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Yorodumi- EMDB-37091: Cryo-EM structure of human C-terminally bound ATG9A-ATG2A-WIPI4 c... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37091 | |||||||||
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Title | Cryo-EM structure of human C-terminally bound ATG9A-ATG2A-WIPI4 complex | |||||||||
Map data | Cryo-EM map of C-terminally bound ATG9A-ATG2A-WIPI4 complex. | |||||||||
Sample |
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Keywords | Lipid transfer / ATG9A-ATG2A-WIPI4 complex / single particle cryo-EM / autophagy / LIPID TRANSPORT-MEMBRANE PROTEIN complex | |||||||||
Function / homology | Function and homology information phagophore / protein lipidation / lipid transfer activity / organelle membrane contact site / glycophagy / phosphatidylinositol phosphate binding / phospholipid scramblase activity / nucleophagy / programmed necrotic cell death / positive regulation of autophagosome assembly ...phagophore / protein lipidation / lipid transfer activity / organelle membrane contact site / glycophagy / phosphatidylinositol phosphate binding / phospholipid scramblase activity / nucleophagy / programmed necrotic cell death / positive regulation of autophagosome assembly / autophagy of mitochondrion / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phosphatidylinositol-3-phosphate binding / phagophore assembly site / bone morphogenesis / phosphatidylinositol-3,5-bisphosphate binding / reticulophagy / Macroautophagy / extrinsic component of membrane / autophagosome assembly / autophagosome / protein-membrane adaptor activity / cellular response to starvation / lipid droplet / mitochondrial membrane / trans-Golgi network / recycling endosome / autophagy / recycling endosome membrane / late endosome / late endosome membrane / endosome / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / protein kinase binding / Golgi apparatus / mitochondrion / membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.0 Å | |||||||||
Authors | Wang Y / Stjepanovic G | |||||||||
Funding support | China, 2 items
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Citation | Journal: To Be Published Title: Structural basis for lipid transfer by the ATG2A-ATG9A complex Authors: Wang Y / Stjepanovic G | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37091.map.gz | 776.1 MB | EMDB map data format | |
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Header (meta data) | emd-37091-v30.xml emd-37091.xml | 18.2 KB 18.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37091_fsc.xml | 20.1 KB | Display | FSC data file |
Images | emd_37091.png | 53.2 KB | ||
Filedesc metadata | emd-37091.cif.gz | 7.4 KB | ||
Others | emd_37091_half_map_1.map.gz emd_37091_half_map_2.map.gz | 765 MB 765 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37091 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37091 | HTTPS FTP |
-Validation report
Summary document | emd_37091_validation.pdf.gz | 711 KB | Display | EMDB validaton report |
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Full document | emd_37091_full_validation.pdf.gz | 710.6 KB | Display | |
Data in XML | emd_37091_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | emd_37091_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37091 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37091 | HTTPS FTP |
-Related structure data
Related structure data | 8kc3MC 8kbxC 8kbyC 8kbzC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_37091.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of C-terminally bound ATG9A-ATG2A-WIPI4 complex. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map B of C-terminally bound ATG9A-ATG2A-WIPI4 complex.
File | emd_37091_half_map_1.map | ||||||||||||
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Annotation | Half map B of C-terminally bound ATG9A-ATG2A-WIPI4 complex. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A of C-terminally bound ATG9A-ATG2A-WIPI4 complex.
File | emd_37091_half_map_2.map | ||||||||||||
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Annotation | Half map A of C-terminally bound ATG9A-ATG2A-WIPI4 complex. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : C-terminally bound ATG9A-ATG2A-WIPI4 complex
Entire | Name: C-terminally bound ATG9A-ATG2A-WIPI4 complex |
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Components |
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-Supramolecule #1: C-terminally bound ATG9A-ATG2A-WIPI4 complex
Supramolecule | Name: C-terminally bound ATG9A-ATG2A-WIPI4 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 536 KDa |
-Macromolecule #1: Autophagy-related protein 9A
Macromolecule | Name: Autophagy-related protein 9A / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 94.551031 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAQFDTEYQR LEASYSDSPP GEEDLLVHVA EGSKSPWHHI ENLDLFFSRV YNLHQKNGFT CMLIGEIFEL MQFLFVVAFT TFLVSCVDY DILFANKMVN HSLHPTEPVK VTLPDAFLPA QVCSARIQEN GSLITILVIA GVFWIHRLIK FIYNICCYWE I HSFYLHAL ...String: MAQFDTEYQR LEASYSDSPP GEEDLLVHVA EGSKSPWHHI ENLDLFFSRV YNLHQKNGFT CMLIGEIFEL MQFLFVVAFT TFLVSCVDY DILFANKMVN HSLHPTEPVK VTLPDAFLPA QVCSARIQEN GSLITILVIA GVFWIHRLIK FIYNICCYWE I HSFYLHAL RIPMSALPYC TWQEVQARIV QTQKEHQICI HKRELTELDI YHRILRFQNY MVALVNKSLL PLRFRLPGLG EA VFFTRGL KYNFELILFW GPGSLFLNEW SLKAEYKRGG QRLELAQRLS NRILWIGIAN FLLCPLILIW QILYAFFSYA EVL KREPGA LGARCWSLYG RCYLRHFNEL EHELQSRLNR GYKPASKYMN CFLSPLLTLL AKNGAFFAGS ILAVLIALTI YDED VLAVE HVLTTVTLLG VTVTVCRSFI PDQHMVFCPE QLLRVILAHI HYMPDHWQGN AHRSQTRDEF AQLFQYKAVF ILEEL LSPI VTPLILIFCL RPRALEIIDF FRNFTVEVVG VGDTCSFAQM DVRQHGHPQW LSAGQTEASV YQQAEDGKTE LSLMHF AIT NPGWQPPRES TAFLGFLKEQ VQRDGAAASL AQGGLLPENA LFTSIQSLQS ESEPLSLIAN VVAGSSCRGP PLPRDLQ GS RHRAEVASAL RSFSPLQPGQ APTGRAHSTM TGSGVDARTA SSGSSVWEGQ LQSLVLSEYA STEMSLHALY MHQLHKQQ A QAEPERHVWH RRESDESGES APDEGGEGAR APQSIPRSAS YPCAAPRPGA PETTALHGGF QRRYGGITDP GTVPRVPSH FSRLPLGGWA EDGQSASRHP EPVPEEGSED ELPPQVHKV UniProtKB: Autophagy-related protein 9A |
-Macromolecule #2: WD repeat domain phosphoinositide-interacting protein 4
Macromolecule | Name: WD repeat domain phosphoinositide-interacting protein 4 type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 39.916539 KDa |
Recombinant expression | Organism: Baculovirus expression vector pFastBac1-HM |
Sequence | String: MTQQPLRGVT SLRFNQDQSC FCCAMETGVR IYNVEPLMEK GHLDHEQVGS MGLVEMLHRS NLLALVGGGS SPKFSEISVL IWDDAREGK DSKEKLVLEF TFTKPVLSVR MRHDKIVIVL KNRIYVYSFP DNPRKLFEFD TRDNPKGLCD LCPSLEKQLL V FPGHKCGS ...String: MTQQPLRGVT SLRFNQDQSC FCCAMETGVR IYNVEPLMEK GHLDHEQVGS MGLVEMLHRS NLLALVGGGS SPKFSEISVL IWDDAREGK DSKEKLVLEF TFTKPVLSVR MRHDKIVIVL KNRIYVYSFP DNPRKLFEFD TRDNPKGLCD LCPSLEKQLL V FPGHKCGS LQLVDLASTK PGTSSAPFTI NAHQSDIACV SLNQPGTVVA SASQKGTLIR LFDTQSKEKL VELRRGTDPA TL YCINFSH DSSFLCASSD KGTVHIFALK DTRLNRRSAL ARVGKVGPMI GQYVDSQWSL ASFTVPAESA CICAFGRNTS KNV NSVIAI CVDGTFHKYV FTPDGNCNRE AFDVYLDICD DDDF UniProtKB: WD repeat domain phosphoinositide-interacting protein 4 |
-Macromolecule #3: Autophagy-related protein 2 homolog A
Macromolecule | Name: Autophagy-related protein 2 homolog A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 213.100281 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSRWLWPWSN CVKERVCRYL LHHYLGHFFQ EHLSLDQLSL DLYKGSVALR DIHLEIWSVN EVLESMESPL ELVEGFVGSI EVAVPWAAL LTDHCTVRVS GLQLTLQPRR GPAPGAADSQ SWASCMTTSL QLAQECLRDG LPEPSEPPQP LEGLEMFAQT I ETVLRRIK ...String: MSRWLWPWSN CVKERVCRYL LHHYLGHFFQ EHLSLDQLSL DLYKGSVALR DIHLEIWSVN EVLESMESPL ELVEGFVGSI EVAVPWAAL LTDHCTVRVS GLQLTLQPRR GPAPGAADSQ SWASCMTTSL QLAQECLRDG LPEPSEPPQP LEGLEMFAQT I ETVLRRIK VTFLDTVVRV EHSPGDGERG VAVEVRVQRL EYCDEAVRDP SQAPPVDVHQ PPAFLHKLLQ LAGVRLHYEE LP AQEEPPE PPLQIGSCSG YMELMVKLKQ NEAFPGPKLE VAGQLGSLHL LLTPRQLQQL QELLSAVSLT DHEGLADKLN KSR PLGAED LWLIEQDLNQ QLQAGAVAEP LSPDPLTNPL LNLDNTDLFF SMAGLTSSVA SALSELSLSD VDLASSVRSD MASR RLSAQ AHPAGKMAPN PLLDTMRPDS LLKMTLGGVT LTLLQTSAPS SGPPDLATHF FTEFDATKDG PFGSRDFHHL RPRFQ RACP CSHVRLTGTA VQLSWELRTG SRGRRTTSME VHFGQLEVLE CLWPRGTSEP EYTEILTFPG TLGSQASARP CAHLRH TQI LRRVPKSRPR RSVACHCHSE LALDLANFQA DVELGALDRL AALLRLATVP AEPPAGLLTE PLPAMEQQTV FRLSAPR AT LRLRFPIADL RPEPDPWAGQ AVRAEQLRLE LSEPQFRSEL SSGPGPPVPT HLELTCSDLH GIYEDGGKPP VPCLRVSK A LDPKSTGRKY FLPQVVVTVN PQSSSTQWEV APEKGEELEL SVESPCELRE PEPSPFSSKR TMYETEEMVI PGDPEEMRT FQSRTLALSR CSLEVILPSV HIFLPSKEVY ESIYNRINND LLMWEPADLL PTPDPAAQPS GFPGPSGFWH DSFKMCKSAF KLANCFDLT PDSDSDDEDA HFFSVGASGG PQAAAPEAPS LHLQSTFSTL VTVLKGRITA LCETKDEGGK RLEAVHGELV L DMEHGTLF SVSQYCGQPG LGYFCLEAEK ATLYHRAAVD DYPLPSHLDL PSFAPPAQLA PTIYPSEEGV TERGASGRKG QG RGPHMLS TAVRIHLDPH KNVKEFLVTL RLHKATLRHY MALPEQSWHS QLLEFLDVLD DPVLGYLPPT VITILHTHLF SCS VDYRPL YLPVRVLITA ETFTLSSNII MDTSTFLLRF ILDDSALYLS DKCEVETLDL RRDYVCVLDV DLLELVIKTW KGST EGKLS QPLFELRCSN NVVHVHSCAD SCALLVNLLQ YVMSTGDLHP PPRPPSPTEI AGQKLSESPA SLPSCPPVET ALINQ RDLA DALLDTERSL RELAQPSGGH LPQASPISVY LFPGERSGAP PPSPPVGGPA GSLGSCSEEK EDEREEEGDG DTLDSD EFC ILDAPGLGIP PRDGEPVVTQ LHPGPIVVRD GYFSRPIGST DLLRAPAHFP VPSTRVVLRE VSLVWHLYGG RDFGPHP GH RARTGLSGPR SSPSRCSGPN RPQNSWRTQG GSGRQHHVLM EIQLSKVSFQ HEVYPAEPAT GPAAPSQELE ERPLSRQV F IVQELEVRDR LASSQINKFL YLHTSERMPR RAHSNMLTIK ALHVAPTTNL GGPECCLRVS LMPLRLNVDQ DALFFLKDF FTSLVAGINP VVPGETSAEA RPETRAQPSS PLEGQAEGVE TTGSQEAPGG GHSPSPPDQQ PIYFREFRFT SEVPIWLDYH GKHVTMDQV GTFAGLLIGL AQLNCSELKL KRLCCRHGLL GVDKVLGYAL NEWLQDIRKN QLPGLLGGVG PMHSVVQLFQ G FRDLLWLP IEQYRKDGRL MRGLQRGAAS FGSSTASAAL ELSNRLVQAI QATAETVYDI LSPAAPVSRS LQDKRSARRL RR GQQPADL REGVAKAYDT VREGILDTAQ TICDVASRGH EQKGLTGAVG GVIRQLPPTV VKPLILATEA TSSLLGGMRN QIV PDAHKD HALKWRSDSA QD UniProtKB: Autophagy-related protein 2 homolog A |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 65.17 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |