+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17828 | ||||||||||||
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Title | Cytoplasmic dynein-1 motor domain bound to LIS1 | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Dynein / AAA-Atpase / p150 / LIS1 / MOTOR PROTEIN | ||||||||||||
Function / homology | Function and homology information corpus callosum morphogenesis / establishment of planar polarity of embryonic epithelium / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / interneuron migration / 1-alkyl-2-acetylglycerophosphocholine esterase complex / maintenance of centrosome location / microtubule sliding / platelet activating factor metabolic process / acrosome assembly ...corpus callosum morphogenesis / establishment of planar polarity of embryonic epithelium / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / interneuron migration / 1-alkyl-2-acetylglycerophosphocholine esterase complex / maintenance of centrosome location / microtubule sliding / platelet activating factor metabolic process / acrosome assembly / radial glia-guided pyramidal neuron migration / microtubule organizing center organization / cerebral cortex neuron differentiation / central region of growth cone / positive regulation of intracellular transport / positive regulation of embryonic development / reelin-mediated signaling pathway / regulation of metaphase plate congression / establishment of centrosome localization / positive regulation of cytokine-mediated signaling pathway / cortical microtubule organization / establishment of spindle localization / astral microtubule / positive regulation of spindle assembly / layer formation in cerebral cortex / nuclear membrane disassembly / auditory receptor cell development / positive regulation of dendritic spine morphogenesis / vesicle transport along microtubule / stem cell division / stereocilium / P-body assembly / myeloid leukocyte migration / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / microtubule plus-end binding / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / negative regulation of JNK cascade / retrograde axonal transport / dynein light intermediate chain binding / brain morphogenesis / motile cilium / nuclear migration / osteoclast development / microtubule associated complex / kinesin complex / dynein intermediate chain binding / dynein complex binding / cochlea development / transmission of nerve impulse / cell leading edge / germ cell development / dynactin binding / establishment of mitotic spindle orientation / phospholipase binding / neuromuscular process controlling balance / neuroblast proliferation / protein secretion / positive regulation of axon extension / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / microtubule-based process / COPI-mediated anterograde transport / lipid catabolic process / regulation of microtubule cytoskeleton organization / stress granule assembly / cytoplasmic microtubule organization / Mitotic Prometaphase / regulation of mitotic spindle organization / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / JNK cascade / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Anchoring of the basal body to the plasma membrane / MHC class II antigen presentation / positive regulation of mitotic cell cycle / adult locomotory behavior / AURKA Activation by TPX2 / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / hippocampus development / phosphoprotein binding / neuron migration / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / cerebral cortex development / microtubule cytoskeleton organization / kinetochore / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Singh K / Lau CK / Manigrasso G / Gassmann R / Carter AP | ||||||||||||
Funding support | United Kingdom, European Union, 3 items
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Citation | Journal: Science / Year: 2024 Title: Molecular mechanism of dynein-dynactin complex assembly by LIS1. Authors: Kashish Singh / Clinton K Lau / Giulia Manigrasso / José B Gama / Reto Gassmann / Andrew P Carter / Abstract: Cytoplasmic dynein is a microtubule motor vital for cellular organization and division. It functions as a ~4-megadalton complex containing its cofactor dynactin and a cargo-specific coiled-coil ...Cytoplasmic dynein is a microtubule motor vital for cellular organization and division. It functions as a ~4-megadalton complex containing its cofactor dynactin and a cargo-specific coiled-coil adaptor. However, how dynein and dynactin recognize diverse adaptors, how they interact with each other during complex formation, and the role of critical regulators such as lissencephaly-1 (LIS1) protein (LIS1) remain unclear. In this study, we determined the cryo-electron microscopy structure of dynein-dynactin on microtubules with LIS1 and the lysosomal adaptor JIP3. This structure reveals the molecular basis of interactions occurring during dynein activation. We show how JIP3 activates dynein despite its atypical architecture. Unexpectedly, LIS1 binds dynactin's p150 subunit, tethering it along the length of dynein. Our data suggest that LIS1 and p150 constrain dynein-dynactin to ensure efficient complex formation. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17828.map.gz | 77.8 MB | EMDB map data format | |
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Header (meta data) | emd-17828-v30.xml emd-17828.xml | 23.3 KB 23.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17828_fsc.xml | 19.1 KB | Display | FSC data file |
Images | emd_17828.png | 51.4 KB | ||
Masks | emd_17828_msk_1.map | 83.7 MB | Mask map | |
Filedesc metadata | emd-17828.cif.gz | 9.2 KB | ||
Others | emd_17828_additional_1.map.gz emd_17828_half_map_1.map.gz emd_17828_half_map_2.map.gz | 77.9 MB 77.8 MB 77.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17828 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17828 | HTTPS FTP |
-Related structure data
Related structure data | 8pqyMC 8pqvC 8pqwC 8pqzC 8pr0C 8pr1C 8pr2C 8pr3C 8pr4C 8pr5C 8ptkC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17828.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17828_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: unsharpened map
File | emd_17828_additional_1.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_17828_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17828_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cytoplasmic dynein-1 bound to LIS1
Entire | Name: Cytoplasmic dynein-1 bound to LIS1 |
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Components |
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-Supramolecule #1: Cytoplasmic dynein-1 bound to LIS1
Supramolecule | Name: Cytoplasmic dynein-1 bound to LIS1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Cytoplasmic dynein 1 heavy chain 1
Macromolecule | Name: Cytoplasmic dynein 1 heavy chain 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 533.055125 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MSEPGGGGGE DGSAGLEVSA VQNVADVSVL QKHLRKLVPL LLEDGGEAPA ALEAALEEKS ALEQMRKFLS DPQVHTVLVE RSTLKEDVG DEGEEEKEFI SYNINIDIHY GVKSNSLAFI KRTPVIDADK PVSSQLRVLT LSEDSPYETL HSFISNAVAP F FKSYIRES ...String: MSEPGGGGGE DGSAGLEVSA VQNVADVSVL QKHLRKLVPL LLEDGGEAPA ALEAALEEKS ALEQMRKFLS DPQVHTVLVE RSTLKEDVG DEGEEEKEFI SYNINIDIHY GVKSNSLAFI KRTPVIDADK PVSSQLRVLT LSEDSPYETL HSFISNAVAP F FKSYIRES GKADRDGDKM APSVEKKIAE LEMGLLHLQQ NIEIPEISLP IHPMITNVAK QCYERGEKPK VTDFGDKVED PT FLNQLQS GVNRWIREIQ KVTKLDRDPA SGTALQEISF WLNLERALYR IQEKRESPEV LLTLDILKHG KRFHATVSFD TDT GLKQAL ETVNDYNPLM KDFPLNDLLS ATELDKIRQA LVAIFTHLRK IRNTKYPIQR ALRLVEAISR DLSSQLLKVL GTRK LMHVA YEEFEKVMVA CFEVFQTWDD EYEKLQVLLR DIVKRKREEN LKMVWRINPA HRKLQARLDQ MRKFRRQHEQ LRAVI VRVL RPQVTAVAQQ NQGEVPEPQD MKVAEVLFDA ADANAIEEVN LAYENVKEVD GLDVSKEGTE AWEAAMKRYD ERIDRV ETR ITARLRDQLG TAKNANEMFR IFSRFNALFV RPHIRGAIRE YQTQLIQRVK DDIESLHDKF KVQYPQSQAC KMSHVRD LP PVSGSIIWAK QIDRQLTAYM KRVEDVLGKG WENHVEGQKL KQDGDSFRMK LNTQEIFDDW ARKVQQRNLG VSGRIFTI E STRVRGRTGN VLKLKVNFLP EIITLSKEVR NLKWLGFRVP LAIVNKAHQA NQLYPFAISL IESVRTYERT CEKVEERNT ISLLVAGLKK EVQALIAEGI ALVWESYKLD PYVQRLAETV FNFQEKVDDL LIIEEKIDLE VRSLETCMYD HKTFSEILNR VQKAVDDLN LHSYSNLPIW VNKLDMEIER ILGVRLQAGL RAWTQVLLGQ AEDKAEVDMD TDAPQVSHKP GGEPKIKNVV H ELRITNQV IYLNPPIEEC RYKLYQEMFA WKMVVLSLPR IQSQRYQVGV HYELTEEEKF YRNALTRMPD GPVALEESYS AV MGIVSEV EQYVKVWLQY QCLWDMQAEN IYNRLGEDLN KWQALLVQIR KARGTFDNAE TKKEFGPVVI DYGKVQSKVN LKY DSWHKE VLSKFGQMLG SNMTEFHSQI SKSRQELEQH SVDTASTSDA VTFITYVQSL KRKIKQFEKQ VELYRNGQRL LEKQ RFQFP PSWLYIDNIE GEWGAFNDIM RRKDSAIQQQ VANLQMKIVQ EDRAVESRTT DLLTDWEKTK PVTGNLRPEE ALQAL TIYE GKFGRLKDDR EKCAKAKEAL ELTDTGLLSG SEERVQVALE ELQDLKGVWS ELSKVWEQID QMKEQPWVSV QPRKLR QNL DALLNQLKSF PARLRQYASY EFVQRLLKGY MKINMLVIEL KSEALKDRHW KQLMKRLHVN WVVSELTLGQ IWDVDLQ KN EAIVKDVLLV AQGEMALEEF LKQIREVWNT YELDLVNYQN KCRLIRGWDD LFNKVKEHIN SVSAMKLSPY YKVFEEDA L SWEDKLNRIM ALFDVWIDVQ RRWVYLEGIF TGSADIKHLL PVETQEFQSI STEFLALMKK VSKSPLVMDV LNIQGVQRS LERLADLLGE IQKALGEYLE RERSSFPRFY FVGDEDLLEI IGNSKNVAKL QKHFKKMFAG VSSIILNEDN SVVLGISSRE GEEVMFKTP VSITEHPKIN EWLTLVEKEM RVTLAKLLAE SVTEVEIFGK ATSIDPNTYI TWIDKYQAQL VVLSAQIAWS E NVETALSS MGGGGDAAPL HSVLSNVEVT LNVLADSVLM EQPPLRRRKL EHLITELVHQ RDVTRSLIKS KIDNAKSFEW LS QMRFYFD PKQTDVLQQL SIQMANAKFN YGFEYLGVQD KLVQTPLTDR CYLTMTQALE ARLGGSPFGP AGTGKTESVK ALG HQLGRF VLVFNCDETF DFQAMGRIFV GLCQVGAWGC FDEFNRLEER MLSAVSQQVQ CIQEALREHS NPNYDKTSAP ITCE LLNKQ VKVSPDMAIF ITMNPGYAGR SNLPDNLKKL FRSLAMTKPD RQLIAQVMLY SQGFRTAEVL ANKIVPFFKL CDEQL SSQS HYDFGLRALK SVLVSAGNVK RERIQKIKRE KEERGEAVDE GEIAENLPEQ EILIQSVCET MVPKLVAEDI PLLFSL LSD VFPGVQYHRG EMTALREELK KVCQEMYLTY GDGEEVGGMW VEKVLQLYQI TQINHGLMMV GPSGSGKSMA WRVLLKA LE RLEGVEGVAH IIDPKAISKD HLYGTLDPNT REWTDGLFTH VLRKIIDSVR GELQKRQWIV FDGDVDPEWV ENLNSVLD D NKLLTLPNGE RLSLPPNVRI MFEVQDLKYA TLATVSRCGM VWFSEDVLST DMIFNNFLAR LRSIPLDEGE DEAQRRRKG KEDEGEEAAS PMLQIQRDAA TIMQPYFTSN GLVTKALEHA FQLEHIMDLT RLRCLGSLFS MLHQACRNVA QYNANHPDFP MQIEQLERY IQRYLVYAIL WSLSGDSRLK MRAELGEYIR RITTVPLPTA PNIPIIDYEV SISGEWSPWQ AKVPQIEVET H KVAAPDVV VPTLDTVRHE ALLYTWLAEH KPLVLCGPPG SGKTMTLFSA LRALPDMEVV GLNFSSATTP ELLLKTFDHY CE YRRTPNG VVLAPVQLGK WLVLFCDEIN LPDMDKYGTQ RVISFIRQMV EHGGFYRTSD QTWVKLERIQ FVGACNPPTD PGR KPLSHR FLRHVPVVYV DYPGPASLTQ IYGTFNRAML RLIPSLRTYA EPLTAAMVEF YTMSQERFTQ DTQPHYIYSP REMT RWVRG IFEALRPLET LPVEGLIRIW AHEALRLFQD RLVEDEERRW TDENIDTVAL KHFPNIDREK AMSRPILYSN WLSKD YIPV DQEELRDYVK ARLKVFYEEE LDVPLVLFNE VLDHVLRIDR IFRQPQGHLL LIGVSGAGKT TLSRFVAWMN GLSVYQ IKV HRKYTGEDFD EDLRTVLRRS GCKNEKIAFI MDESNVLDSG FLERMNTLLA NGEVPGLFEG DEYATLMTQC KEGAQKE GL MLDSHEELYK WFTSQVIRNL HVVFTMNPSS EGLKDRAATS PALFNRCVLN WFGDWSTEAL YQVGKEFTSK MDLEKPNY I VPDYMPVVYD KLPQPPSHRE AIVNSCVFVH QTLHQANARL AKRGGRTMAI TPRHYLDFIN HYANLFHEKR SELEEQQMH LNVGLRKIKE TVDQVEELRR DLRIKSQELE VKNAAANDKL KKMVKDQQEA EKKKVMSQEI QEQLHKQQEV IADKQMSVKE DLDKVEPAV IEAQNAVKSI KKQHLVEVRS MANPPAAVKL ALESICLLLG ESTTDWKQIR SIIMRENFIP TIVNFSAEEI S DAIREKMK KNYMSNPSYN YEIVNRASLA CGPMVKWAIA QLNYADMLKR VEPLRNELQK LEDDAKDNQQ KANEVEQMIR DL EASIARY KEEYAVLISE AQAIKADLAA VEAKVNRSTA LLKSLSAERE RWEKTSETFK NQMSTIAGDC LLSAAFIAYA GYF DQQMRQ NLFTTWSHHL QQANIQFRTD IARTEYLSNA DERLRWQASS LPADDLCTEN AIMLKRFNRY PLIIDPSGQA TEFI MNEYK DRKITRTSFL DDAFRKNLES ALRFGNPLLV QDVESYDPVL NPVLNREVRR TGGRVLITLG DQDIDLSPSF VIFLS TRDP TVEFPPDLCS RVTFVNFTVT RSSLQSQCLN EVLKAERPDV DEKRSDLLKL QGEFQLRLRQ LEKSLLQALN EVKGRI LDD DTIITTLENL KREAAEVTRK VEETDIVMQE VETVSQQYLP LSTACSSIYF TMESLKQIHF LYQYSLQFFL DIYHNVL YE NPNLKGVTDH TQRLSIITKD LFQVAFNRVA RGMLHQDHIT FAMLLARIKL KGTVGEPTYD AEFQHFLRGN EIVLSAGS T PRIQGLTVEQ AEAVVRLSCL PAFKDLIAKV QADEQFGIWL DSSSPEQTVP YLWSEETPAT PIGQAIHRLL LIQAFRPDR LLAMAHMFVS TNLGESFMSI MEQPLDLTHI VGTEVKPNTP VLMCSVPGYD ASGHVEDLAA EQNTQITSIA IGSAEGFNQA DKAINTAVK SGRWVMLKNV HLAPGWLMQL EKKLHSLQPH ACFRLFLTME INPKVPVNLL RAGRIFVFEP PPGVKANMLR T FSSIPVSR ICKSPNERAR LYFLLAWFHA IIQERLRYAP LGWSKKYEFG ESDLRSACDT VDTWLDDTAK GRQNISPDKI PW SALKTLM AQSIYGGRVD NEFDQRLLNT FLERLFTTRS FDSEFKLACK VDGHKDIQMP DGIRREEFVQ WVELLPDTQT PSW LGLPNN AERVLLTTQG VDMISKMLKM QMLEDEDDLA YAETEKKTRT DSTSDGRPAW MRTLHTTASN WLHLIPQTLS HLKR TVENI KDPLFRFFER EVKMGAKLLQ DVRQDLADVV QVCEGKKKQT NYLRTLINEL VKGILPRSWS HYTVPAGMTV IQWVS DFSE RIKQLQNISL AAASGGAKEL KNIHVCLGGL FVPEAYITAT RQYVAQANSW SLEELCLEVN VTTSQGATLD ACSFGV TGL KLQGATCNNN KLSLSNAIST ALPLTQLRWV KQTNTEKKAS VVTLPVYLNF TRADLIFTVD FEIATKEDPR SFYERGV AV LCTE UniProtKB: Cytoplasmic dynein 1 heavy chain 1 |
-Macromolecule #2: Platelet-activating factor acetylhydrolase IB subunit beta
Macromolecule | Name: Platelet-activating factor acetylhydrolase IB subunit beta type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 46.709984 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MVLSQRQRDE LNRAIADYLR SNGYEEAYSV FKKEAELDVN EELDKKYAGL LEKKWTSVIR LQKKVMELES KLNEAKEEFT SGGPLGQKR DPKEWIPRPP EKYALSGHRS PVTRVIFHPV FSVMVSASED ATIKVWDYET GDFERTLKGH TDSVQDISFD H SGKLLASC ...String: MVLSQRQRDE LNRAIADYLR SNGYEEAYSV FKKEAELDVN EELDKKYAGL LEKKWTSVIR LQKKVMELES KLNEAKEEFT SGGPLGQKR DPKEWIPRPP EKYALSGHRS PVTRVIFHPV FSVMVSASED ATIKVWDYET GDFERTLKGH TDSVQDISFD H SGKLLASC SADMTIKLWD FQGFECIRTM HGHDHNVSSV AIMPNGDHIV SASRDKTIKM WEVQTGYCVK TFTGHREWVR MV RPNQDGT LIASCSNDQT VRVWVVATKE CKAELREHEH VVECISWAPE SSYSSISEAT GSETKKSGKP GPFLLSGSRD KTI KMWDVS TGMCLMTLVG HDNWVRGVLF HSGGKFILSC ADDKTLRVWD YKNKRCMKTL NAHEHFVTSL DFHKTAPYVV TGSV DQTVK VWECR UniProtKB: Platelet-activating factor acetylhydrolase IB subunit beta |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 3 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-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 / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |