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Yorodumi- EMDB-12237: Subtomogram average reconstruction of humanVPS34 complex II bound... -
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-Basic information
Entry | Database: EMDB / ID: EMD-12237 | ||||||||||||||||||||||||||||||
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Title | Subtomogram average reconstruction of humanVPS34 complex II bound to Rab5a on a lipid membrane | ||||||||||||||||||||||||||||||
Map data | A reconstruction of the VPS34 complex II bound to Rab5a on lipid vesicles created by subtomogram averaging. The map was sharpened with LAFTER and resampled onto the map from EMD-12214 | ||||||||||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information lytic vacuole / maintenance of Golgi location / regulation of protein serine/threonine kinase activity / autophagy of peroxisome / regulation of endosome size / postsynaptic early endosome / nucleus-vacuole junction / cellular response to aluminum ion / cytoplasmic side of early endosome membrane / Toll Like Receptor 9 (TLR9) Cascade ...lytic vacuole / maintenance of Golgi location / regulation of protein serine/threonine kinase activity / autophagy of peroxisome / regulation of endosome size / postsynaptic early endosome / nucleus-vacuole junction / cellular response to aluminum ion / cytoplasmic side of early endosome membrane / Toll Like Receptor 9 (TLR9) Cascade / protein lipidation / Synthesis of PIPs at the late endosome membrane / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III / synaptic vesicle recycling / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation by host of viral genome replication / response to mitochondrial depolarisation / amyloid-beta clearance by transcytosis / positive regulation of attachment of mitotic spindle microtubules to kinetochore / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization / modulation by host of viral process / Synthesis of PIPs at the Golgi membrane / positive regulation of autophagosome assembly / engulfment of apoptotic cell / regulation of autophagosome assembly / negative regulation of autophagosome assembly / receptor catabolic process / phosphatidylinositol kinase activity / protein localization to phagophore assembly site / protein targeting to vacuole / protein targeting to lysosome / suppression by virus of host autophagy / regulation of filopodium assembly / RAB geranylgeranylation / multivesicular body sorting pathway / early endosome to late endosome transport / cellular response to nitrogen starvation / late endosome to vacuole transport / RAB GEFs exchange GTP for GDP on RABs / double-strand break repair via classical nonhomologous end joining / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / early phagosome / SMAD protein signal transduction / phosphatidylinositol-mediated signaling / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / response to iron(II) ion / negative regulation of programmed cell death / TBC/RABGAPs / centrosome cycle / SNARE complex assembly / positive regulation of autophagosome maturation / autolysosome / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / regulation of synaptic vesicle exocytosis / 1-phosphatidylinositol-3-kinase activity / Macroautophagy / spindle organization / mitotic metaphase chromosome alignment / lysosome organization / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of cardiac muscle hypertrophy / positive regulation of exocytosis / p38MAPK cascade / axoneme / autophagosome maturation / autophagosome membrane / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / mitophagy / autophagosome assembly / chromosome, centromeric region / RHO GTPases Activate NADPH Oxidases / PI3K Cascade / neuron development / autophagosome / canonical Wnt signaling pathway / negative regulation of reactive oxygen species metabolic process / response to vitamin E / regulation of macroautophagy / endomembrane system / cellular response to glucose starvation / cellular defense response / phosphatidylinositol 3-kinase binding / phagocytic vesicle / amyloid-beta metabolic process / axon terminus / phagocytosis / positive regulation of autophagy / positive regulation of intrinsic apoptotic signaling pathway / JNK cascade / somatodendritic compartment / Prevention of phagosomal-lysosomal fusion / cellular response to epidermal growth factor stimulus / ruffle Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 13.3 Å | ||||||||||||||||||||||||||||||
Authors | Tremel S / Ohashi Y / Morado DR / Bertram J / Perisic O / Brandt LTL / von Wrisberg M-K / Chen ZA / Maslen SL / Kovtun O ...Tremel S / Ohashi Y / Morado DR / Bertram J / Perisic O / Brandt LTL / von Wrisberg M-K / Chen ZA / Maslen SL / Kovtun O / Skehel M / Rappsilber J / Lang K / Munro S / Briggs JAG / Williams RL | ||||||||||||||||||||||||||||||
Funding support | United Kingdom, Germany, 9 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis for VPS34 kinase activation by Rab1 and Rab5 on membranes. Authors: Shirley Tremel / Yohei Ohashi / Dustin R Morado / Jessie Bertram / Olga Perisic / Laura T L Brandt / Marie-Kristin von Wrisberg / Zhuo A Chen / Sarah L Maslen / Oleksiy Kovtun / Mark Skehel ...Authors: Shirley Tremel / Yohei Ohashi / Dustin R Morado / Jessie Bertram / Olga Perisic / Laura T L Brandt / Marie-Kristin von Wrisberg / Zhuo A Chen / Sarah L Maslen / Oleksiy Kovtun / Mark Skehel / Juri Rappsilber / Kathrin Lang / Sean Munro / John A G Briggs / Roger L Williams / Abstract: The lipid phosphatidylinositol-3-phosphate (PI3P) is a regulator of two fundamental but distinct cellular processes, endocytosis and autophagy, so its generation needs to be under precise temporal ...The lipid phosphatidylinositol-3-phosphate (PI3P) is a regulator of two fundamental but distinct cellular processes, endocytosis and autophagy, so its generation needs to be under precise temporal and spatial control. PI3P is generated by two complexes that both contain the lipid kinase VPS34: complex II on endosomes (VPS34/VPS15/Beclin 1/UVRAG), and complex I on autophagosomes (VPS34/VPS15/Beclin 1/ATG14L). The endosomal GTPase Rab5 binds complex II, but the mechanism of VPS34 activation by Rab5 has remained elusive, and no GTPase is known to bind complex I. Here we show that Rab5a-GTP recruits endocytic complex II to membranes and activates it by binding between the VPS34 C2 and VPS15 WD40 domains. Electron cryotomography of complex II on Rab5a-decorated vesicles shows that the VPS34 kinase domain is released from inhibition by VPS15 and hovers over the lipid bilayer, poised for catalysis. We also show that the GTPase Rab1a, which is known to be involved in autophagy, recruits and activates the autophagy-specific complex I, but not complex II. Both Rabs bind to the same VPS34 interface but in a manner unique for each. These findings reveal how VPS34 complexes are activated on membranes by specific Rab GTPases and how they are recruited to unique cellular locations. | ||||||||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12237.map.gz | 113.4 MB | EMDB map data format | |
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Header (meta data) | emd-12237-v30.xml emd-12237.xml | 30.5 KB 30.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12237_fsc.xml | 7.5 KB | Display | FSC data file |
Images | emd_12237.png | 136.8 KB | ||
Others | emd_12237_half_map_1.map.gz emd_12237_half_map_2.map.gz | 14.5 MB 14.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12237 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12237 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12237.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | A reconstruction of the VPS34 complex II bound to Rab5a on lipid vesicles created by subtomogram averaging. The map was sharpened with LAFTER and resampled onto the map from EMD-12214 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0665 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: A reconstruction of the VPS34 complex II bound...
File | emd_12237_half_map_1.map | ||||||||||||
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Annotation | A reconstruction of the VPS34 complex II bound to Rab5a on lipid vesicles created by subtomogram averaging. The even half map, before LAFTER sharpening. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: A reconstruction of the VPS34 complex II bound...
File | emd_12237_half_map_2.map | ||||||||||||
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Annotation | A reconstruction of the VPS34 complex II bound to Rab5a on lipid vesicles created by subtomogram averaging. The odd half map, before LAFTER sharpening. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG) bound to human...
Entire | Name: human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG) bound to human Rab5a on lipid vesicles |
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Components |
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-Supramolecule #1: human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG) bound to human...
Supramolecule | Name: human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG) bound to human Rab5a on lipid vesicles type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: The subunits were expressed using transient transfection in HEK293T cells. Cells were transfected with three plasmids: pYO1025 (encoding VPS34 and VPS15 in a pCAG backbone), pYO1124 ...Details: The subunits were expressed using transient transfection in HEK293T cells. Cells were transfected with three plasmids: pYO1025 (encoding VPS34 and VPS15 in a pCAG backbone), pYO1124 (encoding UVGRAG 1-464 fused to the BATS of ATG14, residues 413-492 in pVAG) and pYO1006 (Beclin1 in pCAG) |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 392.16 KDa |
-Macromolecule #1: UV radiation resistance-associated gene protein
Macromolecule | Name: UV radiation resistance-associated gene protein / type: protein_or_peptide / ID: 1 / Details: Human UVRAG / Enantiomer: LEVO / EC number: phosphatidylinositol 3-kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSASASVGGP VPQPPPGPAA ALPPGSAARA LHVELPSQQR RLRHLRNIAA RNIVNRNGHQ LLDTYFTLHL CSTEKIYKEF YRSEVIKNS LNPTWRSLDF GIMPDRLDTS VSCFVVKIWG GKENIYQLLI EWKVCLDGLK YLGQQIHARN QNEIIFGLND G YYGAPFEH ...String: MSASASVGGP VPQPPPGPAA ALPPGSAARA LHVELPSQQR RLRHLRNIAA RNIVNRNGHQ LLDTYFTLHL CSTEKIYKEF YRSEVIKNS LNPTWRSLDF GIMPDRLDTS VSCFVVKIWG GKENIYQLLI EWKVCLDGLK YLGQQIHARN QNEIIFGLND G YYGAPFEH KGYSNAQKTI LLQVDQNCVR NSYDVFSLLR LHRAQCAIKQ TQVTVQKIGK EIEEKLRLTS TSNELKKKSE CL QLKILVL QNELERQKKA LGREVALLHK QQIALQDKGS AFSAEHLKLQ LQKESLNELR KECTAKRELF LKTNAQLTIR CRQ LLSELS YIYPIDLNEH KDYFVCGVKL PNSEDFQAKD DGSIAVALGY TAHLVSMISF FLQVPLRYPI IHKGSRSTIK DNIN DKLTE KEREFPLYPK GGEKLQFDYG VYLLNKNIAQ LRYQHGLGTP DLRQTLPNLK NFMEHGLMVR CDRHHTSSAI PVPKR QSSI FGGADVGFSG GIPSPDKGHR KRASSENERL QYKTPPPSYN SALAQPVTTV PSMGETERKI TSLSSSLDTS LDFSKE NKK KGEDLVGSLN GGHANVHPSQ EQGEALSGHR ATVNGTLLPS EQAGSASVQL PGEFHPVSEA ELCCTVEQAE EIIGLEA TG FASGDQLEAF NCIPVDSAVA VECDEQVLGE FEEFSRRIYA LNENVSSFRR PRRSSDK |
-Macromolecule #2: Phosphatidylinositol 3-kinase catalytic subunit type 3
Macromolecule | Name: Phosphatidylinositol 3-kinase catalytic subunit type 3 type: protein_or_peptide / ID: 2 / Details: human vps34 / Enantiomer: LEVO / EC number: phosphatidylinositol 3-kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGEAEKFHYI YSCDLDINVQ LKIGSLEGKR EQKSYKAVLE DPMLKFSGLY QETCSDLYVT CQVFAEGKPL ALPVRTSYKA FSTRWNWNE WLKLPVKYPD LPRNAQVALT IWDVYGPGKA VPVGGTTVSL FGKYGMFRQG MHDLKVWPNV EADGSEPTKT P GRTSSTLS ...String: MGEAEKFHYI YSCDLDINVQ LKIGSLEGKR EQKSYKAVLE DPMLKFSGLY QETCSDLYVT CQVFAEGKPL ALPVRTSYKA FSTRWNWNE WLKLPVKYPD LPRNAQVALT IWDVYGPGKA VPVGGTTVSL FGKYGMFRQG MHDLKVWPNV EADGSEPTKT P GRTSSTLS EDQMSRLAKL TKAHRQGHMV KVDWLDRLTF REIEMINESE KRSSNFMYLM VEFRCVKCDD KEYGIVYYEK DG DESSPIL TSFELVKVPD PQMSMENLVE SKHHKLARSL RSGPSDHDLK PNAATRDQLN IIVSYPPTKQ LTYEEQDLVW KFR YYLTNQ EKALTKFLKC VNWDLPQEAK QALELLGKWK PMDVEDSLEL LSSHYTNPTV RRYAVARLRQ ADDEDLLMYL LQLV QALKY ENFDDIKNGL EPTKKDSQSS VSENVSNSGI NSAEIDSSQI ITSPLPSVSS PPPASKTKEV PDGENLEQDL CTFLI SRAC KNSTLANYLY WYVIVECEDQ DTQQRDPKTH EMYLNVMRRF SQALLKGDKS VRVMRSLLAA QQTFVDRLVH LMKAVQ RES GNRKKKNERL QALLGDNEKM NLSDVELIPL PLEPQVKIRG IIPETATLFK SALMPAQLFF KTEDGGKYPV IFKHGDD LR QDQLILQIIS LMDKLLRKEN LDLKLTPYKV LATSTKHGFM QFIQSVPVAE VLDTEGSIQN FFRKYAPSEN GPNGISAE V MDTYVKSCAG YCVITYILGV GDRHLDNLLL TKTGKLFHID FGYILGRDPK PLPPPMKLNK EMVEGMGGTQ SEQYQEFRK QCYTAFLHLR RYSNLILNLF SLMVDANIPD IALEPDKTVK KVQDKFRLDL SDEEAVHYMQ SLIDESVHAL FAAVVEQIHK FAQYWRK |
-Macromolecule #3: Phosphoinositide 3-kinase regulatory subunit 4
Macromolecule | Name: Phosphoinositide 3-kinase regulatory subunit 4 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGNQLAGIAP SQILSVESYF SDIHDFEYDK SLGSTRFFKV ARAKHREGLV VVKVFAIQDP TLPLTSYKQE LEELKIRLNS AQNCLPFQK ASEKASEKAA MLFRQYVRDN LYDRISTRPF LNNIEKRWIA FQILTAVDQA HKSGVRHGDI KTENVMVTSW N WVLLTDFA ...String: MGNQLAGIAP SQILSVESYF SDIHDFEYDK SLGSTRFFKV ARAKHREGLV VVKVFAIQDP TLPLTSYKQE LEELKIRLNS AQNCLPFQK ASEKASEKAA MLFRQYVRDN LYDRISTRPF LNNIEKRWIA FQILTAVDQA HKSGVRHGDI KTENVMVTSW N WVLLTDFA SFKPTYLPED NPADFNYFFD TSRRRTCYIA PERFVDGGMF ATELEYMRDP STPLVDLNSN QRTRGELKRA MD IFSAGCV IAELFTEGVP LFDLSQLLAY RNGHFFPEQV LNKIEDHSIR ELVTQMIHRE PDKRLEAEDY LKQQRGNAFP EIF YTFLQP YMAQFAKETF LSADERILVI RKDLGNIIHN LCGHDLPEKA EGEPKENGLV ILVSVITSCL QTLKYCDSKL AALE LILHL APRLSVEILL DRITPYLLHF SNDSVPRVRA EALRTLTKVL ALVKEVPRND INIYPEYILP GIAHLAQDDA TIVRL AYAE NIALLAETAL RFLELVQLKN LNMENDPNNE EIDEVTHPNG NYDTELQALH EMVQQKVVTL LSDPENIVKQ TLMENG ITR LCVFFGRQKA NDVLLSHMIT FLNDKNDWHL RGAFFDSIVG VAAYVGWQSS SILKPLLQQG LSDAEEFVIV KALYALT CM CQLGLLQKPH VYEFASDIAP FLCHPNLWIR YGAVGFITVV ARQISTADVY CKLMPYLDPY ITQPIIQIER KLVLLSVL K EPVSRSIFDY ALRSKDITSL FRHLHMRQKK RNGSLPDCPP PEDPAIAQLL KKLLSQGMTE EEEDKLLALK DFMMKSNKA KANIVDQSHL HDSSQKGVID LAALGITGRQ VDLVKTKQEP DDKRARKHVK QDSNVNEEWK SMFGSLDPPN MPQALPKGSD QEVIQTGKP PRSESSAGIC VPLSTSSQVP EVTTVQNKKP VIPVLSSTIL PSTYQIRITT CKTELQQLIQ QKREQCNAER I AKQMMENA EWESKPPPPG WRPKGLLVAH LHEHKSAVNR IRVSDEHSLF ATCSNDGTVK IWNSQKMEGK TTTTRSILTY SR IGGRVKT LTFCQGSHYL AIASDNGAVQ LLGIEASKLP KSPKIHPLQS RILDQKEDGC VVDMHHFNSG AQSVLAYATV NGS LVGWDL RSSSNAWTLK HDLKSGLITS FAVDIHQCWL CIGTSSGTMA CWDMRFQLPI SSHCHPSRAR IRRLSMHPLY QSWV IAAVQ GNNEVSMWDM ETGDRRFTLW ASSAPPLSEL QPSPHSVHGI YCSPADGNPI LLTAGSDMKI RFWDLAYPER SYVVA GSTS SPSVSYYRKI IEGTEVVQEI QNKQKVGPSD DTPRRGPESL PVGHHDIITD VATFQTTQGF IVTASRDGIV KVWKSR PTT ASENLYFQ |
-Macromolecule #4: Beclin-1
Macromolecule | Name: Beclin-1 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MEGSKTSNNS TMQVSFVCQR CSQPLKLDTS FKILDRVTIQ ELTAPLLTTA QAKPGETQEE ETNSGEEPFI ETPRQDGVSR RFIPPARMM STESANSFTL IGEASDGGTM ENLSRRLKVT GDLFDIMSGQ TDVDHPLCEE CTDTLLDQLD TQLNVTENEC Q NYKRCLEI ...String: MEGSKTSNNS TMQVSFVCQR CSQPLKLDTS FKILDRVTIQ ELTAPLLTTA QAKPGETQEE ETNSGEEPFI ETPRQDGVSR RFIPPARMM STESANSFTL IGEASDGGTM ENLSRRLKVT GDLFDIMSGQ TDVDHPLCEE CTDTLLDQLD TQLNVTENEC Q NYKRCLEI LEQMNEDDSE QLQMELKELA LEEERLIQEL EDVEKNRKIV AENLEKVQAE AERLDQEEAQ YQREYSEFKR QQ LELDDEL KSVENQMRYA QTQLDKLKKT NVFNATFHIW HSGQFGTINN FRLGRLPSVP VEWNEINAAW GQTVLLLHAL ANK MGLKFQ RYRLVPYGNH SYLESLTDKS KELPLYCSGG LRFFWDNKFD HAMVAFLDCV QQFKEEVEKG ETRFCLPYRM DVEK GKIED TGGSGGSYSI KTQFNSEEQW TKALKFMLTN LKWGLAWVSS QFYNK |
-Macromolecule #5: Ras-related protein Rab-5A
Macromolecule | Name: Ras-related protein Rab-5A / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO / EC number: small monomeric GTPase |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: NKISQFKLVL LGESAVGKSS LVLRFVKGQF HEFQESTIGA AFLTQTVSLD DTTVKFEIWD TAGLERYHSL APMYYRGAQA AIVVYDITN EESFARAKNW VKELQRQASP NIVIALSGNK ADLANKRAVD FQEAQSYADD NSLLFMETSA KTSMNVNEIF M AIAKKLPK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | 3D array |
-Sample preparation
Concentration | 6.2 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: Quorum SC7620 | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 316 K / Instrument: FEI VITROBOT MARK I / Details: blot force was 20, with a blot time of 6 s. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 6000 pixel / Digitization - Dimensions - Height: 4000 pixel / Digitization - Sampling interval: 5.0 µm / Number grids imaged: 1 / Average exposure time: 0.55 sec. / Average electron dose: 2.99 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model |
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Details | The model in PDB 7BL1 was built and refined into the subtomogram averaged density map in EMD-12214. This map had the membrane portion of the reconstruction masked out. The reconstruction described in the final reconstruction described above includes the membrane that was masked out in EMD-12214. The final reconstruction was sharpened in LAFTER then resampled onto the density of EMD-12214, for ease of fitting the 7BL1 model. | ||||||||||||||
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 320 / Target criteria: Correlation coefficient |