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- EMDB-34898: head module state 2 of Tetrahymena IFT-A -

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Basic information

Entry
Database: EMDB / ID: EMD-34898
Titlehead module state 2 of Tetrahymena IFT-A
Map data
Sample
  • Complex: IFT-A_head-2
    • Protein or peptide: Intraflagellar transport protein 122 homolog
    • Protein or peptide: Intraflagellar transporter
    • Protein or peptide: WD40 repeat protein
  • Ligand: ZINC ION
Keywordsintraflagellar transport complex / PROTEIN TRANSPORT
Function / homology
Function and homology information


intraciliary retrograde transport / cilium assembly / cilium
Similarity search - Function
WDR19, WD40 repeat / WD repeat-containing protein 19/dyf-2 / WD domain, G-beta repeat / Intraflagellar transport protein 122 homolog / Tetratricopeptide-like helical domain superfamily / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...WDR19, WD40 repeat / WD repeat-containing protein 19/dyf-2 / WD domain, G-beta repeat / Intraflagellar transport protein 122 homolog / Tetratricopeptide-like helical domain superfamily / 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
Similarity search - Domain/homology
Intraflagellar transporter / WD40 repeat protein / Intraflagellar transporter
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsMa Y / Wu J / Lei M
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
Title: Structural insight into the intraflagellar transport complex IFT-A and its assembly in the anterograde IFT train.
Authors: Yuanyuan Ma / Jun He / Shaobai Li / Deqiang Yao / Chenhui Huang / Jian Wu / Ming Lei /
Abstract: Intraflagellar transport (IFT) trains, the polymers composed of two multi-subunit complexes, IFT-A and IFT-B, carry out bidirectional intracellular transport in cilia, vital for cilia biogenesis and ...Intraflagellar transport (IFT) trains, the polymers composed of two multi-subunit complexes, IFT-A and IFT-B, carry out bidirectional intracellular transport in cilia, vital for cilia biogenesis and signaling. IFT-A plays crucial roles in the ciliary import of membrane proteins and the retrograde cargo trafficking. However, the molecular architecture of IFT-A and the assembly mechanism of the IFT-A into the IFT trains in vivo remains elusive. Here, we report the cryo-electron microscopic structures of the IFT-A complex from protozoa Tetrahymena thermophila. We find that IFT-A complexes present two distinct, elongated and folded states. Remarkably, comparison with the in situ cryo-electron tomography structure of the anterograde IFT train unveils a series of adjustments of the flexible arms in apo IFT-A when incorporated into the anterograde train. Our results provide an atomic-resolution model for the IFT-A complex and valuable insights into the assembly mechanism of anterograde IFT trains.
History
DepositionDec 3, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateJun 14, 2023-
Current statusJun 14, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34898.png

Downloads & links

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Map

FileDownload / File: emd_34898.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.0037
Minimum - Maximum-0.010355707 - 0.036536746
Average (Standard dev.)0.0000403551 (±0.0009537901)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 457.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34898_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_34898_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 : IFT-A_head-2

EntireName: IFT-A_head-2
Components
  • Complex: IFT-A_head-2
    • Protein or peptide: Intraflagellar transport protein 122 homolog
    • Protein or peptide: Intraflagellar transporter
    • Protein or peptide: WD40 repeat protein
  • Ligand: ZINC ION

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Supramolecule #1: IFT-A_head-2

SupramoleculeName: IFT-A_head-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Tetrahymena thermophila (eukaryote)

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Macromolecule #1: Intraflagellar transport protein 122 homolog

MacromoleculeName: Intraflagellar transport protein 122 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 143.939422 KDa
SequenceString: MKCSELWTEI IPKNDPNSNI TNQVWSCSFN NDGSILLACV GDAILVYDSF TGNLVNKAIR GGQKEQINCI KFSKDGKRFA TASNDKTVW VWSFDVNKNP KLAPEVKYSH TDKVLCLAFN PLTHQIFSGG AQDYALWTPD QQSIEKSKFK DKIITCAWSW D GLYLGFGT ...String:
MKCSELWTEI IPKNDPNSNI TNQVWSCSFN NDGSILLACV GDAILVYDSF TGNLVNKAIR GGQKEQINCI KFSKDGKRFA TASNDKTVW VWSFDVNKNP KLAPEVKYSH TDKVLCLAFN PLTHQIFSGG AQDYALWTPD QQSIEKSKFK DKIITCAWSW D GLYLGFGT MGGIIGIRNR ALEQLAEIQR SFPIWCMDWT PITPDYQNSV LVVGVWEQSI AHYNIQGQQL GSDKKLTYDP ID INFSTQG EFLLVSGTNN KCTLYTREGG FLIDVATKND WVWNNKLKPV IKEAGSVAVQ DQLHVALTTN DGEISMFKIQ QLT VHALEG DKYAYRDNLT DIVVQSMSSN QRIRLKCKEL VKNISIYKDK LAAHLTERIL IYGTSSEDSQ MKYKLHKRIV KKVE AHILE IVSNHLIACV KNKVQLYQLS GDLEKEWVFD SRVNCIKIIG GMPNKEGAYV GLKNGQIFKI FVDNSFPIPI LNHNI SIKN IDASQKRKRL AVVDKNSNLT VYDLSNKEQV FQEMNIVSCA FNNNFDDLLA FSSTDTTFIR CSNHPPLSQK ISGQVV GFK ANKLFVLNDN VMSTIDVSMT QTMIKYLERK EFQSAYEISL LGVTDQDFLY LGNEALIATQ FAIARKCYTR IKKLDFI YL LEKAEKDFKK NTFVEGFYQG EIYALQTKFY EAENALTKSN LASQAKEMWI ILKEFDKAMR ITDTGASPIN RGQNKEIN S DASRKDLLIQ RAEWEVKQGN WKKGGELYIQ AEVYKKAIEV YVTNNFSEGI VEVCRNADAE TQRKEIEQCA AYFKKAKLH QYTKEAYLKL QDNKALLQLN IDLEKWDEAM TLAKAHPEFM EIVKLPYANW LAKQDRYEES LKAYRKIGKH DMATKMLYNL SQNAVFEKR FSDAALFTWM IATEHLGLIR NMKAPTPEDI ENLMKFYQYR DDAEIYFAYS KVQSFVDEPF LPLSGHAYML N IFNAARFA INKLGNRQLY GVQHSYLYYS LGKVSKQLEG YKTARICYEK LASYKIPTEW SEEIELSTLL IRSKPYSDQE SL LPICNRC YNQNPALTEG NRCSSCMHQF QNCFISFENL PLVEFKLDPK ITHKRFIELI NSDKSKTQPN KKKKKANDGW QES HQGDQQ VLTFNNSPQK GGNDNESSPF LDKLNEVFEI QQTTQEYIPV TLDENIVSSL SIDEVYWVDY TKYCYTAEIK YYKS MLTDI PLKNCQECGT FYILDEYEFE ISKTQKCPFC RSVDERAGPQ KDVFDF

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Macromolecule #2: Intraflagellar transporter

MacromoleculeName: Intraflagellar transporter / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 161.644859 KDa
SequenceString: MSLFSELPLD AGTDEQITQI AVSNVSINPS LAIITPHKIL LFNECGEKHD YELSRNIRCT YVQWHPSQPI IALGWETGAI TLWSEETKV AKEEPNGHKS EICLIQFNPS GSRMVSADID GNVTVWRGIN IVSQYKKEQS ITHAIFCELN IDSKLKSGNL F FFGGKSGV ...String:
MSLFSELPLD AGTDEQITQI AVSNVSINPS LAIITPHKIL LFNECGEKHD YELSRNIRCT YVQWHPSQPI IALGWETGAI TLWSEETKV AKEEPNGHKS EICLIQFNPS GSRMVSADID GNVTVWRGIN IVSQYKKEQS ITHAIFCELN IDSKLKSGNL F FFGGKSGV VCLADDANHC SDVCKVGGSI KSLLFYEKEN SVIIITSTLL LVMFKISTSV KTGPSKRVKL SISGDPQKLQ SI WIGSCLL ATCSHENMLR MWHLDQDDNY VLTLHQLAQQ TQTQQGAATV IQSTNTNDQI TSIQYEKRGK VLVAGTREGR IIF WKNLSI GSESPLDVDE WKMLPYVSVR QGVNSIAVGQ NNGLIAVQYG NQISLVQETV INGKMTDQVR LLQSSANTIK IYIN NDISN QVLHFQSKGN IKGLDCNDQF MLLWTSKTIE IHEIIINPKE SQTKLVASIQ EKCLRSVIHK ENIILVNDME LNVLN FKGI QKQNLKFSES EGKILNVNVL NNHLIMWTSN NYIRLFDISR REVKQIGVTR RFENSQGQLG QIRYCAVNSD GSKIVI TAD QRGKSGPQAD NKFYIYDVQT DNFLLYEMPA KCIPLQPYCD RKDRKFFGIS CIINKNIQQE KNADENNDEN EDNKSDK SR NEDDDEKDKS NLEFYTFFVT SENGIRKQDQ YQLESSIEAV FAIDIPKLYF IKRNKKTNSS GQNYKIVEKY LNDFVGLE K IDNQIKEAIM NFSFYLTMDN LDEAYKSVKQ IQNPSIWEKM ASMCVKTKRI DVAEICLGNM RFARGSKAIR EQKKEPELD AQLAMVAIQL NMKDEAVKLY EQSKRYDLYN KMLQAEGNWE KAIQISENHD RINLKNTYYR TAQMYEVSNN YEQAILYYEK SGTHVKEVP RMLLEAGQTE QLERYIIDKN EKPLFKWWAQ YLESNYRIEL AVKFYRQSED YDQMVRLFLT KNDVQTASSI C SETNNSAA CYILAKYLEM NGQIPEAIQY YWKSQHYTQA VRLAREKGMD NEVMSISLQG PNQVKLQSAA YFEEKGFKQK AV ELYKKGG NLIKAYNLAQ EEKLYDEAKQ IARQIEQEED QRNKKRDPND LAGIIDDFIE KGQPERAVPL MIKAKQFERA IET CIRFNI PITQDLVDKI IPTEPAKNAA EENKRKELMK LIADTSIKQG DYRLSSKLYT KLGNQVEAMK CLINLGAIDE VVNY ATMAR MPQLYILAGN FLQTTDWHKN PQLMKHIITF YNKAKAYDNL AGFFDACSSV EIDEYRDYEK AAAALNEALK HAKKS TSES RDFRIEQLET KLNLVQKFVQ ARALFSSDPQ QMKQICEDLL AQPGIDQSVR SGDIYAQIIE YYYQVKNFSQ AFDYIK KMQ QKRIILAPYL DQEMLQQILE SQGVSLNSKN KNNDDEFIEE DVPE

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Macromolecule #3: WD40 repeat protein

MacromoleculeName: WD40 repeat protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 158.411969 KDa
SequenceString: MASSKKVFEF KDDLNGSGKV LFSWSQDCSY IAVCGQSKVV YVLDKRGRKL KETVLKSKNK VIGLEWDKDQ EFLAILQENS TCFLLWNVF QNSFEQQDLE EKSKGSFIKW SKTHPVLVIG TEKGILYFYN KKTQKKIPTM GKHSKKITTG DWNDEGLLIT G SEEKVLTV ...String:
MASSKKVFEF KDDLNGSGKV LFSWSQDCSY IAVCGQSKVV YVLDKRGRKL KETVLKSKNK VIGLEWDKDQ EFLAILQENS TCFLLWNVF QNSFEQQDLE EKSKGSFIKW SKTHPVLVIG TEKGILYFYN KKTQKKIPTM GKHSKKITTG DWNDEGLLIT G SEEKVLTV SSHNSDSKGE SITVQHEPSN LQWARQKTDD RDSSQRTITA ILSNKSILMY DLNTKKQPLE LVYEPKYGKI VD YQLFGDG YIVTGFTEGY VAHVSSHLYE LRDEIQSKRI FQSSLDALCT NDIIYKLAVA GENQIHIYNL GTWEEVKSQR IEL PKAAGN VTKMQWANNG QLLVVATANG HLYGYLTSIP FLTSTYGSIV SVLSSFTEVS IVDTSRINQI QNVSSINLET EPGF LSLGL YHLAAGINNN VWYYLWLDQK RNGIIKGGEM IQKRDYLGSV KDIRLNEFWA AVLTDGKCIL HTIQPNNNVK DQKFP QIET DKAISGIGLT NDFLIMLDSS GKIRYYHLED QQFVVEYKPA DCQLVKIYPN FSGTRVVCFD NKGSAYLFEP AQEQFY PLE HFPQRAEKVL WDQKDPNLFA VLQNDTLITF IINKNNINGT LIQPVKELLA IEDIKNPGPP VQTILDRGVK PLTLSNG LL KCFTPSGSIN GQNLTSHSYL GSYKGRDDTD QGHYRFFLQN LQLHKYNNCL IAAQFLHNAV LYKELGRKAL EFVDLDVA L KSYQLAGSLS MVMTIQSFQH INEKNIIYGN IAMILGQYDL AQELFLKSSQ PILALEMRSD IQDYLTALNL AKSIAPQEE PFICRRLAFQ IENQGNNQEA RKLYERAVLN KDDRPSDRSK IDNHNQLCFA GISRTSIKLG DIQRGVTIAK ELIDNNIVIE IAVVCENMK QYLEAAELYQ KSGMLEKAAS LYIESKDFKK AAPLISMIKS PNLLKQYAKA KESEGAYNEA EQTYEQAESW E DVVRLNLD KLDNLRKAIA VLRTKCDTST VCLMVANVCE KQGNYGELVE FLLKAGKKEE AFQKAQQYNV MDAYSDNMKD FT LEERLRI AQYYENQGIW VKAAKHFEQA KNPTKSLKLY LKAGDQYIDD MIDLVCRNKQ QESLQQTLLD YLLEGEKPKD PIY LLKLYD KLGNIQSLVK IAITIASDEH DQGNYKIAHE RLFETYQKVK EHNVAIPFDL EQKLMIIHSY ILARKYLAYK EEDK EIELA AWLLNRVCKN ISQFPTHAVN ILTSAVIAAM KSKNRPLAYK WSVELVRPEY RSHINEKYKT RIENIARKPL KEEPV ENKT ECPFCKEYVG EFQLVCESCQ NVIPFCIASG THVIADQLCF CPSCRFPANI NYFIKYAESE EGRCPMCSVQ INLNEV KVE NPEQAASILK QLRATRQSSE QKKK

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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 TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 199946

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