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- EMDB-4918: Structure of the dynein-2 complex; tail domain -

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Basic information

Entry
Database: EMDB / ID: EMD-4918
TitleStructure of the dynein-2 complex; tail domain
Map dataTail domain map, sharpened and masked
Sample
  • Complex: Dynein-2 complex; tail domain
    • Protein or peptide: O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein
    • Protein or peptide: WD repeat-containing protein 60
    • Protein or peptide: WD repeat-containing protein 34
    • Protein or peptide: Cytoplasmic dynein 2 light intermediate chain 1
    • Protein or peptide: Dynein light chain roadblock-type 1
    • Protein or peptide: Dynein light chain 1, cytoplasmic
Function / homology
Function and homology information


intraciliary transport involved in cilium assembly / positive regulation of non-motile cilium assembly / organelle organization / intraciliary retrograde transport / visual behavior / ciliary transition zone / dynein light chain binding / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / intraciliary transport ...intraciliary transport involved in cilium assembly / positive regulation of non-motile cilium assembly / organelle organization / intraciliary retrograde transport / visual behavior / ciliary transition zone / dynein light chain binding / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / intraciliary transport / mitocytosis / motile cilium assembly / dynein heavy chain binding / regulation of cilium assembly / Activation of BIM and translocation to mitochondria / embryonic skeletal system morphogenesis / ciliary tip / DNA modification / Intraflagellar transport / negative regulation of nitric oxide biosynthetic process / negative regulation of phosphorylation / cell projection organization / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / ciliary plasm / enzyme inhibitor activity / motile cilium / determination of left/right symmetry / microtubule motor activity / ciliary base / Macroautophagy / dynein intermediate chain binding / microtubule-based movement / pericentriolar material / spermatid development / axoneme / positive regulation of insulin secretion involved in cellular response to glucose stimulus / tertiary granule membrane / ficolin-1-rich granule membrane / cilium assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / 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 / substantia nigra development / MHC class II antigen presentation / centriole / nitric-oxide synthase regulator activity / AURKA Activation by TPX2 / regulation of mitochondrial membrane potential / ciliary basal body / filopodium / RHO GTPases Activate Formins / cilium / mitotic spindle / kinetochore / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / apical part of cell / methylation / scaffold protein binding / microtubule / cytoskeleton / protein domain specific binding / DNA repair / centrosome / apoptotic process / Neutrophil degranulation / protein-containing complex binding / Golgi apparatus / enzyme binding / ATP hydrolysis activity / mitochondrion / extracellular space / ATP binding / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cytoplasmic dynein 2 light intermediate chain 1 / Cytoplasmic dynein 2 intermediate chain 1 / : / Cytoplasmic dynein 2 heavy chain 1, AAA+ ATPase domain / Methylguanine DNA methyltransferase, ribonuclease-like domain / Dynein family light intermediate chain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Dynein light intermediate chain (DLIC) / Dynein light chain roadblock-type 1/2 / Methylated DNA-protein cysteine methyltransferase domain superfamily ...Cytoplasmic dynein 2 light intermediate chain 1 / Cytoplasmic dynein 2 intermediate chain 1 / : / Cytoplasmic dynein 2 heavy chain 1, AAA+ ATPase domain / Methylguanine DNA methyltransferase, ribonuclease-like domain / Dynein family light intermediate chain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Dynein light intermediate chain (DLIC) / Dynein light chain roadblock-type 1/2 / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Methylated-DNA--protein-cysteine methyltransferase active site. / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding domain / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Dynein light chain type 1 / Dynein light chain, type 1/2 / Dynein light chain superfamily / Dynein light chain type 1 / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / 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 / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cytoplasmic dynein 2 heavy chain 1 / Methylated-DNA--protein-cysteine methyltransferase / Dynein light chain 1, cytoplasmic / Cytoplasmic dynein 2 light intermediate chain 1 / Cytoplasmic dynein 2 intermediate chain 1 / Cytoplasmic dynein 2 intermediate chain 2 / Dynein light chain roadblock-type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsToropova K / Zalyte R / Mukhopadhyay AG / Mladenov M / Carter AP / Roberts AJ
Funding support United Kingdom, 8 items
OrganizationGrant numberCountry
Wellcome Trust104196/Z/14/Z United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P008348/1 United Kingdom
Royal Society104196/Z/14/Z United Kingdom
Wellcome TrustWT100387 United Kingdom
Royal SocietyRG170260 United Kingdom
Wellcome Trust079605/Z/06/Z United Kingdom
Medical Research Council (United Kingdom)MC_UP_A025_1011 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L014211/1 United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Structure of the dynein-2 complex and its assembly with intraflagellar transport trains.
Authors: Katerina Toropova / Ruta Zalyte / Aakash G Mukhopadhyay / Miroslav Mladenov / Andrew P Carter / Anthony J Roberts /
Abstract: Dynein-2 assembles with polymeric intraflagellar transport (IFT) trains to form a transport machinery that is crucial for cilia biogenesis and signaling. Here we recombinantly expressed the ~1.4-MDa ...Dynein-2 assembles with polymeric intraflagellar transport (IFT) trains to form a transport machinery that is crucial for cilia biogenesis and signaling. Here we recombinantly expressed the ~1.4-MDa human dynein-2 complex and solved its cryo-EM structure to near-atomic resolution. The two identical copies of the dynein-2 heavy chain are contorted into different conformations by a WDR60-WDR34 heterodimer and a block of two RB and six LC8 light chains. One heavy chain is steered into a zig-zag conformation, which matches the periodicity of the anterograde IFT-B train. Contacts between adjacent dyneins along the train indicate a cooperative mode of assembly. Removal of the WDR60-WDR34-light chain subcomplex renders dynein-2 monomeric and relieves autoinhibition of its motility. Our results converge on a model in which an unusual stoichiometry of non-motor subunits controls dynein-2 assembly, asymmetry, and activity, giving mechanistic insight into the interaction of dynein-2 with IFT trains and the origin of diverse functions in the dynein family.
History
DepositionMay 1, 2019-
Header (metadata) releaseJul 31, 2019-
Map releaseAug 28, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0318
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0318
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rlb
  • Surface level: 0.0318
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4918.png

Downloads & links

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Map

FileDownload / File: emd_4918.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTail domain map, sharpened and masked
Voxel sizeX=Y=Z: 1.39 Å
Density
Contour LevelBy AUTHOR: 0.0318 / Movie #1: 0.0318
Minimum - Maximum-0.06406755 - 0.1417825
Average (Standard dev.)0.0005537674 (±0.004941398)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 389.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z389.200389.200389.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-39-149-104
NX/NY/NZ201201211
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0640.1420.001

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Supplemental data

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Mask #1

Fileemd_4918_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Tail domain map, unmasked and unsharpened

Fileemd_4918_additional_1.map
AnnotationTail domain map, unmasked and unsharpened
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Additional map: Focused refinement of tail domain encompassing the DHC2...

Fileemd_4918_additional_2.map
AnnotationFocused refinement of tail domain encompassing the DHC2 TAIL-A, LIC3-A, WDR60, WDR34, RB and LC8 subunits
Projections & Slices
AxesZYX

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Additional map: Focused refinement of tail domain encompassing DHC2 N-terminal...

Fileemd_4918_additional_3.map
AnnotationFocused refinement of tail domain encompassing DHC2 N-terminal domain (ND), DHC2 TAIL-A (bundles 1-5), DHC2 TAIL-B (bundles 1-3), WDR60, WDR34 and RB subunits
Projections & Slices
AxesZYX

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Additional map: Focused refinement of tail domain encompassing DHC2 TAIL-A...

Fileemd_4918_additional_4.map
AnnotationFocused refinement of tail domain encompassing DHC2 TAIL-A (bundles 5-8), DHC2 TAIL-B (bundles 3-8), LIC3-A and -B, and LC8 subunits
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Tail domain half map 2, unmasked

Fileemd_4918_half_map_1.map
AnnotationTail domain half map 2, unmasked
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Tail domain half map 1, unmasked

Fileemd_4918_half_map_2.map
AnnotationTail domain half map 1, unmasked
Projections & Slices
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Sample components

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Entire : Dynein-2 complex; tail domain

EntireName: Dynein-2 complex; tail domain
Components
  • Complex: Dynein-2 complex; tail domain
    • Protein or peptide: O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein
    • Protein or peptide: WD repeat-containing protein 60
    • Protein or peptide: WD repeat-containing protein 34
    • Protein or peptide: Cytoplasmic dynein 2 light intermediate chain 1
    • Protein or peptide: Dynein light chain roadblock-type 1
    • Protein or peptide: Dynein light chain 1, cytoplasmic

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Supramolecule #1: Dynein-2 complex; tail domain

SupramoleculeName: Dynein-2 complex; tail domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein

MacromoleculeName: O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 515.223031 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GDKDCEMKRT TLDSPLGKLE LSGCEQGLHR IIFLGKGTSA ADAVEVPAPA AVLGGPEPLM QATAWLNAYF HQPEAIEEFP VPALHHPVF QQESFTRQVL WKLLKVVKFG EVISYSHLAA LAGNPAATAA VKTALSGNPV PILIPCHRVV QGDLDVGGYE G GLAVKEWL ...String:
GDKDCEMKRT TLDSPLGKLE LSGCEQGLHR IIFLGKGTSA ADAVEVPAPA AVLGGPEPLM QATAWLNAYF HQPEAIEEFP VPALHHPVF QQESFTRQVL WKLLKVVKFG EVISYSHLAA LAGNPAATAA VKTALSGNPV PILIPCHRVV QGDLDVGGYE G GLAVKEWL LAHEGHRLGK PGLGGSLEVL FQGPDYDIPT TLEVLFQGPA NGTADVRKLF IFTTTQNYFG LMSELWDQPL LC NCLEINN FLDDGNQMLL RVQRSDAGIS FSNTIEFGDT KDKVLVFFKL RPEVITDENL HDNILVSSML ESPISSLYQA VRQ VFAPML LKDQEWSRNF DPKLQNLLSE LEAGLGIVLR RSDTNLTKLK FKEDDTRGIL TPSDEFQFWI EQAHRGNKQI SKER ANYFK ELFETIAREF YNLDSLSLLE VVDLVETTQD VVDDVWRQTE HDHYPESRML HLLDIIGGSF GRFVQKKLGT LNLWE DPYY LVKESLKAGI SICEQWVIVC NHLTGQVWQR YVPHPWKNEK YFPETLDKLG KRLEEVLAIR TIHEKFLYFL PASEEK IIC LTRVFEPFTG LNPVQYNPYT EPLWKAAVSQ YEKIIAPAEQ KIAGKLKNYI SEIQDSPQQL LQAFLKYKEL VKRPTIS KE LMLERETLLA RLVDSIKDFR LDFENRCRGI PGDASGPLSG KNLSEVVNSI VWVRQLELKV DDTIKIAEAL LSDLPGFR C FHQSAKDLLD QLKLYEQEQF DDWSRDIQSG LSDSRSGLCI EASSRIMELD SNDGLLKVHY SDRLVILLRE VRQLSALGF VIPAKIQQVA NIAQKFCKQA IILKQVAHFY NSIDQQMIQS QRPMMLQSAL AFEQIIKNSK AGSGGKSQIT WDNPKELEGY IQKLQNAAE RLATENRKLR KWHTTFCEKV VVLMNIDLLR QQQRWKDGLQ ELRTGLATVE AQGFQASDMH AWKQHWNHQL Y KALEHQYQ MGLEALNENL PEINIDLTYK QGRLQFRPPF EEIRAKYYRE MKRFIGIPNQ FKGVGEAGDE SIFSIMIDRN AS GFLTIFS KAEDLFRRLS AVLHQHKEWI VIGQVDMEAL VEKHLFTVHD WEKNFKALKI KGKEVERLPS AVKVDCLNIN CNP VKTVID DLIQKLFDLL VLSLKKSIQA HLHEIDTFVT EAMEVLTIMP QSVEEIGDAN LQYSKLQERK PEILPLFQEA EDKN RLLRT VAGGGLETIS NLKAKWDKFE LMMESHQLMI KDQIEVMKGN VKSRLQIYYQ ELEKFKARWD QLKPGDDVIE TGQHN TLDK SAKLIKEKKI EFDDLEVTRK KLVDDCHHFR LEEPNFSLAS SISKDIESCA QIWAFYEEFQ QGFQEMANED WITFRT KTY LFEEFLMNWH DRLRKVEEHS VMTVKLQSEV DKYKIVIPIL KYVRGEHLSP DHWLDLFRLL GLPRGTSLEK LLFGDLL RV ADTIVAKAAD LKDLNSRAQG EVTIREALRE LDLWGVGAVF TLIDYEDSQS RTMKLIKDWK DIVNQVGDNR CLLQSLKD S PYYKGFEDKV SIWERKLAEL DEYLQNLNHI QRKWVYLEPI FGRGALPKEQ TRFNRVDEDF RSIMTDIKKD NRVTTLTTH AGIRNSLLTI LDQLQRCQRS LNEFLEEKRS AFPRFYFIGD DDLLEILGQS TNPSVIQSHL KKLFAGINSV CFDEKSKHIT AMKSLEGEV VPFKNKVPLS NNVETWLNDL ALEMKKTLEQ LLKECVTTGR SSQGAVDPSL FPSQILCLAE QIKFTEDVEN A IKDHSLHQ IETQLVNKLE QYTNIDTSSE DPGNTESGIL ELKLKALILD IIHNIDVVKQ LNQIQVHTTE DWAWKKQLRF YM KSDHTCC VQMVDSEFQY TYEYQGNASK LVYTPLTDKC YLTLTQAMKM GLGGNPYGPA GTGKTESVKA LGGLLGRQVL VFN CDEGID VKSMGRIFVG LVKCGAWGCF DEFNRLEESV LSAVSMQIQT IQDALKNHRT VCELLGKEVE VNSNSGIFIT MNPA GKGYG GRQKLPDNLK QLFRPVAMSH PDNELIAEVI LYSEGFKDAK VLSRKLVAIF NLSRELLTPQ QHYDWGLRAL KTVLR GSGN LLRQLNKSGT TQNANESHIV VQALRLNTMS KFTFTDCTRF DALIKDVFPG IELKEVEYDE LSAALKQVFE EANYEI IPN QIKKALELYE QLCQRMGVVI VGPSGAGKST LWRMLRAALC KTGKVVKQYT MNPKAMPRYQ LLGHIDMDTR EWSDGVL TN SARQVVREPQ DVSSWIICDG DIDPEWIESL NSVLDDNRLL TMPSGERIQF GPNVNFVFET HDLSCASPAT ISRMGMIF L SDEETDLNSL IKSWLRNQPA EYRNNLENWI GDYFEKALQW VLKQNDYVVE TSLVGTVMNG LSHLHGCRDH DEFIINLIR GLGGNLNMKS RLEFTKEVFH WARESPPDFH KPMDTYYDST RGRLATYVLK KPEDLTADDF SNGLTLPVIQ TPDMQRGLDY FKPWLSSDT KQPFILVGPE GCGKGMLLRY AFSQLRSTQI ATVHCSAQTT SRHLLQKLSQ TCMVISTNTG RVYRPKDCER L VLYLKDIN LPKLDKWGTS TLVAFLQQVL TYQGFYDENL EWVGLENIQI VASMSAGGRL GRHKLTTRFT SIVRLCSIDY PE REQLQTI YGAYLEPVLH KNLKNHSIWG SSSKIYLLAG SMVQVYEQVR AKFTVDDYSH YFFTPCILTQ WVLGLFRYDL EGG SSNHPL DYVLEIVAYE ARRLFRDKIV GAKELHLFDI ILTSVFQGDW GSDILDNMSD SFYVTWGARH NSGARAAPGQ PLPP HGKPL GKLNSTDLKD VIKKGLIHYG RDNQNLDILL FHEVLEYMSR IDRVLSFPGG SLLLAGRSGV GRRTITSLVS HMHGA VLFS PKISRGYELK QFKNDLKHVL QLAGIEAQQV VLLLEDYQFV HPTFLEMINS LLSSGEVPGL YTLEELEPLL LPLKDQ ASQ DGFFGPVFNY FTYRIQQNLH IVLIMDSANS NFMINCESNP ALHKKCQVLW MEGWSNSSMK KIPEMLFSET GGGEKYN DK KRKEEKKKNS VDPDFLKSFL LIHESCKAYG ATPSQYMTFL HVYSAISSSK KKELLKRQSH LQAGVSKLNE AKALVDEL N RKAGEQSVLL KTKQDEADAA LQMITVSMQD ASEQKTELER LKHRIAEEVV KIEERKNKID DELKEVQPLV NEAKLAVGN IKPESLSEIR SLRMPPDVIR DILEGVLRLM GIFDTSWVSM KSFLAKRGVR EDIATFDARN ISKEIRESVE ELLFKNKGSF DPKNAKRAS TAAAPLAAWV KANIQYSHVL ERIHPLETEQ AGLESNLKKT EDRKRKLEEL LNSVGQKVSE LKEKFQSRTS E AAKLEAEV SKAQETIKAA EVLINQLDRE HKRWNAQVVE ITEELATLPK RAQLAAAFIT YLSAAPESLR KTCLEEWTKS AG LEKFDLR RFLCTESEQL IWKSEGLPSD DLSIENALVI LQSRVCPFLI DPSSQATEWL KTHLKDSRLE VINQQDSNFI TAL ELAVRF GKTLIIQEMD GVEPVLYPLL RRDLVAQGPR YVVQIGDKII DYNEEFRLFL STRNPNPFIP PDAASIVTEV NFTT TRSGL RGQLLALTIQ HEKPDLEEQK TKLLQQEEDK KIQLAKLEES LLETLATSQG NILENKDLIE SLNQTKASSA LIQES LKES YKLQISLDQE RDAYLPLAES ASKMYFIISD LSKINNMYRF SLAAFLRLFQ RALQNKQDSE NTEQRIQSLI SSLQHM VYE YICRCLFKAD QLMFALHFVR GMHPELFQEN EWDTFTGVVV GDMLRKADSQ QKIRDQLPSW IDQERSWAVA TLKIALP SL YQTLCFEDAA LWRTYYNNSM CEQEFPSILA KKVSLFQQIL VVQVLRPDRL QSAMALFACK TLGLKEVSPL PLNLKRLY K ETLEIEPILI IISPGADPSQ ELQELANAER SGECYHQVAM GQGQADLAIQ MLKECARNGD WLCLKNLHLV VSWLPVLEK ELNTLQPKDT FRLWLTAEVH PNFTPILLQS SLKITYESPP GLKKNLMRTY ESWTPEQISK KDNTHRAHAL FSLAWFHAAC QERRNYIPQ GWTKFYEFSL SDLRAGYNII DRLFDGAKDV QWEFVHGLLE NAIYGGRIDN YFDLRVLQSY LKQFFNSSVI D VFNQRNKK SIFPYSVSLP QSCSILDYRA VIEKIPEDDK PSFFGLPANI ARSSQRMISS QVISQLRILG RSITAGSKFD RE IWSNELS PVLNLWKKLN QNSNLIHQKV PPPNDRQGSP ILSFIILEQF NAIRLVQSVH QSLAALSKVI RGTTLLSSEV QKL ASALLN QKCPLAWQSK WEGPEDPLQY LRGLVARALA IQNWVDKAEK QALLSETLDL SELFHPDTFL NALRQETARA VGRS VDSLK FVASWKGRLQ EAKLQIKISG LLLEGCSFDG NQLSENQLDS PSVSSVLPCF MGWIPQDACG PYSPDECISL PVYTS AERD RVVTNIDVPC GGNQDQWIQC GAALFLKNQ

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Macromolecule #2: WD repeat-containing protein 60

MacromoleculeName: WD repeat-containing protein 60 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 122.865156 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEPGKRRTKD DTWKADDLRK HLWAIQSGGS KEERKHREKK LRKESEMDLP EHKEPRCRDP DQDARSRDRV AEVHTAKESP RGERDRDRQ RERRRDAKDR EKEKLKEKHR EAEKSHSRGK DREKEKDRRA RKEELRQTVA HHNLLGQETR DRQLLERAER K GRSVSKVR ...String:
MEPGKRRTKD DTWKADDLRK HLWAIQSGGS KEERKHREKK LRKESEMDLP EHKEPRCRDP DQDARSRDRV AEVHTAKESP RGERDRDRQ RERRRDAKDR EKEKLKEKHR EAEKSHSRGK DREKEKDRRA RKEELRQTVA HHNLLGQETR DRQLLERAER K GRSVSKVR SEEKDEDSER GDEDRERRYR ERKLQYGDSK DNPLKYWLYK EEGERRHRKP REPDRDKKHR EKSSTREKRE KY SKEKSNS FSDKGEERHK EKRHKEGFHF DDERHQSNVD RKEKSAKDEP RKREFQNGEH RNRGASSKRD GTSSQHAENL VRN HGKDKD SRRKHGHEEG SSVWWKLDQR PGGEETVEIE KEETDLENAR ADAYTASCED DFEDYEDDFE VCDGDDDESS NEPE SREKL EELPLAQKKE IQEIQRAINA ENERIGELSL KLFQKRGRTE FEKEPRTDTN SSPSRASVCG IFVDFASASH RQKSR TQAL KQKMRSTKLL RLIDLDFSFT FSLLDLPPVN EYDMYIRNFG KKNTKQAYVQ CNEDNVERDI QTEEIETREV WTQHPG EST VVSGGSEQRD TSDAVVMPKI DTPRLCSFLR AACQVMAVLL EEDRLAAEPS WNLRAQDRAL YFSDSSSQLN TSLPFLQ NR KVSSLHTSRV QRQMVVSVHD LPEKSFVPLL DSKYVLCVWD IWQPSGPQKV LICESQVTCC CLSPLKAFLL FAGTAHGS V VVWDLREDSR LHYSVTLSDG FWTFRTATFS TDGILTSVNH RSPLQAVEPI STSVHKKQSF VLSPFSTQEE MSGLSFHIA SLDESGVLNV WVVVELPKAD IAGSISDLGL MPGGRVKLVH SALIQLGDSL SHKGNEFWGT TQTLNVKFLP SDPNHFIIGT DMGLISHGT RQDLRVAPKL FKPQQHGIRP VKVNVIDFSP FGEPIFLAGC SDGSIRLHQL SSAFPLLQWD SSTDSHAVTG L QWSPTRPA VFLVQDDTSN IYIWDLLQSD LGPVAKQQVS PNRLVAMAAV GEPEKAGGSF LALVLARASG SIDIQHLKRR WA APEVDEC NRLRLLLQEA LWPEGKLHK

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Macromolecule #3: WD repeat-containing protein 34

MacromoleculeName: WD repeat-containing protein 34 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.768293 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MATRAQPGPL SQAGSAGVAA LATVGVASGP GPGRPGPLQD ETLGVASVPS QWRAVQGIRW ETKSCQTASI ATASASAQAR NHVDAQVQT EAPVPVSVQP PSQYDIPRLA AFLRRVEAMV IRELNKNWQS HAFDGFEVNW TEQQQMVSCL YTLGYPPAQA Q GLHVTSIS ...String:
MATRAQPGPL SQAGSAGVAA LATVGVASGP GPGRPGPLQD ETLGVASVPS QWRAVQGIRW ETKSCQTASI ATASASAQAR NHVDAQVQT EAPVPVSVQP PSQYDIPRLA AFLRRVEAMV IRELNKNWQS HAFDGFEVNW TEQQQMVSCL YTLGYPPAQA Q GLHVTSIS WNSTGSVVAC AYGRLDHGDW STLKSFVCAW NLDRRDLRPQ QPSAVVEVPS AVLCLAFHPT QPSHVAGGLY SG EVLVWDL SRLEDPLLWR TGLTDDTHTD PVSQVVWLPE PGHSHRFQVL SVATDGKVLL WQGIGVGQLQ LTEGFALVMQ QLP RSTKLK KHPRGETEVG ATAVAFSSFD PRLFILGTEG GFPLKCSLAA GEAALTRMPS SVPLRAPAQF TFSPHGGPIY SVSC SPFHR NLFLSAGTDG HVHLYSMLQA PPLTSLQLSL KYLFAVRWSP VRPLVFAAAS GKGDVQLFDL QKSSQKPTVL IKQTQ DESP VYCLEFNSQQ TQLLAAGDAQ GTVKVWQLST EFTEQGPREA EDLDCLAAEV AAWSHPQFEK GSAGSAAGSG AGWSHP QFE K

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Macromolecule #4: Cytoplasmic dynein 2 light intermediate chain 1

MacromoleculeName: Cytoplasmic dynein 2 light intermediate chain 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.681621 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPSETLWEIA KAEVEKRGIN GSEGDGAEIA EKFVFFIGSK NGGKTTIILR CLDRDEPPKP TLALEYTYGR RAKGHNTPKD IAHFWELGG GTSLLDLISI PITGDTLRTF SLVLVLDLSK PNDLWPTMEN LLQATKSHVD KVIMKLGKTN AKAVSEMRQK I WNNMPKDH ...String:
MPSETLWEIA KAEVEKRGIN GSEGDGAEIA EKFVFFIGSK NGGKTTIILR CLDRDEPPKP TLALEYTYGR RAKGHNTPKD IAHFWELGG GTSLLDLISI PITGDTLRTF SLVLVLDLSK PNDLWPTMEN LLQATKSHVD KVIMKLGKTN AKAVSEMRQK I WNNMPKDH PDHELIDPFP VPLVIIGSKY DVFQDFESEK RKVICKTLRF VAHYYGASLM FTSKSEALLL KIRGVINQLA FG IDKSKSI CVDQNKPLFI TAGLDSFGQI GSPPVPENDI GKLHAHSPME LWKKVYEKLF PPKSINTLKD IKDPARDPQY AEN EVDEMR IQKDLELEQY KRSSSKSWKQ IELDS

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Macromolecule #5: Dynein light chain roadblock-type 1

MacromoleculeName: Dynein light chain roadblock-type 1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.934576 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MAEVEETLKR LQSQKGVQGI IVVNTEGIPI KSTMDNPTTT QYASLMHSFI LKARSTVRDI DPQNDLTFLR IRSKKNEIMV APDKDYFLI VIQNPTE

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Macromolecule #6: Dynein light chain 1, cytoplasmic

MacromoleculeName: Dynein light chain 1, cytoplasmic / type: protein_or_peptide / ID: 6 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.381899 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MCDRKAVIKN ADMSEEMQQD SVECATQALE KYNIEKDIAA HIKKEFDKKY NPTWHCIVGR NFGSYVTHET KHFIYFYLGQ VAILLFKSG

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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: 7.5
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsDynein-2 complex; tail domain

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 49.6 e/Å2
Details: Average electron dose per image (e-/A2) for additional datasets was 46.8 and 45.4
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware: (Name: Gctf, RELION (ver. 2.1))
Startup modelType of model: EMDB MAP
EMDB ID:

3707


Details: EMD-3707 map was low pass filtered to 60A and used as a reference model for 3D classification and reconstruction of an initial, in-house collected cryo-EM dataset (Polara 300kV instrument). ...Details: EMD-3707 map was low pass filtered to 60A and used as a reference model for 3D classification and reconstruction of an initial, in-house collected cryo-EM dataset (Polara 300kV instrument). This initial map was then used as a reference model for the dataset described in this entry.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 68623
FSC plot (resolution estimation)

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