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- EMDB-28866: Structure of Leishmania tarentolae IFT-A (state 1) -

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Basic information

Entry
Database: EMDB / ID: EMD-28866
TitleStructure of Leishmania tarentolae IFT-A (state 1)
Map dataComposite map
Sample
  • Complex: IFT-A
    • Protein or peptide: Intraflagellar transport protein 122B, putative
    • Protein or peptide: Intraflagellar transport protein 122 homolog
    • Protein or peptide: WD_REPEATS_REGION domain-containing protein
    • Protein or peptide: NET domain-containing protein
    • Protein or peptide: WD_REPEATS_REGION domain-containing protein
    • Protein or peptide: TPR_REGION domain-containing protein
  • Ligand: ZINC ION
KeywordsCilia / IFT / PROTEIN TRANSPORT
Function / homology
Function and homology information


intraciliary retrograde transport / motile cilium / cilium assembly / cilium
Similarity search - Function
Tetratricopeptide repeat protein 21A/21B / WD repeat protein 35 / WDR19, WD40 repeat / WD repeat-containing protein 19/dyf-2 / WD domain, G-beta repeat / Intraflagellar transport protein 122 homolog / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat profile. ...Tetratricopeptide repeat protein 21A/21B / WD repeat protein 35 / WDR19, WD40 repeat / WD repeat-containing protein 19/dyf-2 / WD domain, G-beta repeat / Intraflagellar transport protein 122 homolog / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / 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
Uncharacterized protein / Intraflagellar transport protein 122B, putative / Wd repeat-containing protein 19 / Intraflagellar transport protein 43 / Intraflagellar transport protein 140 / Uncharacterized protein
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhou H / Brown A
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141109 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143183 United States
CitationJournal: Cell / Year: 2022
Title: Mechanism of IFT-A polymerization into trains for ciliary transport.
Authors: Shimi Meleppattu / Haixia Zhou / Jin Dai / Miao Gui / Alan Brown /
Abstract: Intraflagellar transport (IFT) is the highly conserved process by which proteins are transported along ciliary microtubules by a train-like polymeric assembly of IFT-A and IFT-B complexes. IFT-A is ...Intraflagellar transport (IFT) is the highly conserved process by which proteins are transported along ciliary microtubules by a train-like polymeric assembly of IFT-A and IFT-B complexes. IFT-A is sandwiched between IFT-B and the ciliary membrane, consistent with its putative role in transporting transmembrane and membrane-associated cargoes. Here, we have used single-particle analysis electron cryomicroscopy (cryo-EM) to determine structures of native IFT-A complexes. We show that subcomplex rearrangements enable IFT-A to polymerize laterally on anterograde IFT trains, revealing a cooperative assembly mechanism. Surprisingly, we discover that binding of IFT-A to IFT-B shields the preferred lipid-binding interface from the ciliary membrane but orients an interconnected network of β-propeller domains with the capacity to accommodate diverse cargoes toward the ciliary membrane. This work provides a mechanistic basis for understanding IFT-train assembly and cargo interactions.
History
DepositionNov 14, 2022-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28866.png

Downloads & links

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Map

FileDownload / File: emd_28866.map.gz / Format: CCP4 / Size: 909.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 9.0
Minimum - Maximum-36.983130000000003 - 86.419579999999996
Average (Standard dev.)0.019767707 (±1.3594165)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions620620620
Spacing620620620
CellA=B=C: 514.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Consensus refinement

Fileemd_28866_additional_1.map
AnnotationConsensus refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IFT121 IFT122 half map 1

Fileemd_28866_additional_10.map
AnnotationIFT121_IFT122 half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IFT139 IFT122 half map 2

Fileemd_28866_additional_11.map
AnnotationIFT139_IFT122 half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IFT139 mask

Fileemd_28866_additional_12.map
AnnotationIFT139 mask
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IFT121 IFT122 mask

Fileemd_28866_additional_13.map
AnnotationIFT121_IFT122 mask
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IFT139 IFT122 mask

Fileemd_28866_additional_14.map
AnnotationIFT139_IFT122 mask
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: A1 subcomplex mask

Fileemd_28866_additional_15.map
AnnotationA1 subcomplex mask
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: A1 V subcomplex mask

Fileemd_28866_additional_16.map
AnnotationA1_V subcomplex mask
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Consensus refinement half map 2

Fileemd_28866_additional_17.map
AnnotationConsensus refinement half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Consensus refinement half map 1

Fileemd_28866_additional_18.map
AnnotationConsensus refinement half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: A1 subcomplex half 1

Fileemd_28866_additional_2.map
AnnotationA1 subcomplex half 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: A1 subcomplex half 2

Fileemd_28866_additional_3.map
AnnotationA1 subcomplex half 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: A1 V subcomplex half 2

Fileemd_28866_additional_4.map
AnnotationA1_V subcomplex half 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: A1 V subcomplex half 1

Fileemd_28866_additional_5.map
AnnotationA1_V subcomplex half 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IFT121 IFT122 half map 2

Fileemd_28866_additional_6.map
AnnotationIFT121_IFT122 half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IFT139 half map 1

Fileemd_28866_additional_7.map
AnnotationIFT139 half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IFT139 IFT122 half map 1

Fileemd_28866_additional_8.map
AnnotationIFT139_IFT122 half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IFT139 half map 2

Fileemd_28866_additional_9.map
AnnotationIFT139 half map 2
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

EntireName: IFT-A
Components
  • Complex: IFT-A
    • Protein or peptide: Intraflagellar transport protein 122B, putative
    • Protein or peptide: Intraflagellar transport protein 122 homolog
    • Protein or peptide: WD_REPEATS_REGION domain-containing protein
    • Protein or peptide: NET domain-containing protein
    • Protein or peptide: WD_REPEATS_REGION domain-containing protein
    • Protein or peptide: TPR_REGION domain-containing protein
  • Ligand: ZINC ION

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Supramolecule #1: IFT-A

SupramoleculeName: IFT-A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Leishmania tarentolae (eukaryote)

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Macromolecule #1: Intraflagellar transport protein 122B, putative

MacromoleculeName: Intraflagellar transport protein 122B, putative / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 139.24675 KDa
SequenceString: MFVYLSKRIA MPNGVKVTSI AWNDGQGWLA CGGEKGLLKV LKVDGGPQGQ RSGGLSSSQT LEGHDTTVDL VTWNQQYCKL TSSDVSGRI IVWVLHKGMW FEEMVNNRNS SRVVDFAWNP SGTKICITYE DGAVIVGGVD GNRYWGRELP YKLAKVCWGA D GNSILFGT ...String:
MFVYLSKRIA MPNGVKVTSI AWNDGQGWLA CGGEKGLLKV LKVDGGPQGQ RSGGLSSSQT LEGHDTTVDL VTWNQQYCKL TSSDVSGRI IVWVLHKGMW FEEMVNNRNS SRVVDFAWNP SGTKICITYE DGAVIVGGVD GNRYWGRELP YKLAKVCWGA D GNSILFGT ATGEVYVHDA SSGEHLSQVE IKCNDGKAPS PLAGLSWHPA WVERPEPLAT LAVCYQSGKL QLMTSIGDET PC NVDRDLP AHFISWNPSG TVLAVTAATP ATEENGPGIV TQFFSTEGVH LRTLRVSGKQ CGGITWEGGG LRVAIGVDSS VYF ANVRPN YKYCYFKKTA VFAFTVPDKV EESVMFWNVN TNERRTKSVR GLQYMNACKD ACVLISRPDT TQQQRMIQLV NAIG SPLET RFIDMELYTY DMNSSAVVCC GDESIYIWQF RDPSTAVDAL DPISMQASRA ESQERVIHVC DLVRGDTAPT MKVRS ALTN DLISAMCVSE THMFVSLESG TLHVYQLSPL QLVSKYILFA RAQSMSVNCN STQLAVIHLG GITNVYCIER EKFSLV PCK ADTIDGVELK DVWNLRWAVD DPHRFAVMEK TRMLVYNHGV AEEPVQSCAN LCKFKSLKIR TLQLDELLLD PERPRKD YI VDFEAQLLRD MRAVLRDGTA KEAYEFAESH NTKKLWELLA EHTLFQLDFT YAEVAFIHCK DYAAIQFVKR VRSLDDPK K QLAEVNAYYR RFDEAERLYK DVDRKDLALD LRYRLGDWFG VVRLVQEGGG DEALLFQAWE NIGDHYASRQ KWSKAAQYY TQCRHYRKLA RIFYIIEDYE MLTQLISMGE HDKELMVTLG NMLLTVGLAE EAAKAFIAAN EPRMAVNGCV QVNMWNRAIA LAKEHRLED VGQLLEKYAK YLIHRERLTE AIELYRKAGK HDEAATLLAQ LGKRAALRDA LKAKKFYVLS ALEVQKYRTT A IALNRDGV AVVSEMLNKD RSTVSERTLD AAWRGAEAYH FLLMCQQQMA DRNFKAALVL AMRLIEYDDL VAPVDGYSLI AL TAYLVKN FGLCSKAFAR LEQAERNDEA GGVAAAATTQ LENFSLDLDV THRTMASTCG GSTGGSTGML SGGGGSALSG TTT SLQLTN PGKGVTRMAP MTYPTVSLRD PPRPFADLAR HIFMTHSPVD TSVDSVPCPT CGSFNKEWAQ RCIKCQQPFN TCIV SGCAI VSEDGAWQCS VCHRKALEAV VDKYRNCPLC HTPRKGRMRR GI

UniProtKB: Intraflagellar transport protein 122B, putative

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Macromolecule #2: Intraflagellar transport protein 122 homolog

MacromoleculeName: Intraflagellar transport protein 122 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 144.971953 KDa
SequenceString: MHTSVRWSET ADAVKGIRPP VNSLCYSPSG DYVVASCGVR VLVYAASTGT LLHSLMGHQD TIYCVDYSSD GKNFASGGAD RTVIVWSSQ GEGIVKYQHT EAIQALAHNP TSSQLASVSS VDWGIWSPEQ PKVSKYSLPS KGLCAAWTPN GKTLAIGMLD G TVMMLSKT ...String:
MHTSVRWSET ADAVKGIRPP VNSLCYSPSG DYVVASCGVR VLVYAASTGT LLHSLMGHQD TIYCVDYSSD GKNFASGGAD RTVIVWSSQ GEGIVKYQHT EAIQALAHNP TSSQLASVSS VDWGIWSPEQ PKVSKYSLPS KGLCAAWTPN GKTLAIGMLD G TVMMLSKT SEEKVIIRRP APVWALAFTP LRENGIDVLA IGSWDQRLSF YNLSGTAVGR ERELDFDPCS VSYFNDGEYI LL SGSDHKV TLFTKDGNRL IELASADDWI WSARQRPRQK QFCYGTNDGT ISCIDITIST VHTIYDDQYV FRKDMTNLVV HQL LVDRKM VIPCNEYVQK IATFLDKLAV QLQERVIVFE FFYDDDRTMR YQDIAQIRRR LECSLLCVTT GAIIVSNDKR ITMY DFQGN KRREWSMESP VQLMKVVGGM EGREILLVGL NGGQVMKVFV DNPFPTLLHK GTAPVKSAEL SSSRSRLAVI DSTNT LQVL ELGEKNELLF SEDNVTAVAF NIDVDDNIAF TTGDNTLHIK TGSLPAYQQA VRGIVVGFKA NHVFNLHYSN MMVLDV PHA HALYKYVEMR DFDRAYEVAC LGVADADWKM LGLHAMSQLR LDIARKAFTH IQDTKLVELL KSLELRRRQS GAEDGLS LT LGKASGTPDT VEGPENKGYG STNGELAAAR VAAKDSVLYG SILAFQGKYN DAARQFMKTG CELKAVEMYC DLKMWDNA K KICTDEKVLK DLIRQQARWA EESQNFVEAA SLYESCGDYA KAIGMMGQAG QVEKLMKMCR SLPTSEVTLI TECANFFRK HNAIPFAIEA YEKVQDHQAL IGIYVAKGDW RNAFTILEKT PTLAREVYVP WATWLADNDK FDEALEAFRA AKWPKEAMRL METLATNSV TCRKFRDAAF YYIHLAEEYG RFEETEKPTD VEKAARIRRS KECVRRADIY YAFSGVYAHT TQPLPYNELS L FRTAKYLF GMCAESAIPI NVGKGAILYT LSRIANRLEM VRTARAVFEK LQGVILPVSM MEQVDIETLL VRSKPVKDRD EL LDRCFRC NQLIAQLPMA GDRCPNCFHP CVRSFVNFEC LPLVEFVLAD ELTDEEAERI IVSGVGRRRS ADDENSKDHS DGA DAKAKE WKSDNGANVI SFDDGNIDYE IDQQLVAMGR SKAAANKGND PFFTQLQYVL RPGRPTATYQ PFVASADILK GFRR DEVFI VRPRYGTLPV PNRYYRLMRS DVSVCLCNGC QHFFIAEDYE AECMRGSGCP LCRYRPGKQV SRSMKQILFD METAA AASK TSSAAAAL

UniProtKB: Uncharacterized protein

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Macromolecule #3: WD_REPEATS_REGION domain-containing protein

MacromoleculeName: WD_REPEATS_REGION domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 182.580078 KDa
SequenceString: MSLFVVNAPG HEGQLKEQLI VAHKRRPLLA TAWVNPPSVL ITNSEGEVLT QVADPPGSTG RTHQPTALTW HPNEELLVIG WSNGEMSLW SMPSVSSLAL GEDYTTAAAR SAVQLIAAKA ATQSSAEGAT REHASGAVVA SEWSTRGLYL VSASQQRHVV M WMLEKIPA ...String:
MSLFVVNAPG HEGQLKEQLI VAHKRRPLLA TAWVNPPSVL ITNSEGEVLT QVADPPGSTG RTHQPTALTW HPNEELLVIG WSNGEMSLW SMPSVSSLAL GEDYTTAAAR SAVQLIAAKA ATQSSAEGAT REHASGAVVA SEWSTRGLYL VSASQQRHVV M WMLEKIPA ETSVTFKLKP LWSVQSREPV ARIIHVPSKA SHPSTAFKLN NGATAAAAAE GGDDDISFLL ADGGTSVTAI NE DQQLFPC VTQQEQIASV LYDAATRTLV TLTTTSMIEV YAVGEDIKGT STLRRKLSAP ATTPTVSTTT GERIAMSMVW ASP GVVAFG SGDDRLRILD LSSGSLDVLL LPQPDLHVSS LATFAAKGTM IVGTVEGFLV VFQHHAASLL TSRHVSVARE TVTS SSPFA PAATEASQWE AMTVHQVGKC VDRVVLTALG DVALCCGGSE LQVLHEIIRK RAWDGVAAAT QISSDMVVIE SITGC QCLL QNKGNVHGVS IAFPNIALWN GSQIDFYMID EATSEITFIN FVLTTSPAFA IHREGLIYVK GNRIVFETMQ LAPIAQ MTF TESEGVPVIM DIMNDYLVVV SSKNYLRLAR ISTRDLQQLG PARPLTFPSI LQPDAVEASS GASEMTPFVE DISTLEV SV SGARVNAQGR RVALMSTLGP LALPDTRIWV YDSDTDKMSF FDFGSRNEIP NSVYWNTPEP NTTTVGEFEY ILLACETY Q IHMDDKKSAS EEAESPKACT DTTNDGNKIA DHPVGQENLP EALPDMENYA EKKAELEDAR RESVGTTNYV SQRPHNIVT FFATHDGLVL QNFAPLRRYQ ICLVGLTIPD FLLASVKING DPNNAEDYVI EQKRLRDFEG LKSDKDVAVR EALMKFSYYA TIGNMDEAY RCVKSIKNPA AWQGLARLCV TSGRLDVAAV CLATMEDCVA ARALREAKED YPDDQDVQLA TLALGLSMTE E AVELLRKS KRYDLLTDVY MACGKFEHAQ RHSERFDRAR IRPVAYKYAQ FMESLQNMDA AIMWYYNAKC ASTDVPRIFF QT NRMHELR QLMMIQSQPP SPTAGDSAQR PQPGIGEQQS TFATIFPQNR ELLLWWAQHS ERRHNVQEAL RFYNAGEDVY NIV RILCSL TPPKLDSALQ LVNKEMDKAK MRFQQQQAFA ATASARFGDD DHGEPDPVGS AYFVAQLYER QGDDQLALQY YQAA GAYRS GVRVAWKMEQ YGVVANLAMK SSDERLMLET AMALEKHQAY DKAVQLYRRI GAVQCALDAC VQGGLYETLH EVSAA FASG STDPAVFLGM ADHFQSESDY QKAVEMLLFA KHFEEALKLC ETQNATLTEE MAESMTSNIG ELSMEERQAV LRRVAH IAK DQGRWSLACK KYTQAGDRVK AMRMLMRGGE TEKVIFFANH SRNVEIYTMA ANFLQSQNWS ADANIYKSIV LFYTKAK AW MNLLAFYESC AQLHIDENRN YPEALRALED CIAMAESVRG GKANIEMEKV EQLKQRVEIL KAFVKAQKTV DSMVVAER G SVAEKAKADS VIACCSGLIK RSRPSSPDHS LIQDALRIGD VFALMVRFYF DKLGEPHNAL KVMESMPKHG ADPQLFIEA DYMERVCQAN GKSLANVLPG GIATEAPGAV WEGARKFSTD TRRSSVIDEV DRVV

UniProtKB: Intraflagellar transport protein 140

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Macromolecule #4: NET domain-containing protein

MacromoleculeName: NET domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 38.742742 KDa
SequenceString: MSTTSMTAPA TSPSRLESMR AASSTTSSKP APTGPSKKSD APAKTKRQDK PNVNSANDSN AADTGTAAAA TRPDHGRRSR RTEDANWLN AEKPGNAYRP ADKELSQNVK VVQDDILNRE QAQREQAERA QRQKEKLEQH ISESPAGFQA ALPRLNELDV A NSWDKLLR ...String:
MSTTSMTAPA TSPSRLESMR AASSTTSSKP APTGPSKKSD APAKTKRQDK PNVNSANDSN AADTGTAAAA TRPDHGRRSR RTEDANWLN AEKPGNAYRP ADKELSQNVK VVQDDILNRE QAQREQAERA QRQKEKLEQH ISESPAGFQA ALPRLNELDV A NSWDKLLR MMRSEYDMSC LTSCLARELD EDVAWNPEML LVQLTSDMLD AAELQKDSGE AYVPVDASDI GQMTGGEVAR KR KAKRTKA AGGAEGEPEK DTEMPATASP PPTSQAATSK TPRKKATTDP AAAEPKKTQT GKAQNAGPTS AGNSSLPQKG SAA GSTSGA AGGGGGSKTS AAPSTAKRDA SKDANATKSS SSKKKTSKQV SK

UniProtKB: Intraflagellar transport protein 43

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Macromolecule #5: WD_REPEATS_REGION domain-containing protein

MacromoleculeName: WD_REPEATS_REGION domain-containing protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 152.393281 KDa
SequenceString: MVLTQQFVIS NADLGRGHVV EALHPSSPLI ALAGSKGRVL ILNKTGKVEH QLPMQNVVAM EWECSTDTLA IITSSSSDVH LYTHRTRQT DTIDTKLKDL CFVCWSQSQP LFAIGSKSGQ FVLYNRRTLR LVPVADTHKQ RLISGMWVPA QDSRLLIISE D PSLSISDA ...String:
MVLTQQFVIS NADLGRGHVV EALHPSSPLI ALAGSKGRVL ILNKTGKVEH QLPMQNVVAM EWECSTDTLA IITSSSSDVH LYTHRTRQT DTIDTKLKDL CFVCWSQSQP LFAIGSKSGQ FVLYNRRTLR LVPVADTHKQ RLISGMWVPA QDSRLLIISE D PSLSISDA EGKVLTTIPL PSVPKSVCVS GMANSPKSSS FAAVNLDNTL LIVDLRSYAT AAGQFNSALG QITCLTAGIN GE FLAGFAS GTVALLDLAG SEVRLRGSLR LLKNAVEMVN FGEGSGVVAA VADNRVGLLR ITEDGIAPTG DEASLESERG VPD LLAWSR DGQQLFVGTN QGNVTVFTLK VLNVSASYGT LVFSFTSNRT IGVKNLQDNR VVCTVPVNSD PAFISAGMAM LAAG VNNQV SYYEYFIPNS LPYPMVDPAK NVSQSSQQAH SVFLRTVEYP SPVTDLKVNS NLAAVVYDGR VQLSPIRDTP EAAAP VYFP ESGDTRLVSI ALSEVFFLYA TTSRVSVYAL HNLQQVATFT CNTGLKRAFA NPACTRVAYV DDSSELFNVN LVTEVA NKA EGYDPDQKMV LWDQAEATVF ITYDSEKCAT FVNTPHSRHG ATCESVLVKD SSEDNLYTPL PPGYTPVTLF RGTVVCQ TP NGTLETVPLQ THNNIFLRTP NAEAFYNNFS LNRLRWSSNN ITSPQEAEDL AVKSLHMLDV ELAIRVYRQL SQPSLVLC L EKIRHIHEKN LLLGHVSMIM GYMKDAQNFF LRSSQPLRAL EMRRDMMQWE RALTLAEQLA PEEVPIISRD YAQHLEYRG VYAKALEMYQ KGLRQLPTGH ASTELSVTVQ EVERHNEQCR QGAARSQIRI GNIADAMKTV KESSEVSFVK ECAKLCEENQ KHEEAAQLY EKAGDIERAA TIYIERCKNL KAAERLLPFI KSRNIIGIYA RGKEAEGAFV EAEKAFAQAE DWDNAVRLRI E KLNDLHGA YVIVRQTRSA NAAALVAKKC TAQKEYGTAV EFLVLAKSLD EAFELAKTHD CMFNFESALL NQVQLKDGIA PL SNQADFT MIAEYYDNDG KAGQAGMYYH ISGHYAKALN KYLESGQPED IEKAVEVVGK AHSDSLTNKF IDYLMGETDG EPK DPSYIF KLYLAMGSYE KAAKTSVIIS AKEQEIGNYK SAHKTLVEAY RILQQRNMHV SNDLRRALML LHSYIIVKDL LKIM KDDDT ACRMLLRVSR NIQKFPKHIT TIVTTTVLQC LKSNFKKSAF EYACYLIQNE KHRAEMTEKS RKKIEGIVRR HSKDD AVDP VEPMLPCPYC DAPVAETELD CGACKNTIPF CIVTGKHIVK SDYTSTPCCG FPAIYSALMT RLSGTLTCPM CEATID ISN VNRETNPELK ALL

UniProtKB: Wd repeat-containing protein 19

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Macromolecule #6: TPR_REGION domain-containing protein

MacromoleculeName: TPR_REGION domain-containing protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 180.805828 KDa
SequenceString: MQPSSSFLPD VWMAVTREPH IPEITPLSRI LAAAAISTYS RQVEYDLDTG CKKKRTAPPP SPPPPSSPPP SPRLTLANAA AMTTTILRT NYALLLFYVR EKYWHHAEEV CLSVIQSTDD HMFRVWRALT LERQGMANDA IREYKAVESR RTTAVPALMG M QLIYKHNR ...String:
MQPSSSFLPD VWMAVTREPH IPEITPLSRI LAAAAISTYS RQVEYDLDTG CKKKRTAPPP SPPPPSSPPP SPRLTLANAA AMTTTILRT NYALLLFYVR EKYWHHAEEV CLSVIQSTDD HMFRVWRALT LERQGMANDA IREYKAVESR RTTAVPALMG M QLIYKHNR DQEGVAQTEA KLDGFEIAAN MGGWVQAAAL CWAMGDINAA RDILLRFTDN EAAMAYRDEY TNYGTIRGWV DL LSGRGAL LEKAGALFTS VMDMEEAQYS YFQADNESGS GSRGTTKWID LNAALGYVAF LERKTQLAKA QSLLDRLFVL YPN CSIPPL VGKARLLMQA EDWEQAIEVT HRILAHDKSN VEALALEALY AMAKDTRHDA APVRVRRLLD AVRAKEPRNV ALLH QFALV FSRLAGDRLD LLSLTTQFSD MAYALDSRNG DVLCGLGYQQ LYRHDDKAAT ETFRKAATLT DSLDPLLGTV TCLLR QGDM EAAATQLQLC NQLQPAAQRN AELSMLNAQL RWHRRGMEEE TAVLRYLDQA AEAIKQDVKE RAGVGMEVYV HLNAPV ALA IAHAYIMHCR NEPPDPMFKH ADVVGEKCGR HLEFIVQHLP ACMEAQLMLA KVWFVTGEVR KAQNLLKSTL IVQEQPL PD AFLLSSQICQ YMGDTKLACQ ALAQARTLDF SLQEKPLYNL LLGTVKGTTG EYAEALASLQ RAYNTVKSAA TAPSAGKP T NPLSVPETVT LYLQLAQAQL RVRDVDAARE TLTEAALKFR GSAQIGRVII AQAMLAARTD VDKSIELLRQ VSSKSEFYI AAHSQLGKLF LTHKHNVAMY IQCFQEMAES VPSAQSYVEL GEAYTTIQEP EQAIAAYEKA KALSPSSSEL SVRVGRALVA AHDYAKAIR YYQDALVTDP HLSIVRADLA TLQWRLGHIE EARETIVASP VYELPSTDGA GAGVASAAAA GSAEAVGTAI E RINLYLLL YKVLRDQPWT VPLSEEGTAA ADSDDNHGDA ALTALLTARS LQRRLLEHQL RTTEAPEVIT EQRVVMSRIC TE AGARCIY STPAPPPFSV VMTDKKVEAA AALAVQSAIA SRLTNAREYL REAIAFDESN ERAQLESAQL CYRTGDTEGC EQH CTTVLR MAEGSANTAD AAILLANLYT EQNRDEDARN MFEDLLRKTP QHYEALVYYL ILLYHAGQLP EAKEALERAA AAVP IGQRA DPGLSYVRGL YEHLCNNNAE ALRHFNLARL PAGNPWCTRA LVRMIRIYLV PTTQDLWVRG TSPAAAAATA VADPP RAKE QQQKSATPGK VPLAAATTGS TELHDNIRHA EQLLLLLPVH SEERRILQAY CTMATRRPEE LETALHLFLE CIVAAE TGG VSAAMTAEKN GGSGSPKKTA AEERKQPRRG KGGDSDDDED LQLLASMHEA AAELAQRSSG NSTATLAFAL QCKVIHP EA FLGLAICLFI SGQETAARNV LARLLESKDI TTKMSAMKQA EDKEDAASKD AASKEAAEPA APMVLSPPIA ILTCSEDD T IERAMLFEAY MDTQEGRLKD ARFVLQQVLS ANEGCSSAWN ELGLIYERNQ KHKNASQCYQ KAWKLVQEAD PDVGYKLGF NYLRGGQPVK AIDVCKRVLT HHATYPRIEA DIMDAAYSML RP

UniProtKB: Uncharacterized protein

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 4 / 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

Concentration1.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMHEPES
5.0 mMMagnesium sulfateMgSO4
1.0 mMCalcium chlorideCaCl2
50.0 mMPotassium chlorideKCl
1.0 mMDTT
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / 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: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 57.8 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: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 239280

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-8f5o:
Structure of Leishmania tarentolae IFT-A (state 1)

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