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- EMDB-27833: Cryo-EM structure of helical arch of BIRC6 (from local refinement 1) -

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Basic information

Entry
Database: EMDB / ID: EMD-27833
TitleCryo-EM structure of helical arch of BIRC6 (from local refinement 1)
Map datamain map
Sample
  • Complex: Baculoviral IAP repeat-containing protein 6
    • Protein or peptide: Baculoviral IAP repeat-containing protein 6
  • Ligand: water
KeywordsUbiquitin / E3 ligase / Apoptosis / Autophagy / IAP / LIGASE
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 / regulation of cytokinesis / negative regulation of extrinsic apoptotic signaling pathway / trans-Golgi network ...spongiotrophoblast layer development / labyrinthine layer development / ALK mutants bind TKIs / Flemming body / microtubule organizing center / cysteine-type endopeptidase inhibitor activity / ubiquitin conjugating enzyme activity / regulation of cytokinesis / negative regulation of extrinsic apoptotic signaling pathway / trans-Golgi network / RING-type E3 ubiquitin transferase / spindle pole / ubiquitin-protein transferase activity / Signaling by ALK fusions and activated point mutants / regulation of cell population proliferation / midbody / cell population proliferation / endosome / protein ubiquitination / protein phosphorylation / cell division / centrosome / positive regulation of cell population proliferation / negative regulation of apoptotic process / 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 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / 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: 1.98 Å
AuthorsHunkeler M / Fischer ES
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA066996 United States
The Mark Foundation19-001-ELA United States
CitationJournal: Science / Year: 2023
Title: Structures of BIRC6-client complexes provide a mechanism of SMAC-mediated release of caspases.
Authors: Moritz Hunkeler / Cyrus Y Jin / Eric S Fischer /
Abstract: Tight regulation of apoptosis is essential for metazoan development and prevents diseases such as cancer and neurodegeneration. Caspase activation is central to apoptosis, and inhibitor of apoptosis ...Tight regulation of apoptosis is essential for metazoan development and prevents diseases such as cancer and neurodegeneration. Caspase activation is central to apoptosis, and inhibitor of apoptosis proteins (IAPs) are the principal actors that restrain caspase activity and are therefore attractive therapeutic targets. IAPs, in turn, are regulated by mitochondria-derived proapoptotic factors such as SMAC and HTRA2. Through a series of cryo-electron microscopy structures of full-length human baculoviral IAP repeat-containing protein 6 (BIRC6) bound to SMAC, caspases, and HTRA2, we provide a molecular understanding for BIRC6-mediated caspase inhibition and its release by SMAC. The architecture of BIRC6, together with near-irreversible binding of SMAC, elucidates how the IAP inhibitor SMAC can effectively control a processive ubiquitin ligase to respond to apoptotic stimuli.
History
DepositionAug 15, 2022-
Header (metadata) releaseFeb 15, 2023-
Map releaseFeb 15, 2023-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27833.png

Downloads & links

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Map

FileDownload / File: emd_27833.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 480 pix.
= 422.4 Å		0.88 Å/pix.
x 480 pix.
= 422.4 Å		0.88 Å/pix.
x 480 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.33
Minimum - Maximum-4.0353637 - 7.166699
Average (Standard dev.)-0.0032015468 (±0.13369595)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 422.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27833_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: main map post-processed with deepEMhancer

Fileemd_27833_additional_1.map
Annotationmain map post-processed with deepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_27833_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_27833_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Baculoviral IAP repeat-containing protein 6

EntireName: Baculoviral IAP repeat-containing protein 6
Components
  • Complex: Baculoviral IAP repeat-containing protein 6
    • Protein or peptide: Baculoviral IAP repeat-containing protein 6
  • Ligand: water

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Supramolecule #1: Baculoviral IAP repeat-containing protein 6

SupramoleculeName: Baculoviral IAP repeat-containing protein 6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.067 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: Ligases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 534.158312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKL AAANSSIDLI STSLYKKAGL TMVTGGGAAP PGTVTEPLPS VIVLSAGRKM AAAAAAASGP GCSSAAGAGA AGVSEWLVL RDGCMHCDAD GLHSLSYHPA LNAILAVTSR GTIKVIDGTS GATLQASALS AKPGGQVKCQ YISAVDKVIF V DDYAVGCR ...String:
MDYKDDDDKL AAANSSIDLI STSLYKKAGL TMVTGGGAAP PGTVTEPLPS VIVLSAGRKM AAAAAAASGP GCSSAAGAGA AGVSEWLVL RDGCMHCDAD GLHSLSYHPA LNAILAVTSR GTIKVIDGTS GATLQASALS AKPGGQVKCQ YISAVDKVIF V DDYAVGCR KDLNGILLLD TALQTPVSKQ DDVVQLELPV TEAQQLLSAC LEKVDISSTE GYDLFITQLK DGLKNTSHET AA NHKVAKW ATVTFHLPHH VLKSIASAIV NELKKINQNV AALPVASSVM DRLSYLLPSA RPELGVGPGR SVDRSLMYSE ANR RETFTS WPHVGYRWAQ PDPMAQAGFY HQPASSGDDR AMCFTCSVCL VCWEPTDEPW SEHERHSPNC PFVKGEHTQN VPLS VTLAT SPAQFPCTDG TDRISCFGSG SCPHFLAAAT KRGKICIWDV SKLMKVHLKF EINAYDPAIV QQLILSGDPS SGVDS RRPT LAWLEDSSSC SDIPKLEGDS DDLLEDSDSE EHSRSDSVTG HTSQKEAMEV SLDITALSIL QQPEKLQWEI VANVLE DTV KDLEELGANP CLTNSKSEKT KEKHQEQHNI PFPCLLAGGL LTYKSPATSP ISSNSHRSLD GLSRTQGESI SEQGSTD NE SCTNSELNSP LVRRTLPVLL LYSIKESDEK AGKIFSQMNN IMSKSLHDDG FTVPQIIEME LDSQEQLLLQ DPPVTYIQ Q FADAAANLTS PDSEKWNSVF PKPGTLVQCL RLPKFAEEEN LCIDSITPCA DGIHLLVGLR TCPVESLSAI NQVEALNNL NKLNSALCNR RKGELESNLA VVNGANISVI QHESPADVQT PLIIQPEQRN VSGGYLVLYK MNYATRIVTL EEEPIKIQHI KDPQDTITS LILLPPDILD NREDDCEEPI EDMQLTSKNG FEREKTSDIS TLGHLVITTQ GGYVKILDLS NFEILAKVEP P KKEGTEEQ DTFVSVIYCS GTDRLCACTK GGELHFLQIG GTCDDIDEAD ILVDGSLSKG IEPSSEGSKP LSNPSSPGIS GV DLLVDQP FTLEILTSLV ELTRFETLTP RFSATVPPCW VEVQQEQQQR RHPQHLHQQH HGDAAQHTRT WKLQTDSNSW DEH VFELVL PKACMVGHVD FKFVLNSNIT NIPQIQVTLL KNKAPGLGKV NALNIEVEQN GKPSLVDLNE EMQHMDVEES QCLR LCPFL EDHKEDILCG PVWLASGLDL SGHAGMLTLT SPKLVKGMAG GKYRSFLIHV KAVNERGTEE ICNGGMRPVV RLPSL KHQS NKGYSLASLL AKVAAGKEKS SNVKNENTSG TRKSENLRGC DLLQEVSVTI RRFKKTSISK ERVQRCAMLQ FSEFHE KLV NTLCRKTDDG QITEHAQSLV LDTLCWLAGV HSNGPGSSKE GNENLLSKTR KFLSDIVRVC FFEAGRSIAH KCARFLA LC ISNGKCDPCQ PAFGPVLLKA LLDNMSFLPA ATTGGSVYWY FVLLNYVKDE DLAGCSTACA SLLTAVSRQL QDRLTPME A LLQTRYGLYS SPFDPVLFDL EMSGSSCKNV YNSSIGVQSD EIDLSDVLSG NGKVSSCTAA EGSFTSLTGL LEVEPLHFT CVSTSDGTRI ERDDAMSSFG VTPAVGGLSS GTVGEASTAL SSAAQVALQS LSHAMASAEQ QLQVLQEKQQ QLLKLQQQKA KLEAKLHQT TAAAAAAASA VGPVHNSVPS NPVAAPGFFI HPSDVIPPTP KTTPLFMTPP LTPPNEAVSV VINAELAQLF P GSVIDPPA VNLAAHNKNS NKSRMNPLGS GLALAISHAS HFLQPPPHQS IIIERMHSGA RRFVTLDFGR PILLTDVLIP TC GDLASLS IDIWTLGEEV DGRRLVVATD ISTHSLILHD LIPPPVCRFM KITVIGRYGS TNARAKIPLG FYYGHTYILP WES ELKLMH DPLKGEGESA NQPEIDQHLA MMVALQEDIQ CRYNLACHRL ETLLQSIDLP PLNSANNAQY FLRKPDKAVE EDSR VFSAY QDCIQLQLQL NLAHNAVQRL KVALGASRKM LSETSNPEDL IQTSSTEQLR TIIRYLLDTL LSLLHASNGH SVPAV LQST FHAQACEELF KHLCISGTPK IRLHTGLLLV QLCGGERWWG QFLSNVLQEL YNSEQLLIFP QDRVFMLLSC IGQRSL SNS GVLESLLNLL DNLLSPLQPQ LPMHRRTEGV LDIPMISWVV MLVSRLLDYV ATVEDEAAAA KKPLNGNQWS FINNNLH TQ SLNRSSKGSS SLDRLYSRKI RKQLVHHKQQ LNLLKAKQKA LVEQMEKEKI QSNKGSSYKL LVEQAKLKQA TSKHFKDL I RLRRTAEWSR SNLDTEVTTA KESPEIEPLP FTLAHERCIS VVQKLVLFLL SMDFTCHADL LLFVCKVLAR IANATRPTI HLCEIVNEPQ LERLLLLLVG TDFNRGDISW GGAWAQYSLT CMLQDILAGE LLAPVAAEAM EEGTVGDDVG ATAGDSDDSL QQSSVQLLE TIDEPLTHDI TGAPPLSSLE KDKEIDLELL QDLMEVDIDP LDIDLEKDPL AAKVFKPISS TWYDYWGADY G TYNYNPYI GGLGIPVAKP PANTEKNGSQ TVSVSVSQAL DARLEVGLEQ QAELMLKMMS TLEADSILQA LTNTSPTLSQ SP TGTDDSL LGGLQAANQT SQLIIQLSSV PMLNVCFNKL FSMLQVHHVQ LESLLQLWLT LSLNSSSTGN KENGADIFLY NAN RIPVIS LNQASITSFL TVLAWYPNTL LRTWCLVLHS LTLMTNMQLN SGSSSAIGTQ ESTAHLLVSD PNLIHVLVKF LSGT SPHGT NQHSPQVGPT ATQAMQEFLT RLQVHLSSTC PQIFSEFLLK LIHILSTERG AFQTGQGPLD AQVKLLEFTL EQNFE VVSV STISAVIESV TFLVHHYITC SDKVMSRSGS DSSVGARACF GGLFANLIRP GDAKAVCGEM TRDQLMFDLL KLVNIL VQL PLSGNREYSA RVSVTTNTTD SVSDEEKVSG GKDGNGSSTS VQGSPAYVAD LVLANQQIMS QILSALGLCN SSAMAMI IG ASGLHLTKHE NFHGGLDAIS VGDGLFTILT TLSKKASTVH MMLQPILTYM ACGYMGRQGS LATCQLSEPL LWFILRVL D TSDALKAFHD MGGVQLICNN MVTSTRAIVN TARSMVSTIM KFLDSGPNKA VDSTLKTRIL ASEPDNAEGI HNFAPLGTI TSSSPTAQPA EVLLQATPPH RRARSAAWSY IFLPEEAWCD LTIHLPAAVL LKEIHIQPHL ASLATCPSSV SVEVSADGVN MLPLSTPVV TSGLTYIKIQ LVKAEVASAV CLRLHRPRDA STLGLSQIKL LGLTAFGTTS SATVNNPFLP SEDQVSKTSI G WLRLLHHC LTHISDLEGM MASAAAPTAN LLQTCAALLM SPYCGMHSPN IEVVLVKIGL QSTRIGLKLI DILLRNCAAS GS DPTDLNS PLLFGRLNGL SSDSTIDILY QLGTTQDPGT KDRIQALLKW VSDSARVAAM KRSGRMNYMC PNSSTVEYGL LMP SPSHLH CVAAILWHSY ELLVEYDLPA LLDQELFELL FNWSMSLPCN MVLKKAVDSL LCSMCHVHPN YFSLLMGWMG ITPP PVQCH HRLSMTDDSK KQDLSSSLTD DSKNAQAPLA LTESHLATLA SSSQSPEAIK QLLDSGLPSL LVRSLASFCF SHISS SESI AQSIDISQDK LRRHHVPQQC NKMPITADLV APILRFLTEV GNSHIMKDWL GGSEVNPLWT ALLFLLCHSG STSGSH NLG AQQTSARSAS LSSAATTGLT TQQRTAIENA TVAFFLQCIS CHPNNQKLMA QVLCELFQTS PQRGNLPTSG NISGFIR RL FLQLMLEDEK VTMFLQSPCP LYKGRINATS HVIQHPMYGA GHKFRTLHLP VSTTLSDVLD RVSDTPSITA KLISEQKD D KEKKNHEEKE KVKAENGFQD NYSVVVASGL KSQSKRAVSA TPPRPPSRRG RTIPDKIGST SGAEAANKII TVPVFHLFH KLLAGQPLPA EMTLAQLLTL LYDRKLPQGY RSIDLTVKLG SRVITDPSLS KTDSYKRLHP EKDHGDLLAS CPEDEALTPG DECMDGILD ESLLETCPIQ SPLQVFAGMG GLALIAERLP MLYPEVIQQV SAPVVTSTTQ EKPKDSDQFE WVTIEQSGEL V YEAPETVA AEPPPIKSAV QTMSPIPAHS LAAFGLFLRL PGYAEVLLKE RKHAQCLLRL VLGVTDDGEG SHILQSPSAN VL PTLPFHV LRSLFSTTPL TTDDGVLLRR MALEIGALHL ILVCLSALSH HSPRVPNSSV NQTEPQVSSS HNPTSTEEQQ LYW AKGTGF GTGSTASGWD VEQALTKQRL EEEHVTCLLQ VLASYINPVS SAVNGEAQSS HETRGQNSNA LPSVLLELLS QSCL IPAMS SYLRNDSVLD MARHVPLYRA LLELLRAIAS CAAMVPLLLP LSTENGEEEE EQSECQTSVG TLLAKMKTCV DTYTN RLRS KRENVKTGVK PDASDQEPEG LTLLVPDIQK TAEIVYAATT SLRQANQEKK LGEYSKKAAM KPKPLSVLKS LEEKYV AVM KKLQFDTFEM VSEDEDGKLG FKVNYHYMSQ VKNANDANSA ARARRLAQEA VTLSTSLPLS SSSSVFVRCD EERLDIM KV LITGPADTPY ANGCFEFDVY FPQDYPSSPP LVNLETTGGH SVRFNPNLYN DGKVCLSILN TWHGRPEEKW NPQTSSFL Q VLVSVQSLIL VAEPYFNEPG YERSRGTPSG TQSSREYDGN IRQATVKWAM LEQIRNPSPC FKEVIHKHFY LKRVEIMAQ CEEWIADIQQ YSSDKRVGRT MSHHAAALKR HTAQLREELL KLPCPEGLDP DTDDAPEVCR ATTGAEETLM HDQVKPSSSK ELPSDFQL

UniProtKB: Baculoviral IAP repeat-containing protein 6

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 377 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
30.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium chloride
3.0 mMC9H15O6PTCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283.15 K / Instrument: LEICA EM GP
Detailsadded CHAPSO to 0.8 mM

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
DetailsData collection in counting mode, using multi-shot scheme (9 holes per stage position, 3 movies per hole)
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 19647 / Average exposure time: 2.4 sec. / Average electron dose: 52.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
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

Particle selectionNumber selected: 4058599
Startup modelType of model: OTHER / Details: ab initio
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 1.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1116480
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 6 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8e2e:
Cryo-EM structure of helical arch of BIRC6 (from local refinement 1)

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