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- EMDB-15954: Structure of the IFT-A complex; IFT-A2 module -

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Basic information

Entry
Database: EMDB / ID: EMD-15954
TitleStructure of the IFT-A complex; IFT-A2 module
Map dataIFT-A2 module, locally sharpened with LocScale
Sample
  • Complex: IFT-A complex; IFT-A2 module
    • Protein or peptide: Intraflagellar transport protein 122 homolog
    • Protein or peptide: SNAP-tag,Tetratricopeptide repeat protein 21B
    • Protein or peptide: WD repeat-containing protein 35
    • Protein or peptide: Intraflagellar transport protein 43 homolog
Function / homology
Function and homology information


protein localization to non-motile cilium / regulation of intraciliary retrograde transport / : / forebrain dorsal/ventral pattern formation / intraciliary transport particle A / intraciliary anterograde transport / negative regulation of eating behavior / embryonic heart tube left/right pattern formation / embryonic body morphogenesis / intraciliary retrograde transport ...protein localization to non-motile cilium / regulation of intraciliary retrograde transport / : / forebrain dorsal/ventral pattern formation / intraciliary transport particle A / intraciliary anterograde transport / negative regulation of eating behavior / embryonic heart tube left/right pattern formation / embryonic body morphogenesis / intraciliary retrograde transport / cerebellar Purkinje cell differentiation / intraciliary transport / establishment of protein localization to organelle / spinal cord dorsal/ventral patterning / photoreceptor connecting cilium / ciliary tip / ventricular system development / Intraflagellar transport / camera-type eye morphogenesis / protein localization to cilium / non-motile cilium assembly / non-motile cilium / embryonic heart tube development / regulation of smoothened signaling pathway / embryonic forelimb morphogenesis / limb development / smoothened signaling pathway / axoneme / Bergmann glial cell differentiation / cilium assembly / centriolar satellite / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / centriole / cellular response to leukemia inhibitory factor / ciliary basal body / neural tube closure / cilium / positive regulation of canonical Wnt signaling pathway / microtubule cytoskeleton / cytoskeleton / centrosome / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / membrane / cytoplasm
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 / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Tetratricopeptide repeat ...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 / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Tetratricopeptide repeat / TPR repeat region circular profile. / 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 21B / Intraflagellar transport protein 43 homolog / Intraflagellar transport protein 122 homolog / WD repeat-containing protein 35
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHesketh SJ / Mukhopadhyay AG / Nakamura D / Toropova K / Roberts AJ
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
Wellcome Trust217186/Z/19/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S007202/1 United Kingdom
CitationJournal: Cell / Year: 2022
Title: IFT-A structure reveals carriages for membrane protein transport into cilia.
Authors: Sophie J Hesketh / Aakash G Mukhopadhyay / Dai Nakamura / Katerina Toropova / Anthony J Roberts /
Abstract: Intraflagellar transport (IFT) trains are massive molecular machines that traffic proteins between cilia and the cell body. Each IFT train is a dynamic polymer of two large complexes (IFT-A and -B) ...Intraflagellar transport (IFT) trains are massive molecular machines that traffic proteins between cilia and the cell body. Each IFT train is a dynamic polymer of two large complexes (IFT-A and -B) and motor proteins, posing a formidable challenge to mechanistic understanding. Here, we reconstituted the complete human IFT-A complex and obtained its structure using cryo-EM. Combined with AlphaFold prediction and genome-editing studies, our results illuminate how IFT-A polymerizes, interacts with IFT-B, and uses an array of β-propeller and TPR domains to create "carriages" of the IFT train that engage TULP adaptor proteins. We show that IFT-A⋅TULP carriages are essential for cilia localization of diverse membrane proteins, as well as ICK-the key kinase regulating IFT train turnaround. These data establish a structural link between IFT-A's distinct functions, provide a blueprint for IFT-A in the train, and shed light on how IFT evolved from a proto-coatomer ancestor.
History
DepositionOct 12, 2022-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateJan 4, 2023-
Current statusJan 4, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15954.png

Downloads & links

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Map

FileDownload / File: emd_15954.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIFT-A2 module, locally sharpened with LocScale
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 546.304 Å		1.07 Å/pix.
x 512 pix.
= 546.304 Å		1.07 Å/pix.
x 512 pix.
= 546.304 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.29076707 - 0.70104915
Average (Standard dev.)0.00044692642 (±0.008609052)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 546.304 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15954_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IFT-A2 module, unsharpened

Fileemd_15954_additional_1.map
AnnotationIFT-A2 module, unsharpened
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: IFT-A2 module, half map B

Fileemd_15954_half_map_1.map
AnnotationIFT-A2 module, half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: IFT-A2 module, half map A

Fileemd_15954_half_map_2.map
AnnotationIFT-A2 module, half map A
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 complex; IFT-A2 module

EntireName: IFT-A complex; IFT-A2 module
Components
  • Complex: IFT-A complex; IFT-A2 module
    • Protein or peptide: Intraflagellar transport protein 122 homolog
    • Protein or peptide: SNAP-tag,Tetratricopeptide repeat protein 21B
    • Protein or peptide: WD repeat-containing protein 35
    • Protein or peptide: Intraflagellar transport protein 43 homolog

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Supramolecule #1: IFT-A complex; IFT-A2 module

SupramoleculeName: IFT-A complex; IFT-A2 module / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: Homo sapiens (human)
Molecular weightTheoretical: 141.7135 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA YAKDGKRFAS GSADKSVIIW TSKLEGILK YTHNDAIQCV SYNPITHQLA SCSSSDFGLW SPEQKSVSKH KSSSKIICCS WTNDGQYLAL GMFNGIISIR N KNGEEKVK ...String:
MRAVLTWRDK AEHCINDIAF KPDGTQLILA AGSRLLVYDT SDGTLLQPLK GHKDTVYCVA YAKDGKRFAS GSADKSVIIW TSKLEGILK YTHNDAIQCV SYNPITHQLA SCSSSDFGLW SPEQKSVSKH KSSSKIICCS WTNDGQYLAL GMFNGIISIR N KNGEEKVK IERPGGSLSP IWSICWNPSS RWESFWMNRE NEDAEDVIV(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)IPS T LKSAVYSSQG SEAEEEEPEE EDDSPRDDNL EERNDILAVA DWGQKVSFYQ LSGKQIGKDR ALNFDPCCIS YFTKGEYIL LGGSDKQVSL FTKDGVRLGT VGEQNSWVWT CQAKPDSNYV VVGCQDGTIS FYQLIFSTVH GLYKDRYAYR DSMTDVIVQH LITEQKVRI KCKELVKKIA IYRNRLAIQL PEKILIYELY SEDLSDMHYR VKEKIIKKFE CNLLVVCANH IILCQEKRLQ C LSFSGVKE REWQMESLIR YIKVIGGPPG REGLLVGLKN GQILKIFVDN LFAIVLLKQA TAVRCLDMSA SRKKLAVVDE ND TCLVYDI DTKELLFQEP NANSVAWNTQ CEDMLCFSGG GYLNIKASTF PVHRQKLQGF VVGYNGSKIF CLHVFSISAV EVP QSAPMY QYLDRKLFKE AYQIACLGVT DTDWRELAME ALEGLDFETA KKAFIRVQDL RYLELISSIE ERKKRGETNN DLFL ADVFS YQGKFHEAAK LYKRSGHENL ALEMYTDLCM FEYAKDFLGS GDPKETKMLI TKQADWARNI KEPKAAVEMY ISAGE HVKA IEICGDHGWV DMLIDIARKL DKAEREPLLL CATYLKKLDS PGYAAETYLK MGDLKSLVQL HVETQRWDEA FALGEK HPE FKDDIYMPYA QWLAENDRFE EAQKAFHKAG RQREAVQVLE QLTNNAVAES RFNDAAYYYW MLSMQCLDIA QDPAQKD TM LGKFYHFQRL AELYHGYHAI HRHTEDPFSV HRPETLFNIS RFLLHSLPKD TPSGISKVKI LFTLAKQSKA LGAYRLAR H AYDKLRGLYI PARFQKSIEL GTLTIRAKPF HDSEELVPLC YRCSTNNPLL NNLGNVCINC RQPFIFSASS YDVLHLVEF YLEEGITDEE AISLIDLEVL RPKRDDRQLE IANNSSQILR LVETKDSIGD EDPFTAKLSF EQGGSEFVPV VVSRLVLRSM SRRDVLIKR WPPPLRWQYF RSLLPDASIT MCPSCFQMFH SEDYELLVLQ HGCCPYCRRC KDDPGP

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Macromolecule #2: SNAP-tag,Tetratricopeptide repeat protein 21B

MacromoleculeName: SNAP-tag,Tetratricopeptide repeat protein 21B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 170.652609 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 PGLGGSMDSQ ELKTLINYYC QERYFHHVLL VASEGIKRYG SDPVFRFYHA YGTLMEGKTQ EA LREFEAI KNKQDVSLCS LLALIYAHKM SPNPDREAIL ESDARVKEQR KGAGEKALYH AGLFLWHIGR HDKAREYIDR MIK ISDGSK QGHVLKAWLD ITRGKEPYTK KALKYFEEGL QDGNDTFALL GKAQCLEMRQ NYSGALETVN QIIVNFPSFL PAFV KKMKL QLALQDWDQT VETAQRLLLQ DSQNVEALRM QALYYVCREG DIEKASTKLE NLGNTLDAME PQNAQLFYNI TLAFS RTCG RSQLILQKIQ TLLERAFSLN PQQSEFATEL GYQMILQGRV KEALKWYKTA MTLDETSVSA LVGFIQCQLI EGQLQD ADQ QLEFLNEIQQ SIGKSAELIY LHAVLAMKKN KRQEEVINLL NDVLDTHFSQ LEGLPLGIQY FEKLNPDFLL EIVMEYL SF CPMQPASPGQ PLCPLLRRCI SVLETVVRTV PGLLQTVFLI AKVKYLSGDI EAAFNNLQHC LEHNPSYADA HLLLAQVY L SQEKVKLCSQ SLELCLSYDF KVRDYPLYHL IKAQSQKKMG EIADAIKTLH MAMSLPGMKR IGASTKSKDR KTEVDTSHR LSIFLELIDV HRLNGEQHEA TKVLQDAIHE FSGTSEEVRV TIANADLALA QGDIERALSI LQNVTAEQPY FIEAREKMAD IYLKHRKDK MLYITCFREI AERMANPRSF LLLGDAYMNI LEPEEAIVAY EQALNQNPKD GTLASKMGKA LIKTHNYSMA I TYYEAALK TGQKNYLCYD LAELLLKLKW YDKAEKVLQH ALAHEPVNEL SALMEDGRCQ VLLAKVYSKM EKLGDAITAL QQ ARELQAR VLKRVQMEQP DAVPAQKHLA AEICAEIAKH SVAQRDYEKA IKFYREALVH CETDNKIMLE LARLYLAQDD PDS CLRQCA LLLQSDQDNE AATMMMADLM FRKQDYEQAV FHLQQLLERK PDNYMTLSRL IDLLRRCGKL EDVPRFFSMA EKRN SRAKL EPGFQYCKGL YLWYTGEPND ALRHFNKARK DRDWGQNALY NMIEICLNPD NETVGGEVFE NLDGDLGNST EKQES VQLA VRTAEKLLKE LKPQTVQGHV QLRIMENYCL MATKQKSNVE QALNTFTEIA ASEKEHIPAL LGMATAYMIL KQTPRA RNQ LKRIAKMNWN AIDAEEFEKS WLLLADIYIQ SAKYDMAEDL LKRCLRHNRS CCKAYEYMGY IMEKEQAYTD AALNYEM AW KYSNRTNPAV GYKLAFNYLK AKRYVDSIDI CHQVLEAHPT YPKIRKDILD KARASLRP

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Macromolecule #3: WD repeat-containing protein 35

MacromoleculeName: WD repeat-containing protein 35 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 134.037969 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: FQGMFFYLSK KISIPNNVKL QCVSWNKEQG FIACGGEDGL LKVLKLETQT DDAKLRGLAA PSNLSMNQTL EGHSGSVQVV TWNEQYQKL TTSDENGLII VWMLYKGSWI EEMINNRNKS VVRSMSWNAD GQKICIVYED GAVIVGSVDG NRIWGKDLKG I QLSHVTWS ...String:
FQGMFFYLSK KISIPNNVKL QCVSWNKEQG FIACGGEDGL LKVLKLETQT DDAKLRGLAA PSNLSMNQTL EGHSGSVQVV TWNEQYQKL TTSDENGLII VWMLYKGSWI EEMINNRNKS VVRSMSWNAD GQKICIVYED GAVIVGSVDG NRIWGKDLKG I QLSHVTWS ADSKVLLFGM ANGEIHIYDN QGNFMIKMKL SCLVNVTGAI SIAGIHWYHG TEGYVEPDCP CLAVCFDNGR CQ IMRHEND QNPVLIDTGM YVVGIQWNHM GSVLAVAGFQ KAAMQDKDVN IVQFYTPFGE HLGTLKVPGK EISALSWEGG GLK IALAVD SFIYFANIRP NYKWGYCSNT VVYAYTRPDR PEYCVVFWDT KNNEKYVKYV KGLISITTCG DFCILATKAD ENHP QEENE METFGATFVL VLCNSIGTPL DPKYIDIVPL FVAMTKTHVI AASKEAFYTW QYRVAKKLTA LEINQITRSR KEGRE RIYH VDDTPSGSMD GVLDYSKTIQ GTRDPICAIT ASDKILIVGR ESGTIQRYSL PNVGLIQKYS LNCRAYQLSL NCNSSR LAI IDISGVLTFF DLDARVTDST GQQVVGELLK LERRDVWDMK WAKDNPDLFA MMEKTRMYVF RNLDPEEPIQ TSGYICN FE DLEIKSVLLD EILKDPEHPN KDYLINFEIR SLRDSRALIE KVGIKDASQF IEDNPHPRLW RLLAEAALQK LDLYTAEQ A FVRCKDYQGI KFVKRLGKLL SESMKQAEVV GYFGRFEEAE RTYLEMDRRD LAIGLRLKLG DWFRVLQLLK TGSGDADDS LLEQANNAIG DYFADRQKWL NAVQYYVQGR NQERLAECYY MLEDYEGLEN LAISLPENHK LLPEIAQMFV RVGMCEQAVT AFLKCSQPK AAVDTCVHLN QWNKAVELAK NHSMKEIGSL LARYASHLLE KNKTLDAIEL YRKANYFFDA AKLMFKIADE E AKKGSKPL RVKKLYVLSA LLIEQYHEQM KNAQRGKVKG KSSEATSALA GLLEEEVLST TDRFTDNAWR GAEAYHFFIL AQ RQLYEGC VDTALKTALH LKDYEDIIPP VEIYSLLALC ACASRAFGTC SKAFIKLKSL ETLSSEQKQQ YEDLALEIFT KHT SKDNRK PELDSLMEGG EGKLPTCVAT GSPITEYQFW MCSVCKHGVL AQEISHYSFC PLCHSPVG

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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: Homo sapiens (human)
Molecular weightTheoretical: 23.615119 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GMEDLLDLDE ELRYSLATSR AKMGRRAQQE SAQAENHLNG KNSSLTLTGE TSSAKLPRCR QGGWAGDSVK ASKFRRKASE EIEDFRLRP QSLNGSDYGG DIPIIPDLEE VQEEDFVLQV AAPPSIQIKR VMTYRDLDND LMKYSAIQTL DGEIDLKLLT K VLAPEHEV ...String:
GMEDLLDLDE ELRYSLATSR AKMGRRAQQE SAQAENHLNG KNSSLTLTGE TSSAKLPRCR QGGWAGDSVK ASKFRRKASE EIEDFRLRP QSLNGSDYGG DIPIIPDLEE VQEEDFVLQV AAPPSIQIKR VMTYRDLDND LMKYSAIQTL DGEIDLKLLT K VLAPEHEV REDDVGWDWD HLFTEVSSEV LTEWDPLQTE KEDPAGQARH T

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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
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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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: 3.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Details: Average electron dose for additional dataset was 49.5 (e-/A2)
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio model generated from the data
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Resolution range 3.2-8A / Number images used: 242645
FSC plot (resolution estimation)

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