[English] 日本語
Yorodumi
- EMDB-34895: base module state 1 of Tetrahymena IFT-A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34895
Titlebase module state 1 of Tetrahymena IFT-A
Map data
Sample
  • Complex: IFT-A_base-1
    • Protein or peptide: Intraflagellar transport protein 122 homolog
    • Protein or peptide: WD40 repeat protein
    • Protein or peptide: Tetratricopeptide repeat protein
    • Protein or peptide: Intraflagellar transport protein 43 homolog
  • Ligand: ZINC ION
Keywordsintraflagellar transport complex / PROTEIN TRANSPORT
Function / homology
Function and homology information


intraciliary transport particle A / cilium assembly / cilium
Similarity search - Function
Intraflagellar transport protein 43 / Intraflagellar transport protein 43 / Tetratricopeptide repeat protein 21A/21B / WD repeat protein 35 / Intraflagellar transport protein 122 homolog / Tetratricopeptide repeat / Tetratricopeptide repeat / Quinoprotein alcohol dehydrogenase-like superfamily / TPR repeat profile. / Tetratricopeptide repeats ...Intraflagellar transport protein 43 / Intraflagellar transport protein 43 / Tetratricopeptide repeat protein 21A/21B / WD repeat protein 35 / Intraflagellar transport protein 122 homolog / Tetratricopeptide repeat / Tetratricopeptide repeat / Quinoprotein alcohol dehydrogenase-like superfamily / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / 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
Tetratricopeptide repeat protein / Uncharacterized protein / WD40 repeat protein / Intraflagellar transporter
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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

-
Structure visualization

Supplemental images

emd_34895.png

Downloads & links

-
Map

FileDownload / File: emd_34895.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.0196
Minimum - Maximum-0.071930334 - 0.14259094
Average (Standard dev.)0.00004042868 (±0.0037170933)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 369.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_34895_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_34895_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : IFT-A_base-1

EntireName: IFT-A_base-1
Components
  • Complex: IFT-A_base-1
    • Protein or peptide: Intraflagellar transport protein 122 homolog
    • Protein or peptide: WD40 repeat protein
    • Protein or peptide: Tetratricopeptide repeat protein
    • Protein or peptide: Intraflagellar transport protein 43 homolog
  • Ligand: ZINC ION

-
Supramolecule #1: IFT-A_base-1

SupramoleculeName: IFT-A_base-1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Tetrahymena thermophila (eukaryote)

-
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

-
Macromolecule #2: WD40 repeat protein

MacromoleculeName: WD40 repeat protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 138.076984 KDa
SequenceString: MFVFLSKKIG MPNNAKIEAV CWNKEQGWIA AGGEKGILKV LKIEDQRQKD GSNPTTTGQL LVNNTLEYHT SNVYLVTWND RYRKLTSVE ENGIIVVWAY FRELQLWKEE MINDRKKSVV RDLKWSPDGQ KVCIAYEDGA VIVGSVEGSP LWRKEFPHKL A LIEWSPDS ...String:
MFVFLSKKIG MPNNAKIEAV CWNKEQGWIA AGGEKGILKV LKIEDQRQKD GSNPTTTGQL LVNNTLEYHT SNVYLVTWND RYRKLTSVE ENGIIVVWAY FRELQLWKEE MINDRKKSVV RDLKWSPDGQ KVCIAYEDGA VIVGSVEGSP LWRKEFPHKL A LIEWSPDS KMMIFGTPEG EVRVYDSQGM EMQRLKIHCL QKLIDPSKSF SPDLPLAAID WFPQAKMYTD DTPPGLCIAY QC GRVQLMK NEKDDEPVLI DTMMKIFTVK WNPSGSMFAI SGTQDENGEL KGVVQFYSNA GHHLKTLRVP GSDRVTGVSW EGS GLRIAM AVNQAIFFAN IKPDHKWAYM SDGTLAFAYQ KIDRVEYTII FWDTINNKKN LKFVKNLCCL RASGDLCCIV TELI GYDLW QIDLCNSIGS PIDSKQINIY PNAVTMTKTH IIVCSQDHVY AWQYKNQVER LTTFEQQTGL RRVGREQAWF IDKEN DSNN QYDKDTYDVE PQSEDVICTV AANENFLLVA RISGTINVYT FPHISLENKL HIQTRPSQMS LNKDATRLAI IDHNGN LNI LKITPQGDEL LPFEKKECWF VKYSDDIPES FVFMERSRMY IVNDQTPEEP IITEGYICQY KDFQVKIVYL DDIMKSP DG VLRKEELTLE IEANILKDIK DQLYKKSMQE MFIVIKQHDN DCLWRVYAKK ALEDNDFDSA ENAFVQCKDY ASLKFLQR V RELDDRERQR AEIQCYFNKV EEAEEIYNKI ERRDLSIQMR MKLGDWAQVV DQIREGTGQD VELQKARLEL GNYYAENFQ WDKAAKQYAL AKYNPGLIEA YTRIQDYEGL EKLIAEIPER NELLQDMGDR FQQAGLCDAA VKCYEKFGDI KQAIDCCVLL NHWNLAVEL AEQYNFVQIE GLLVQYANQL LEKRRKLEAA ELYRKAKRNT EAAKILSQIA DDLTERDANP LNIKKMYVMA A LEVDLYKK RMLDATMTGQ ATSTAKTLNS LITSTINTSS ADKILNNPWR GAEAWHFFIL AQRQLYNGQF KYALKSALRL GE YELEIDQ KKIYSLIAIA AYYNKSFREC SRAFVKLQNL ENITEDEKER YEAIAVSIFT KHPPLDSPCE YTPCVGKNCS QQV SEYDIH CRACGSNFSP CVASGRPIFQ KEFYQCKNCR HKMIESEVSR LKLYNCALCH SPIDFKRFTE SNNNNNNNI

-
Macromolecule #3: Tetratricopeptide repeat protein

MacromoleculeName: Tetratricopeptide repeat protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 154.216141 KDa
SequenceString: MQNQQQKMQT ILIAQSQVYY YIREGFWSTM QRFCQEQYKA FGDPFFIFWK AYGLYQEGLP NEAINELTSI QHKKEIQYAT IVALITYHL STNIVDRETV QNLKFEESTQ RRLSSDKAIC LAAFFYAFNK EHAKARDLID EIHSDNFNIR IASAWCYLLE G GKFLEKSV ...String:
MQNQQQKMQT ILIAQSQVYY YIREGFWSTM QRFCQEQYKA FGDPFFIFWK AYGLYQEGLP NEAINELTSI QHKKEIQYAT IVALITYHL STNIVDRETV QNLKFEESTQ RRLSSDKAIC LAAFFYAFNK EHAKARDLID EIHSDNFNIR IASAWCYLLE G GKFLEKSV QLFEELYNEQ HEINKNLESL MGRSKANEMI KKFDISLNTI NEINVLYPDF KGGLIEKAKL LMTVDDWEQL VD YCNKILY DDDKNIMALM LLTFYTFARE GDIETGCERL QKLIQAVEFS ESRNMQLMFK ISQVFSRISG RNTQILKFTM KLV NQCKQL SPLNAQYFCE LAQQLLMVNQ FERAEQYFQE ASAIDVDNKE CLMGLILSKI MQGQTEDAES QIDFINQTTN NGER TSEIA YLEALVSTKQ ENVDPRVTIK LLEESLKLHI AQANRLYPSF DFYIVLNPDF LMSLSQAYFF QVGMKEMLAG KQPQN GVAS KGTKLLDFII KKIPGLIPAY LLQAKGKMSM GNTQEALKSV TKVIEQDPKN EEAYILSAMI ASSSKNFSLA QNQLQQ ALS NNFMIRDNPL FMLVKGEVEY AQGSYQACLE TMKAAYEIPE VKDKANQSKV VSAMSVLQFS DKDRCSIFLL YAKALQQ NN NSKEAKKIMT QAISQFTGTT EEVNVLIANS EIALQSGDVK KAISILKGVP QESPYFLRAR QILADVYLDQ LRDRRNYA K CYADLIEIDP SFDNYKMLGD ALMKIREPEE ASRAYEKAAL IKPDDEQIIQ LLGLSLCQTH DYNKALTYYE NALRMNPKR LDLIIDLGKL CIQIKNFNRA EEILKPDIFS DEYQLPTYQN LKRNQEGFYL IAKLNIKRTP PGVFTPIDMY RKALKKSIQI QIDVIEKAK QEGEDVEKER KTLADMYIEL AKYTNQYEKN EKATLDILAE ASKYTNNQDT MSKTVGNQEK ILELEVQMYF K SNQKLECE NKCNLLLKLN PNNDLACLTL AELLLQKDEY SQAIEQFKKI LQDRPNNYGI LAKLIDFFRR SFQINEAKTY IE RAEKKAT NTNDPGLCYC RGLYHKYNRS PKDALNEFSK AKKSSQYAEE SLVNMIDIYL NPDQDLYYSN VEEGPKVVDE VNL RACESL LREMQIRASY LRYIVMESYV FFLGGPRYKG GLEQGLKNLN DILKTNNDYI PAMLALAVGK FIQKKSTDAK NLLK LLWKR QYTTEYGEDL ERAWLLSADS FIAIQKYDSA EEILKKCLKY NQSCGKAEEY MGLIKEKEQS YVDAATHYEK AYKLT NEKS ASIAFRLSFN YLKAKRYVDC INICKKILVL FPNYPKIEKD CLEKARQALK

-
Macromolecule #4: Intraflagellar transport protein 43 homolog

MacromoleculeName: Intraflagellar transport protein 43 homolog / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 16.711193 KDa
SequenceString:
MAAKGKQGWG FGGKDQNVKI DTSQQDQKKQ NIWEQNNEDL IFVPDLTQEA QEQEVSKVSA PPNQPTVQVQ DINELQKFTK INTLPQTEE GVDLSQLMQI LSPVEDIKEK DEAWEFLQLK TQIYEIVSNM YGGNELIDDD DEDDENQ

-
Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

-
Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 538078

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more