine layer development / ALK mutants bind TKIs / Flemming body / microtubule organizing center / cysteine-type endopeptidase inhibitor activity / ubiquitin conjugating enzyme activity / Signaling by ALK fusions and activated point mutants / regulation of cytokinesis / negative regulation of extrinsic apoptotic signaling pathway / RING-type E3 ubiquitin transferase / trans-Golgi network / spindle pole / ubiquitin-protein transferase activity / regulation of cell population proliferation / midbody / cell population proliferation / protein ubiquitination / endosome / cell cycle / cell division / protein phosphorylation / centrosome / apoptotic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / membrane / nucleus / cytosol
Similarity search - Function
Baculoviral IAP repeat-containing protein 6 / Baculoviral IAP repeat-containing protein 6 / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / 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
Similarity search - Domain/homology
Baculoviral IAP repeat-containing protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsEhrmann JF / Grabarczyk DB / Clausen T
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission847548European Union
CitationJournal: Science / Year: 2023
Title: Structural basis for regulation of apoptosis and autophagy by the BIRC6/SMAC complex.
Authors: Julian F Ehrmann / Daniel B Grabarczyk / Maria Heinke / Luiza Deszcz / Robert Kurzbauer / Otto Hudecz / Alexandra Shulkina / Rebeca Gogova / Anton Meinhart / Gijs A Versteeg / Tim Clausen /
Abstract: Inhibitor of apoptosis proteins (IAPs) bind to pro-apoptotic proteases, keeping them inactive and preventing cell death. The atypical ubiquitin ligase BIRC6 is the only essential IAP, additionally ...Inhibitor of apoptosis proteins (IAPs) bind to pro-apoptotic proteases, keeping them inactive and preventing cell death. The atypical ubiquitin ligase BIRC6 is the only essential IAP, additionally functioning as a suppressor of autophagy. We performed a structure-function analysis of BIRC6 in complex with caspase-9, HTRA2, SMAC, and LC3B, which are critical apoptosis and autophagy proteins. Cryo-electron microscopy structures showed that BIRC6 forms a megadalton crescent shape that arcs around a spacious cavity containing receptor sites for client proteins. Multivalent binding of SMAC obstructs client binding, impeding ubiquitination of both autophagy and apoptotic substrates. On the basis of these data, we discuss how the BIRC6/SMAC complex can act as a stress-induced hub to regulate apoptosis and autophagy drivers.
History
DepositionAug 24, 2022-
Header (metadata) releaseFeb 15, 2023-
Map releaseFeb 15, 2023-
UpdateMar 29, 2023-
Current statusMar 29, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15668.png

Downloads & links

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Map

FileDownload / File: emd_15668.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 428. Å		1.07 Å/pix.
x 400 pix.
= 428. Å		1.07 Å/pix.
x 400 pix.
= 428. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0035
Minimum - Maximum-0.0056399335 - 0.015191485
Average (Standard dev.)-6.4477725e-05 (±0.0006049711)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 428.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15668_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15668_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15668_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Human BIRC6 homodimer

EntireName: Human BIRC6 homodimer
Components
  • Complex: Human BIRC6 homodimer
    • Protein or peptide: Baculoviral IAP repeat-containing protein 6
  • Ligand: ZINC ION

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Supramolecule #1: Human BIRC6 homodimer

SupramoleculeName: Human BIRC6 homodimer / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.06 MDa

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Macromolecule #1: Baculoviral IAP repeat-containing protein 6

MacromoleculeName: Baculoviral IAP repeat-containing protein 6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 532.009 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVTGGGAAPP GTVTEPLPSV IVLSAGRKMA AAAAAASGPG CSSAAGAGAA GVSEWLVLRD GCMHCDADGL HSLSYHPALN AILAVTSRG TIKVIDGTSG ATLQASALSA KPGGQVKCQY ISAVDKVIFV DDYAVGCRKD LNGILLLDTA LQTPVSKQDD V VQLELPVT ...String:
MVTGGGAAPP GTVTEPLPSV IVLSAGRKMA AAAAAASGPG CSSAAGAGAA GVSEWLVLRD GCMHCDADGL HSLSYHPALN AILAVTSRG TIKVIDGTSG ATLQASALSA KPGGQVKCQY ISAVDKVIFV DDYAVGCRKD LNGILLLDTA LQTPVSKQDD V VQLELPVT EAQQLLSACL EKVDISSTEG YDLFITQLKD GLKNTSHETA ANHKVAKWAT VTFHLPHHVL KSIASAIVNE LK KINQNVA ALPVASSVMD RLSYLLPSAR PELGVGPGRS VDRSLMYSEA NRRETFTSWP HVGYRWAQPD PMAQAGFYHQ PAS SGDDRA MCFTCSVCLV CWEPTDEPWS EHERHSPNCP FVKGEHTQNV PLSVTLATSP AQFPCTDGTD RISCFGSGSC PHFL AAATK RGKICIWDVS KLMKVHLKFE INAYDPAIVQ QLILSGDPSS GVDSRRPTLA WLEDSSSCSD IPKLEGDSDD LLEDS DSEE HSRSDSVTGH TSQKEAMEVS LDITALSILQ QPEKLQWEIV ANVLEDTVKD LEELGANPCL TNSKSEKTKE KHQEQH NIP FPCLLAGGLL TYKSPATSPI SSNSHRSLDG LSRTQGESIS EQGSTDNESC TNSELNSPLV RRTLPVLLLY SIKESDE KA GKIFSQMNNI MSKSLHDDGF TVPQIIEMEL DSQEQLLLQD PPVTYIQQFA DAAANLTSPD SEKWNSVFPK PGTLVQCL R LPKFAEEENL CIDSITPCAD GIHLLVGLRT CPVESLSAIN QVEALNNLNK LNSALCNRRK GELESNLAVV NGANISVIQ HESPADVQTP LIIQPEQRNV SGGYLVLYKM NYATRIVTLE EEPIKIQHIK DPQDTITSLI LLPPDILDNR EDDCEEPIED MQLTSKNGF EREKTSDIST LGHLVITTQG GYVKILDLSN FEILAKVEPP KKEGTEEQDT FVSVIYCSGT DRLCACTKGG E LHFLQIGG TCDDIDEADI LVDGSLSKGI EPSSEGSKPL SNPSSPGISG VDLLVDQPFT LEILTSLVEL TRFETLTPRF SA TVPPCWV EVQQEQQQRR HPQHLHQQHH GDAAQHTRTW KLQTDSNSWD EHVFELVLPK ACMVGHVDFK FVLNSNITNI PQI QVTLLK NKAPGLGKVN ALNIEVEQNG KPSLVDLNEE MQHMDVEESQ CLRLCPFLED HKEDILCGPV WLASGLDLSG HAGM LTLTS PKLVKGMAGG KYRSFLIHVK AVNERGTEEI CNGGMRPVVR LPSLKHQSNK GYSLASLLAK VAAGKEKSSN VKNEN TSGT RKSENLRGCD LLQEVSVTIR RFKKTSISKE RVQRCAMLQF SEFHEKLVNT LCRKTDDGQI TEHAQSLVLD TLCWLA GVH SNGPGSSKEG NENLLSKTRK FLSDIVRVCF FEAGRSIAHK CARFLALCIS NGKCDPCQPA FGPVLLKALL DNMSFLP AA TTGGSVYWYF VLLNYVKDED LAGCSTACAS LLTAVSRQLQ DRLTPMEALL QTRYGLYSSP FDPVLFDLEM SGSSCKNV Y NSSIGVQSDE IDLSDVLSGN GKVSSCTAAE GSFTSLTGLL EVEPLHFTCV STSDGTRIER DDAMSSFGVT PAVGGLSSG TVGEASTALS SAAQVALQSL SHAMASAEQQ LQVLQEKQQQ LLKLQQQKAK LEAKLHQTTA AAAAAASAVG PVHNSVPSNP VAAPGFFIH PSDVIPPTPK TTPLFMTPPL TPPNEAVSVV INAELAQLFP GSVIDPPAVN LAAHNKNSNK SRMNPLGSGL A LAISHASH FLQPPPHQSI IIERMHSGAR RFVTLDFGRP ILLTDVLIPT CGDLASLSID IWTLGEEVDG RRLVVATDIS TH SLILHDL IPPPVCRFMK ITVIGRYGST NARAKIPLGF YYGHTYILPW ESELKLMHDP LKGEGESANQ PEIDQHLAMM VAL QEDIQC RYNLACHRLE TLLQSIDLPP LNSANNAQYF LRKPDKAVEE DSRVFSAYQD CIQLQLQLNL AHNAVQRLKV ALGA SRKML SETSNPEDLI QTSSTEQLRT IIRYLLDTLL SLLHASNGHS VPAVLQSTFH AQACEELFKH LCISGTPKIR LHTGL LLVQ LCGGERWWGQ FLSNVLQELY NSEQLLIFPQ DRVFMLLSCI GQRSLSNSGV LESLLNLLDN LLSPLQPQLP MHRRTE GVL DIPMISWVVM LVSRLLDYVA TVEDEAAAAK KPLNGNQWSF INNNLHTQSL NRSSKGSSSL DRLYSRKIRK QLVHHKQ QL NLLKAKQKAL VEQMEKEKIQ SNKGSSYKLL VEQAKLKQAT SKHFKDLIRL RRTAEWSRSN LDTEVTTAKE SPEIEPLP F TLAHERCISV VQKLVLFLLS MDFTCHADLL LFVCKVLARI ANATRPTIHL CEIVNEPQLE RLLLLLVGTD FNRGDISWG GAWAQYSLTC MLQDILAGEL LAPVAAEAME EGTVGDDVGA TAGDSDDSLQ QSSVQLLETI DEPLTHDITG APPLSSLEKD KEIDLELLQ DLMEVDIDPL DIDLEKDPLA AKVFKPISST WYDYWGADYG TYNYNPYIGG LGIPVAKPPA NTEKNGSQTV S VSVSQALD ARLEVGLEQQ AELMLKMMST LEADSILQAL TNTSPTLSQS PTGTDDSLLG GLQAANQTSQ LIIQLSSVPM LN VCFNKLF SMLQVHHVQL ESLLQLWLTL SLNSSSTGNK ENGADIFLYN ANRIPVISLN QASITSFLTV LAWYPNTLLR TWC LVLHSL TLMTNMQLNS GSSSAIGTQE STAHLLVSDP NLIHVLVKFL SGTSPHGTNQ HSPQVGPTAT QAMQEFLTRL QVHL SSTCP QIFSEFLLKL IHILSTERGA FQTGQGPLDA QVKLLEFTLE QNFEVVSVST ISAVIESVTF LVHHYITCSD KVMSR SGSD SSVGARACFG GLFANLIRPG DAKAVCGEMT RDQLMFDLLK LVNILVQLPL SGNREYSARV SVTTNTTDSV SDEEKV SGG KDGNGSSTSV QGSPAYVADL VLANQQIMSQ ILSALGLCNS SAMAMIIGAS GLHLTKHENF HGGLDAISVG DGLFTIL TT LSKKASTVHM MLQPILTYMA CGYMGRQGSL ATCQLSEPLL WFILRVLDTS DALKAFHDMG GVQLICNNMV TSTRAIVN T ARSMVSTIMK FLDSGPNKAV DSTLKTRILA SEPDNAEGIH NFAPLGTITS SSPTAQPAEV LLQATPPHRR ARSAAWSYI FLPEEAWCDL TIHLPAAVLL KEIHIQPHLA SLATCPSSVS VEVSADGVNM LPLSTPVVTS GLTYIKIQLV KAEVASAVCL RLHRPRDAS TLGLSQIKLL GLTAFGTTSS ATVNNPFLPS EDQVSKTSIG WLRLLHHCLT HISDLEGMMA SAAAPTANLL Q TCAALLMS PYCGMHSPNI EVVLVKIGLQ STRIGLKLID ILLRNCAASG SDPTDLNSPL LFGRLNGLSS DSTIDILYQL GT TQDPGTK DRIQALLKWV SDSARVAAMK RSGRMNYMCP NSSTVEYGLL MPSPSHLHCV AAILWHSYEL LVEYDLPALL DQE LFELLF NWSMSLPCNM VLKKAVDSLL CSMCHVHPNY FSLLMGWMGI TPPPVQCHHR LSMTDDSKKQ DLSSSLTDDS KNAQ APLAL TESHLATLAS SSQSPEAIKQ LLDSGLPSLL VRSLASFCFS HISSSESIAQ SIDISQDKLR RHHVPQQCNK MPITA DLVA PILRFLTEVG NSHIMKDWLG GSEVNPLWTA LLFLLCHSGS TSGSHNLGAQ QTSARSASLS SAATTGLTTQ QRTAIE NAT VAFFLQCISC HPNNQKLMAQ VLCELFQTSP QRGNLPTSGN ISGFIRRLFL QLMLEDEKVT MFLQSPCPLY KGRINAT SH VIQHPMYGAG HKFRTLHLPV STTLSDVLDR VSDTPSITAK LISEQKDDKE KKNHEEKEKV KAENGFQDNY SVVVASGL K SQSKRAVSAT PPRPPSRRGR TIPDKIGSTS GAEAANKIIT VPVFHLFHKL LAGQPLPAEM TLAQLLTLLY DRKLPQGYR SIDLTVKLGS RVITDPSLSK TDSYKRLHPE KDHGDLLASC PEDEALTPGD ECMDGILDES LLETCPIQSP LQVFAGMGGL ALIAERLPM LYPEVIQQVS APVVTSTTQE KPKDSDQFEW VTIEQSGELV YEAPETVAAE PPPIKSAVQT MSPIPAHSLA A FGLFLRLP GYAEVLLKER KHAQCLLRLV LGVTDDGEGS HILQSPSANV LPTLPFHVLR SLFSTTPLTT DDGVLLRRMA LE IGALHLI LVCLSALSHH SPRVPNSSVN QTEPQVSSSH NPTSTEEQQL YWAKGTGFGT GSTASGWDVE QALTKQRLEE EHV TCLLQV LASYINPVSS AVNGEAQSSH ETRGQNSNAL PSVLLELLSQ SCLIPAMSSY LRNDSVLDMA RHVPLYRALL ELLR AIASC AAMVPLLLPL STENGEEEEE QSECQTSVGT LLAKMKTCVD TYTNRLRSKR ENVKTGVKPD ASDQEPEGLT LLVPD IQKT AEIVYAATTS LRQANQEKKL GEYSKKAAMK PKPLSVLKSL EEKYVAVMKK LQFDTFEMVS EDEDGKLGFK VNYHYM SQV KNANDANSAA RARRLAQEAV TLSTSLPLSS SSSVFVRCDE ERLDIMKVLI TGPADTPYAN GCFEFDVYFP QDYPSSP PL VNLETTGGHS VRFNPNLYND GKVCLSILNT WHGRPEEKWN PQTSSFLQVL VSVQSLILVA EPYFNEPGYE RSRGTPSG T QSSREYDGNI RQATVKWAML EQIRNPSPCF KEVIHKHFYL KRVEIMAQCE EWIADIQQYS SDKRVGRTMS HHAAALKRH TAQLREELLK LPCPEGLDPD TDDAPEVCRA TTGAEETLMH DQVKPSSSKE LPSDFQLSAW SHPQFEK

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / 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

Concentration0.2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 136411
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8atu

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8atx:
Cryo-EM structure of human BIRC6 - no substrate

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