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- EMDB-27783: Structure of human cytoplasmic dynein-1 bound to one Lis1 -

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Basic information

Entry
Database: EMDB / ID: EMD-27783
TitleStructure of human cytoplasmic dynein-1 bound to one Lis1
Map data
Sample
  • Complex: Human cytoplasmic dynein-1 bound to one Lis1
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1
    • Protein or peptide: Platelet-activating factor acetylhydrolase IB subunit beta
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
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 / cytoplasmic microtubule organization / regulation of microtubule cytoskeleton organization / stress granule assembly / 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
Dynein regulator LIS1 / LIS1, N-terminal / LisH / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Lissencephaly type-1-like homology motif / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / P-loop containing dynein motor region ...Dynein regulator LIS1 / LIS1, N-terminal / LisH / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Lissencephaly type-1-like homology motif / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, linker, subdomain 3 / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, N-terminal region 2 / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / LIS1 homology (LisH) motif profile. / LIS1 homology motif / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Platelet-activating factor acetylhydrolase IB subunit beta / Cytoplasmic dynein 1 heavy chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsReimer JM / DeSantis M / Reck-Peterson SL / Leschziner AE
Funding support United States, 2 items
OrganizationGrant numberCountry
Damon Runyon Cancer Research FoundationDRG-2370-19 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM107214 United States
Citation
Journal: Elife / Year: 2023
Title: Structures of human dynein in complex with the lissencephaly 1 protein, LIS1.
Authors: Janice M Reimer / Morgan E DeSantis / Samara L Reck-Peterson / Andres E Leschziner /
Abstract: The lissencephaly 1 protein, LIS1, is mutated in type-1 lissencephaly and is a key regulator of cytoplasmic dynein-1. At a molecular level, current models propose that LIS1 activates dynein by ...The lissencephaly 1 protein, LIS1, is mutated in type-1 lissencephaly and is a key regulator of cytoplasmic dynein-1. At a molecular level, current models propose that LIS1 activates dynein by relieving its autoinhibited form. Previously we reported a 3.1 Å structure of yeast dynein bound to Pac1, the yeast homologue of LIS1, which revealed the details of their interactions (Gillies et al., 2022). Based on this structure, we made mutations that disrupted these interactions and showed that they were required for dynein's function in vivo in yeast. We also used our yeast dynein-Pac1 structure to design mutations in human dynein to probe the role of LIS1 in promoting the assembly of active dynein complexes. These mutations had relatively mild effects on dynein activation, suggesting that there may be differences in how dynein and Pac1/LIS1 interact between yeast and humans. Here, we report cryo-EM structures of human dynein-LIS1 complexes. Our new structures reveal the differences between the yeast and human systems, provide a blueprint to disrupt the human dynein-LIS1 interactions more accurately, and map type-1 lissencephaly disease mutations, as well as mutations in dynein linked to malformations of cortical development/intellectual disability, in the context of the dynein-LIS1 complex.
#1: Journal: Elife / Year: 2022
Title: Structural basis for cytoplasmic dynein-1 regulation by Lis1.
Authors: Gillies JP / Reimer JM / Karasmanis EP / Lahiri I / Htet ZM / Leschziner AE / Reck-Peterson SL
History
DepositionAug 5, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateFeb 1, 2023-
Current statusFeb 1, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27783.png

Downloads & links

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Map

FileDownload / File: emd_27783.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.16 Å
Density
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.5309163 - 0.83650243
Average (Standard dev.)-0.00018260715 (±0.021816276)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 408.31998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27783_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27783_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human cytoplasmic dynein-1 bound to one Lis1

EntireName: Human cytoplasmic dynein-1 bound to one Lis1
Components
  • Complex: Human cytoplasmic dynein-1 bound to one Lis1
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1
    • Protein or peptide: Platelet-activating factor acetylhydrolase IB subunit beta
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Human cytoplasmic dynein-1 bound to one Lis1

SupramoleculeName: Human cytoplasmic dynein-1 bound to one Lis1 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cytoplasmic dynein 1 heavy chain 1

MacromoleculeName: Cytoplasmic dynein 1 heavy chain 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 380.953594 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GQVALEELQD LKGVWSELSK VWEQIDQMKE QPWVSVQPRK LRQNLDALLN QLKSFPARLR QYASYEFVQR LLKGYMKINM LVIELKSEA LKDRHWKQLM KRLHVNWVVS ELTLGQIWDV DLQKNEAIVK DVLLVAQGEM ALEEFLKQIR EVWNTYELDL V NYQNKCRL ...String:
GQVALEELQD LKGVWSELSK VWEQIDQMKE QPWVSVQPRK LRQNLDALLN QLKSFPARLR QYASYEFVQR LLKGYMKINM LVIELKSEA LKDRHWKQLM KRLHVNWVVS ELTLGQIWDV DLQKNEAIVK DVLLVAQGEM ALEEFLKQIR EVWNTYELDL V NYQNKCRL IRGWDDLFNK VKEHINSVSA MKLSPYYKVF EEDALSWEDK LNRIMALFDV WIDVQRRWVY LEGIFTGSAD IK HLLPVET QRFQSISTEF LALMKKVSKS PLVMDVLNIQ GVQRSLERLA DLLGKIQKAL GEYLERERSS FPRFYFVGDE DLL EIIGNS KNVAKLQKHF KKMFAGVSSI ILNEDNSVVL GISSREGEEV MFKTPVSITE HPKINEWLTL VEKEMRVTLA KLLA ESVTE VEIFGKATSI DPNTYITWID KYQAQLVVLS AQIAWSENVE TALSSMGGGG DAAPLHSVLS NVEVTLNVLA DSVLM EQPP LRRRKLEHLI TELVHQRDVT RSLIKSKIDN AKSFEWLSQM RFYFDPKQTD VLQQLSIQMA NAKFNYGFEY LGVQDK LVQ TPLTDRCYLT MTQALEARLG GSPFGPAGTG KTESVKALGH QLGRFVLVFN CDETFDFQAM GRIFVGLCQV GAWGCFD EF NRLEERMLSA VSQQVQCIQE ALREHSNPNY DKTSAPITCE LLNKQVKVSP DMAIFITMNP GYAGRSNLPD NLKKLFRS L AMTKPDRQLI AQVMLYSQGF RTAEVLANKI VPFFKLCDEQ LSSQSHYDFG LRALKSVLVS AGNVKRERIQ KIKREKEER GEAVDEGEIA ENLPEQEILI QSVCETMVPK LVAEDIPLLF SLLSDVFPGV QYHRGEMTAL REELKKVCQE MYLTYGDGEE VGGMWVEKV LQLYQITQIN HGLMMVGPSG SGKSMAWRVL LKALERLEGV EGVAHIIDPK AISKDHLYGT LDPNTREWTD G LFTHVLRK IIDSVRGELQ KRQWIVFDGD VDPEWVENLN SVLDDNKLLT LPNGERLSLP PNVRIMFEVQ DLKYATLATV SR CGMVWFS EDVLSTDMIF NNFLARLRSI PLDEGEDEAQ RRRKGKEDEG EEAASPMLQI QRDAATIMQP YFTSNGLVTK ALE HAFQLE HIMDLTRLRC LGSLFSMLHQ ACRNVAQYNA NHPDFPMQIE QLERYIQRYL VYAILWSLSG DSRLKMRAEL GEYI RRITT VPLPTAPNIP IIDYEVSISG EWSPWQAKVP QIEVETHKVA APDVVVPTLD TVRHEALLYT WLAEHKPLVL CGPPG SGKT MTLFSALRAL PDMEVVGLNF SSATTPELLL KTFDHYCEYR RTPNGVVLAP VQLGKWLVLF CDEINLPDMD KYGTQR VIS FIRQMVEHGG FYRTSDQTWV KLERIQFVGA CNPPTDPGRK PLSHRFLRHV PVVYVDYPGP ASLTQIYGTF NRAMLRL IP SLRTYAEPLT AAMVEFYTMS QERFTQDTQP HYIYSPREMT RWVRGIFEAL RPLETLPVEG LIRIWAHEAL RLFQDRLV E DEERRWTDEN IDTVALKHFP NIDREKAMSR PILYSNWLSK DYIPVDQEEL RDYVKARLKV FYEEELDVPL VLFNEVLDH VLRIDRIFRQ PQGHLLLIGV SGAGKTTLSR FVAWMNGLSV YQIKVHRKYT GEDFDEDLRT VLRRSGCKNE KIAFIMDESN VLDSGFLER MNTLLANGEV PGLFEGDEYA TLMTQCKEGA QKEGLMLDSH EELYKWFTSQ VIRNLHVVFT MNPSSEGLKD R AATSPALF NRCVLNWFGD WSTEALYQVG KEFTSKMDLE KPNYIVPDYM PVVYDKLPQP PSHREAIVNS CVFVHQTLHQ AN ARLAKRG GRTMAITPRH YLDFINHYAN LFHEKRSELE EQQMHLNVGL RKIKETVDQV EELRRDLRIK SQELEVKNAA AND KLKKMV KDQQEAEKKK VMSQEIQEQL HKQQEVIADK QMSVKEDLDK VEPAVIEAQN AVKSIKKQHL VEVRSMANPP AAVK LALES ICLLLGESTT DWKQIRSIIM RENFIPTIVN FSAEEISDAI REKMKKNYMS NPSYNYEIVN RASLACGPMV KWAIA QLNY ADMLKRVEPL RNELQKLEDD AKDNQQKANE VEQMIRDLEA SIARYKEEYA VLISEAQAIK ADLAAVEAKV NRSTAL LKS LSAERERWEK TSETFKNQMS TIAGDCLLSA AFIAYAGYFD QQMRQNLFTT WSHHLQQANI QFRTDIARTE YLSNADE RL RWQASSLPAD DLCTENAIML KRFNRYPLII DPSGQATEFI MNEYKDRKIT RTSFLDDAFR KNLESALRFG NPLLVQDV E SYDPVLNPVL NREVRRTGGR VLITLGDQDI DLSPSFVIFL STRDPTVEFP PDLCSRVTFV NFTVTRSSLQ SQCLNEVLK AERPDVDEKR SDLLKLQGEF QLRLRQLEKS LLQALNEVKG RILDDDTIIT TLENLKREAA EVTRKVEETD IVMQEVETVS QQYLPLSTA CSSIYFTMES LKQIHFLYQY SLQFFLDIYH NVLYENPNLK GVTDHTQRLS IITKDLFQVA FNRVARGMLH Q DHITFAML LARIKLKGTV GEPTYDAEFQ HFLRGNEIVL SAGSTPRIQG LTVEQAEAVV RLSCLPAFKD LIAKVQADEQ FG IWLDSSS PEQTVPYLWS EETPATPIGQ AIHRLLLIQA FRPDRLLAMA HMFVSTNLGE SFMSIMEQPL DLTHIVGTEV KPN TPVLMC SVPGYDASGH VEDLAAEQNT QITSIAIGSA EGFNQADKAI NTAVKSGRWV MLKNVHLAPG WLMQLEKKLH SLQP HACFR LFLTMEINPK VPVNLLRAGR IFVFEPPPGV KANMLRTFSS IPVSRICKSP NERARLYFLL AWFHAIIQER LRYAP LGWS KKYEFGESDL RSACDTVDTW LDDTAKGRQN ISPDKIPWSA LKTLMAQSIY GGRVDNEFDQ RLLNTFLERL FTTRSF DSE FKLACKVDGH KDIQMPDGIR REEFVQWVEL LPDTQTPSWL GLPNNAERVL LTTQGVDMIS KMLKMQMLED EDDLAYA ET EKKTRTDSTS DGRPAWMRTL HTTASNWLHL IPQTLSHLKR TVENIKDPLF RFFEREVKMG AKLLQDVRQD LADVVQVC E GKKKQTNYLR TLINELVKGI LPRSWSHYTV PAGMTVIQWV SDFSERIKQL QNISLAAASG GAKELKNIHV CLGGLFVPE AYITATRQYV AQANSWSLEE LCLEVNVTTS QGATLDACSF GVTGLKLQGA TCNNNKLSLS NAISTALPLT QLRWVKQTNT EKKASVVTL PVYLNFTRAD LIFTVDFEIA TKEDPRSFYE RGVAVLCTE

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Macromolecule #2: Platelet-activating factor acetylhydrolase IB subunit beta

MacromoleculeName: Platelet-activating factor acetylhydrolase IB subunit beta
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.722918 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GSVLSQRQRD ELNRAIADYL RSNGYEEAYS VFKKEAELDV NEELDKKYAG LLEKKWTSVI RLQKKVMELE SKLNEAKEEF TSGGPLGQK RDPKEWIPRP PEKYALSGHR SPVTRVIFHP VFSVMVSASE DATIKVWDYE TGDFERTLKG HTDSVQDISF D HSGKLLAS ...String:
GSVLSQRQRD ELNRAIADYL RSNGYEEAYS VFKKEAELDV NEELDKKYAG LLEKKWTSVI RLQKKVMELE SKLNEAKEEF TSGGPLGQK RDPKEWIPRP PEKYALSGHR SPVTRVIFHP VFSVMVSASE DATIKVWDYE TGDFERTLKG HTDSVQDISF D HSGKLLAS CSADMTIKLW DFQGFECIRT MHGHDHNVSS VAIMPNGDHI VSASRDKTIK MWEVQTGYCV KTFTGHREWV RM VRPNQDG TLIASCSNDQ TVRVWVVATK ECKAELREHE HVVECISWAP ESSYSSISEA TGSETKKSGK PGPFLLSGSR DKT IKMWDV STGMCLMTLV GHDNWVRGVL FHSGGKFILS CADDKTLRVW DYKNKRCMKT LNAHEHFVTS LDFHKTAPYV VTGS VDQTV KVWECR

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 3 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.4000000000000001 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 55.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5nug

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24417
FSC plot (resolution estimation)

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