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- EMDB-23084: Outer dynein arm docking complex bound to doublet microtubules fr... -

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Basic information

Entry
Database: EMDB / ID: EMD-23084
TitleOuter dynein arm docking complex bound to doublet microtubules from C. reinhardtii
Map datacomposite map of ODA-DC bound to doublet microtubules
Sample
  • Complex: ODA docking complex
    • Protein or peptide: Tubulin beta
    • Protein or peptide: Tubulin alpha
    • Protein or peptide: Dynein gamma chain, flagellar outer arm
    • Protein or peptide: Outer dynein arm-docking complex subunit 1
    • Protein or peptide: Outer dynein arm protein 1
    • Protein or peptide: Outer dynein arm-docking complex protein DC3
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
Keywordsdynein / microtubule / cilia / MOTOR PROTEIN
Function / homology
Function and homology information


outer dynein arm / outer dynein arm assembly / cilium movement involved in cell motility / dynein complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / motile cilium / dynein intermediate chain binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton ...outer dynein arm / outer dynein arm assembly / cilium movement involved in cell motility / dynein complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / motile cilium / dynein intermediate chain binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule / hydrolase activity / GTPase activity / calcium ion binding / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
: / ODAD1 central coiled coil region / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain 3, AAA+ lid domain / AAA+ lid 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 ...: / ODAD1 central coiled coil region / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain 3, AAA+ lid domain / AAA+ lid 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 / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Uncharacterized protein / Outer dynein arm protein 1 / Tubulin beta-1/beta-2 chain / Tubulin alpha-1 chain / Dynein gamma chain, flagellar outer arm / Outer dynein arm-docking complex protein DC3
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWalton T / Wu H
CitationJournal: Nat Commun / Year: 2021
Title: Structure of a microtubule-bound axonemal dynein.
Authors: Travis Walton / Hao Wu / Alan Brown /
Abstract: Axonemal dyneins are tethered to doublet microtubules inside cilia to drive ciliary beating, a process critical for cellular motility and extracellular fluid flow. Axonemal dyneins are evolutionarily ...Axonemal dyneins are tethered to doublet microtubules inside cilia to drive ciliary beating, a process critical for cellular motility and extracellular fluid flow. Axonemal dyneins are evolutionarily and biochemically distinct from cytoplasmic dyneins that transport cargo, and the mechanisms regulating their localization and function are poorly understood. Here, we report a single-particle cryo-EM reconstruction of a three-headed axonemal dynein natively bound to doublet microtubules isolated from cilia. The slanted conformation of the axonemal dynein causes interaction of its motor domains with the neighboring dynein complex. Our structure shows how a heterotrimeric docking complex specifically localizes the linear array of axonemal dyneins to the doublet microtubule by directly interacting with the heavy chains. Our structural analysis establishes the arrangement of conserved heavy, intermediate and light chain subunits, and provides a framework to understand the roles of individual subunits and the interactions between dyneins during ciliary waveform generation.
History
DepositionDec 10, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kzo
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7kzo
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23084.png

Downloads & links

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Map

FileDownload / File: emd_23084.map.gz / Format: CCP4 / Size: 93 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map of ODA-DC bound to doublet microtubules
Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum0.0 - 0.121121824
Average (Standard dev.)0.00035386693 (±0.0029214069)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions290290290
Spacing290290290
CellA=B=C: 394.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z290290290
origin x/y/z0.0000.0000.000
length x/y/z394.400394.400394.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS290290290
D min/max/mean0.0000.1210.000

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Supplemental data

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Mask #1

Fileemd_23084_msk_1.map
Projections & Slices
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Additional map: mask for focused refinement of DC1/2

Fileemd_23084_additional_1.map
Annotationmask for focused refinement of DC1/2
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Additional map: half map 1 for focused refinement of gamma HC N-terminal tail

Fileemd_23084_additional_10.map
Annotationhalf map 1 for focused refinement of gamma HC N-terminal tail
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Additional map: focused refinement of gamma HC N-terminal tail

Fileemd_23084_additional_11.map
Annotationfocused refinement of gamma HC N-terminal tail
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Additional map: half map 2 for focused refinement of gamma HC N-terminal tail

Fileemd_23084_additional_12.map
Annotationhalf map 2 for focused refinement of gamma HC N-terminal tail
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Additional map: refinement of entire ODA-DC

Fileemd_23084_additional_13.map
Annotationrefinement of entire ODA-DC
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Additional map: half map 2 for refinement of entire ODA-DC

Fileemd_23084_additional_14.map
Annotationhalf map 2 for refinement of entire ODA-DC
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Additional map: half map 1 for refinement of entire ODA-DC

Fileemd_23084_additional_15.map
Annotationhalf map 1 for refinement of entire ODA-DC
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Additional map: half map 1 for focused refinement of DC1/2

Fileemd_23084_additional_2.map
Annotationhalf map 1 for focused refinement of DC1/2
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Additional map: half map 2 for focused refinement of DC1/2

Fileemd_23084_additional_3.map
Annotationhalf map 2 for focused refinement of DC1/2
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Additional map: focused refinement of DC1/2

Fileemd_23084_additional_4.map
Annotationfocused refinement of DC1/2
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Additional map: half map 1 for focused refinement of DC3

Fileemd_23084_additional_5.map
Annotationhalf map 1 for focused refinement of DC3
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Additional map: mask for focused refinement of DC3

Fileemd_23084_additional_6.map
Annotationmask for focused refinement of DC3
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Additional map: half map 2 for focused refinement of DC3

Fileemd_23084_additional_7.map
Annotationhalf map 2 for focused refinement of DC3
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Additional map: focused refinement of DC3

Fileemd_23084_additional_8.map
Annotationfocused refinement of DC3
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Additional map: mask for focused refinement of gamma HC N-terminal tail

Fileemd_23084_additional_9.map
Annotationmask for focused refinement of gamma HC N-terminal tail
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Sample components

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Entire : ODA docking complex

EntireName: ODA docking complex
Components
  • Complex: ODA docking complex
    • Protein or peptide: Tubulin beta
    • Protein or peptide: Tubulin alpha
    • Protein or peptide: Dynein gamma chain, flagellar outer arm
    • Protein or peptide: Outer dynein arm-docking complex subunit 1
    • Protein or peptide: Outer dynein arm protein 1
    • Protein or peptide: Outer dynein arm-docking complex protein DC3
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: ODA docking complex

SupramoleculeName: ODA docking complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Details: ODA-DC bound to doublet microtubules showing contacts with the N-terminal tail of heavy chain gamma
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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Macromolecule #1: Tubulin beta

MacromoleculeName: Tubulin beta / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 49.665809 KDa
SequenceString: MREIVHIQGG QCGNQIGAKF WEVVSDEHGI DPTGTYHGDS DLQLERINVY FNEATGGRYV PRAILMDLEP GTMDSVRSGP YGQIFRPDN FVFGQTGAGN NWAKGHYTEG AELIDSVLDV VRKEAESCDC LQGFQVCHSL GGGTGSGMGT LLISKIREEY P DRMMLTFS ...String:
MREIVHIQGG QCGNQIGAKF WEVVSDEHGI DPTGTYHGDS DLQLERINVY FNEATGGRYV PRAILMDLEP GTMDSVRSGP YGQIFRPDN FVFGQTGAGN NWAKGHYTEG AELIDSVLDV VRKEAESCDC LQGFQVCHSL GGGTGSGMGT LLISKIREEY P DRMMLTFS VVPSPKVSDT VVEPYNATLS VHQLVENADE CMVLDNEALY DICFRTLKLT TPTFGDLNHL ISAVMSGITC CL RFPGQLN ADLRKLAVNL IPFPRLHFFM VGFTPLTSRG SQQYRALTVP ELTQQMWDAK NMMCAADPRH GRYLTASALF RGR MSTKEV DEQMLNVQNK NSSYFVEWIP NNVKSSVCDI PPKGLKMSAT FIGNSTAIQE MFKRVSEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDASAEEEGE FEGEEEEA

UniProtKB: Tubulin beta-1/beta-2 chain

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Macromolecule #2: Tubulin alpha

MacromoleculeName: Tubulin alpha / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 49.638008 KDa
SequenceString: MREVISIHIG QAGIQVGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDAFN TFFSETGAGK HVPRCIFLDL EPTVVDEVRT GTYRQLFHP EQLISGKEDA ANNFARGHYT IGKEIVDLAL DRIRKLADNC TGLQGFLVFN AVGGGTGSGL GSLLLERLSV D YGKKSKLG ...String:
MREVISIHIG QAGIQVGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDAFN TFFSETGAGK HVPRCIFLDL EPTVVDEVRT GTYRQLFHP EQLISGKEDA ANNFARGHYT IGKEIVDLAL DRIRKLADNC TGLQGFLVFN AVGGGTGSGL GSLLLERLSV D YGKKSKLG FTVYPSPQVS TAVVEPYNSV LSTHSLLEHT DVAVMLDNEA IYDICRRSLD IERPTYTNLN RLIAQVISSL TA SLRFDGA LNVDITEFQT NLVPYPRIHF MLSSYAPIIS AEKAYHEQLS VAEITNAAFE PASMMVKCDP RHGKYMACCL MYR GDVVPK DVNASVATIK TKRTIQFVDW CPTGFKCGIN YQPPTVVPGG DLAKVQRAVC MISNSTAIGE IFSRLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDL AALEKDFEEV GAESAEGAGE GEGEEY

UniProtKB: Tubulin alpha-1 chain

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Macromolecule #3: Dynein gamma chain, flagellar outer arm

MacromoleculeName: Dynein gamma chain, flagellar outer arm / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 513.491406 KDa
SequenceString: MALDNRHRLI VGKLAEAFGL PENVIEKTLT QDKQAVNSFF TPAGPPSLVF VYQVKEDKLK DGSVGPVDNK PTLHRIGPHE RIHNSVYFT RLNPKGINEK TLEADMGSGE LSVLWALENF KAIVSDLYLP IMQEQQQWGK MSTEYLEDFL SSTAKFGSML T EAVATVSG ...String:
MALDNRHRLI VGKLAEAFGL PENVIEKTLT QDKQAVNSFF TPAGPPSLVF VYQVKEDKLK DGSVGPVDNK PTLHRIGPHE RIHNSVYFT RLNPKGINEK TLEADMGSGE LSVLWALENF KAIVSDLYLP IMQEQQQWGK MSTEYLEDFL SSTAKFGSML T EAVATVSG GVEPMPDPRY IDQYGDLRPA GITQAAGDDD TLQEMEECLT EWCREAELLL NQTNKIKDGE ERGPDTELEY WR TRMSNFN SITEHLKTKE CKLVLGICSH AKTKAYLRWR GLDVQITDAA NESKDNVKYL ATLEKSMEPM YQGRVTDITE SLP ALMTNV RMMYTIARFY STAEHMTRLF TKITNQLVRR CKEQIMENGK IWDQDKVTLI GNMKVSVELA NVYRQQYRLA KETL AAQPK SKQFDFDEQA IFLKFDLSSK ALHKLIDMFT TIHQFSSLEQ HTHIEGLDTM LKSLNNIIDD VKRKPYDLLD YSRNA FDTD FLEFNVQIND LELQLQGFVN ASFEHITSTE HALSLLAQFQ AIMQRETLQQ DLENKYMVIF QNYAKDLDAV QKLYEK NKY EPPVPRNAPP VAGNIMWARQ LLRRIEAPMQ LAQNKNLLAA KESKKNIKTY NKVAKALIEF ETLWHQAWIK SIEQCKA GL AAPLLVQHPD TGKILVNFDK EIMQLVREAK YMQRFNIRCS SPSQMVLLQE EKFKFYHNQL THLVREYEHV LGRGATIK P LLRPHLDDME RKIAPGFAVL TWTSLNIDGY LHRFKQGLAR LEELVRKVVD LTENRVDSNL GAISSTLLVE LPTDRSFTY EGFVEQNRFQ KKQAELLAIR NEEVRRAIED LYTLVRNYPR ENTEDVLDEK EVSLLVRHYS KNMYNAIMQC TLNSLQAMKR RLGSKTTTG IFFMERPFFD VDVELKVPSV CMNPTLEEIQ AAINQCAKKV LTISKQLPAW GMDNVATYHE MMRGDRRWVK A VLRLTGSV EGIKTQVGEY IRTFDKYDFL WKEDLQAAYD HFMRSNPTLE AFEAELKKYM AIETEVTMIN GVNNIGALSL ET HPLKNSL KAEAVSWKTQ FAQNLHKQCS DDLKLDNYIR DTNSKFHRKI EDLEDVRNVM AVLKEVREKE SEIDNLIGPI EEM YGLLMR YEVRVPKEET TMVSDLRYGW KKLKKVATEV SDNLTRLQVG FKRELIKEVK TFVVDAQMFR KDWEANAMVP GLDP QEAVD RLRKFQQMFE VRKRKWENYS SGEELFGLPV TQYPELEQTE KEIQMLDRLY SLYVAVITTI KGYGDYFWVD VVEKI DEMG EQVQQYQNQS KKLPKLRDWP AYNACRKTID DFLEMLPLFQ ALTHKSMRER HWKEVMRVTG HELNLAEDHF KLQHLL DCN VLRYREDIED LTGAAVKEEI IEVKLNQLKA DWATANLALA EYKNRGPVIL KPSDTSELME KLEESQMTLG SMATNRY SA PFRDEVQAWS IKLSTVSEII EQWLMVQSMW QYMEAVFSGG DIVKQLPQEA KRFLNIDKNF MKIVSNALET QNVINTCF G NELMKNMLPH LHEQLEMCQK SLSAYLEQKR AEFPRFTCVG PHLLEICRWA HDPPSVVPHF QSGLFDSLSN VTFDRIDKT RMTEMFSQQN EKVEFERPVD AKGNIEVWLQ RLVDGMEDTV KQIIKRAVRN VAEMPLEDFV FGHPAQVSLL GIQFQWTAET QMALSSAKV DKTIMNKNMK KVDALLRDMV NITVRLDLTK NQRTNLETCI TVHMHQKEST EDLVKKKIKD PTDFEWLKQV R FYWRDDKD TVIISICDVD FEYSFEYLGV KERLVITPLT DICYITLSQA LGMFLGGAPA GPAGTGKTET TKDLGNTLGK YV VVFNCSD QFDYTYMGKI YKGLAQSGLW GCFDEFNRIN LDVLSVCAQQ VYCICRTRER KKSFQFTDGT TVSLDPRVGF FIT MNPGYA GAQELPENLK ALFRGVTMMV PNRQIIMKVK LAAAGYQEND ILSKKFFVLY GLCEQQLSKQ AHYDFGLRNI LSVL RTAGA SKRQSPDKSE VFLMMRTVRD MNMSKFVAED VPLFLSLIDD LFPGLKADAT RPDVNKDAEK VVLERGLQVH PTWMN KCIQ LYETYLVRHG IMLVGPSGSG KSAICECLAA ALTELGTKHV IWRMNPKAIT APQMFGRRDD TTGDWTDGIF AVLWRR AAK NKNQNTWIVL DGPVDAIWIE NLNTVLDDNK VLTLANGDRI LMSAAMKAMF EPENLNNASP ATVSRAGIIY VSDVELG WE PPVKSWLQKR DPTEACWARL FSKYIDRMLE FVRISLKPVM YNEQVSIVGT VMTLLNGYLK SMKEAGTAMN DAKYERVF L YCMTWSLGGL LEMKERPLFD QELRTFAHNM PPKEEDSDTI FEFLVNTTDA EWLHWRHCVP VWTYPKNEEK PQYAQLVIP TLDSVRYGAL LNLSYNVDKA TLLVGGPGTA KTNTINQFIS KFNAETTANK TITFSSLTTP GIFQMSIEGA VEKRQGRTFG PPGGKQMCI FVDDISMPYI NEWGHQVTNE IVRQLLEQGG MYSLEKPIGD MKFITDVRYV AAMNTPGGGK NDIPNRLKRQ F AIFNVPLP SVAAINGIFG KLVEGRFSRD VFCEEVVYVA SKLVPLTITL WNRIQTKMLP TPAKFHYLFN MRELSKVFQG VI LATRDRF NLAAGDSAVF GGNVASPEGY LLGLWIHECR RVFSDKLISY EDKNWVDKAV FDLCRDNFSS DLVKQVEEPI YFV DFLREP AVMMRPVEIV TPHPSFYYSV PGGLPEVRAR VEGLQRKFNE ESKVMKLELV LFTDCVTHLM RITRLLAWPG LGLL VGVGG SGKQSLSRLS AYIAGPTFYI TKTYNVSNLF EHIKGLYKIA GFKGQPVYFI FTDAEVKDEG FLEYINQILM TGEVA GLLT KEDQDMIVND IRPVMKHQAP GILDTYDNLY NFFLNRVRDN LHVVLCFSPV GAKFARRAQQ FPGLINGCTI DWFCPG PKK RLTSVSGKFI DKFTMACPKE VKNQLELLMG HAHVFVTAAC KEYFEKYRRY VYVTPKSYLS FLQGYKELYA KKWSFTK EL AYQIEVACQK MFEPKADVNK MKAELAVKNQ TAVSAKEAEA LLKQISESTA IAEKEKQKVA VIVDAVTKKA SEIATVKD D AERDLAAAKP ALDAALEALN SIKDGDIKNL KALKKPPQII TRIFDCVLVL RMLPVTKAEY TDEKGRMVQV GNYPEAQKM MNQMSFLQDL KDFAKEQIND ETVELLEPYF MSEDFTFENA QKGSGNVAGL CNWAESMAKY HNVAKVVEPK IAKLREAEAE LKLATKEKN AAEERMAKVQ AKLDEMQAQF DAAMAHKQAL EDDAAATQRK MDSANALIGA LAGEEARWTA QSKEFDVQIQ R LTGDCALA SAFVSYLGPF NKEFRELLLN RDFYGDCMKL NVPVTPHLQI TKFLVDDSEV GEWNLQGLPT DELSIQNGIM VT RASRYPV LVDPQGQGRE WIKNREEANQ LKTTQLNDKL FRNHLEECLA FGRPLLIENI EEELDPLLDP VLERRLVKKG KTW VVPLAD KEVDFTETFR LFCTTRLPNP HFTPELSAKV TVVDFTVTMA GLEDQLLGKL ISKEKKELED QRQQLLEEVQ SYKK RIKQL EDDLLCRLSN SQGNLLDEHQ ELIDVLAVTK QTAQDVSEKL ANASETNKRI NEACEEYRPV AHRATLLYFL IAEFS VVNC MYQTSLAQFN QLYELAIDRS EKANMPSKRI HNIIEYMTYE IYLYVQRGLF ERHKIIFALM LTNKVLTSAG KVKATD LDV FLKGGAALDI NSVRKKPKDW IPDLVWLNII ALSAMDAFRD IPDSVFRNDG LWRQWYDQEA PEMAKVPDYE DRLNKFE RM CVVKTFREDR TLIAAADYIA EALGQRFVES VPLNMEKRPG RRAMAKCPLI CLLSPGPDPT KLIEDLAKKK KIKTLGVS M GQGQEVIARK HMAAASLEGH WVLLQNTHLG LGYLTEVETF LVKEENVHED FRLWITAEPH PQFPIGLLQM GIKITNEAP VGIKAGLRAS YQWVNQDMLD MVSRQEWRQL LFVMCFLHSV VQEPQFGPIG WNVPYEFNQS DLSACVQFLQ NHLSEMDAKK APQPTWETV RYMISAIQYG SRITDDFDKL LMDTFAEKYF LQPVLQPSYE LFKDTRSSDG FSYRVPDSTD IETFGSYIET L PGTESPEI FGLHPNADIT FRTLQVQESI VTILDTMPKG AGSGSGLSRE DVVDKICEDL LSKAPPLFDK EETKEKLKKL PG GPTLPLT VHLRQEIDRL NIVTRLTTTT LKNLALAIAG TIAAERGLID ALDALFNARI PQQWLSKSWE ASTLGNWFTG LLQ RYDQLN KWLNLGRPKA YWMTGFFNPQ GFLTAMKQEV NRKHRDKWAL DDVVMSSEVT HRPKDFESLK EGAPEGVYVY GLYL DLRLD GRENRLMDSD PKKLFNPLPV LHVDGVLAKD KKRSGLYEAP KPYRVKARKG LNFITTFSVR TEDDKSKWIL PGVGI LCSI D

UniProtKB: Dynein gamma chain, flagellar outer arm

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Macromolecule #4: Outer dynein arm-docking complex subunit 1

MacromoleculeName: Outer dynein arm-docking complex subunit 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
EC number: Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 83.51818 KDa
SequenceString: MAQKSTLKLP RLRTKEELLK TSPELCKLLG EDSDDGRSMS PFTAPPPAGT VKPPSRGLPA VSTKATKGPG MDTPRGLGEE ELTEEELLR LELEKIKNER QVLLDSIKLV KAQAGTAGGE AQQNDIKALR RELELKKAKL NELHEDVRRK ENVLNKQRDD T TDASRLTP ...String:
MAQKSTLKLP RLRTKEELLK TSPELCKLLG EDSDDGRSMS PFTAPPPAGT VKPPSRGLPA VSTKATKGPG MDTPRGLGEE ELTEEELLR LELEKIKNER QVLLDSIKLV KAQAGTAGGE AQQNDIKALR RELELKKAKL NELHEDVRRK ENVLNKQRDD T TDASRLTP GELSEEQAYI QQLQDEMKQI DEELVEAEAK NRLYYLLGER TRREHLAMDM KVRASQQLKK DSADDLYTLT AH FNEMRAA KEQAERELAR MKRMLEETRV DWQKKLRERR REVRELKKRQ QKQLERERKM REKQLERERQ ERELQAKLKM EQD SYEMRV AALAPKVEAM EHSWNRIRTI SGADTPEEVL AYWEGLKAKE EQMRSLVSLA EQRESSAKSE IAALLENRSG MYEK GSAAA ADVGEGSEER ATLITEVERN MEGAKGKFNK LRSVCIGAEQ GLRSLQERLM IALEEIHPDQ LRASHMKGGH DAKAR GKGA ASAGARRGSA HAHTPDRNKR GPATGSRSQS PALVPHSPAG DKPSSPLHGT SPEHGHEPIP EGAEELAGEA EMVSPL GAD GNTIDDEHFF PELPELLTSV TDRLNRVLVL AAELDAQEPA GAGEDGLPLS GEPGADGAEG AAPASPSRGA PEGLSES ER TLVKGMNRRT WTGAPLLETI NASPSEAALT LNIKRKKGKK KEQQVQPDLN RILGYTGSDV EEEEPESEEE TEEEANKD D GVVDRDYIKL RALKMSQRLA NQQRAIKV

UniProtKB: Uncharacterized protein

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Macromolecule #5: Outer dynein arm protein 1

MacromoleculeName: Outer dynein arm protein 1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 62.292305 KDa
SequenceString: MPSADATRGG GSAGSMGKGT LGAGDTLGHK SVLDKQRAAI EKLRAQNEQL KTELLLENKF SVRPGDPFAQ ALINRLQDEG DMLARKIVL EMRKTKMLDQ QLSEMGSTLT TTRNNMGGIF SAKEQSTAVQ KRIKLLENRL EKAYVKYNQS ITHNKQLRES I NNLRRERI ...String:
MPSADATRGG GSAGSMGKGT LGAGDTLGHK SVLDKQRAAI EKLRAQNEQL KTELLLENKF SVRPGDPFAQ ALINRLQDEG DMLARKIVL EMRKTKMLDQ QLSEMGSTLT TTRNNMGGIF SAKEQSTAVQ KRIKLLENRL EKAYVKYNQS ITHNKQLRES I NNLRRERI MFESIQSNLE RELAKLKRDM ADMIQQANGA FEAREKAIGE MNALKAQADK EQQGFEEEWR QLTTIIEEDK KE RERARAQ ELAMRERETQ ELLKMGTLSS AEKKKRITKG SWNVGYNKAM AQNVAAEKVE MYGQAFKRIQ DATGIEDIDQ LVN TFLAAE DQNYTLFNYV NEVNQEIEKL EDQINIMRGE INKYRETGRE LDMTKSRELT EEEARLAASE AQSQLYEKRT DSAL SMTTA LKAGINDLFE RIGCNTPAVR DLLGEEGVTE ANLTAYLGII EQRTNEILQI YAKRKAQQGT DGLAEALLAQ PLTQP GNRI IIEPPSTTQE EEVEGLEPEP VEEDRPLTRE HLESKVQRTL PRKLETAIKV RPAGADATGG KRGSPTRR

UniProtKB: Outer dynein arm protein 1

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Macromolecule #6: Outer dynein arm-docking complex protein DC3

MacromoleculeName: Outer dynein arm-docking complex protein DC3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 21.371311 KDa
SequenceString:
MASAAARERY ARKNEQNELE RAFNTIDSKG DKKIDAEELT ELFLRLGHKP KRGEVEDMIW EVDEDCDGCI SLLEFQTLYT RCRDDKTGY EPRGLFNVVE FVMNDKNNQG FITLEEAMQI MYLRYGRAEL DMQLEQVFGT ADLNSGKILT LTEFLHCLHT N QVKQLLNR VTAKTYKAPP PPQKRK

UniProtKB: Outer dynein arm-docking complex protein DC3

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Macromolecule #7: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 7 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 7 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #9: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 8 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration20 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
30.0 mMHEPES
25.0 mMKCl
5.0 mMMgSO4
0.5 mMEGTA
10.0 mMATPAdenosine triphosphate
0.75 mMCaCl2

Details: Buffer also contained 1x Protease Arrest (G-Biosciences)
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
Details: 2.5 ul of splayed axoneme solution was then dispensed onto glow-discharged C-Flat 1.2/1.3-4Cu grids inside a Vitrobot Mark IV under 100% humidity. After a 10 s delay time, cryo-EM samples ...Details: 2.5 ul of splayed axoneme solution was then dispensed onto glow-discharged C-Flat 1.2/1.3-4Cu grids inside a Vitrobot Mark IV under 100% humidity. After a 10 s delay time, cryo-EM samples were prepared by first blotting for 10 s with blot force set to 16 and immediately plunged into liquid ethane..
DetailsSplayed axonemes isolated from Chlamydomonas reinhardtii flagella.

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 25 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 20524 / Average exposure time: 3.7 sec. / Average electron dose: 61.48 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 5584147 / Software - Name: RELION (ver. 3.1)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6u42

Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Helical parameters - Δz: 82.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 0 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1)
Details: The composite map was generated from three focused refinements of the full ODA-DC map. The three focused refinements centered on DC1/2 (3.1 A), DC3 (3.2 A), and heavy chain gamma (3.2 A).
Number images used: 485694

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Target criteria: Correlation coefficient
Output model

PDB-7kzo:
Outer dynein arm docking complex bound to doublet microtubules from C. reinhardtii

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