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- EMDB-38300: Cryo-EM structure of partial dimeric WDR11-FAM91A1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-38300
TitleCryo-EM structure of partial dimeric WDR11-FAM91A1 complex
Map data
Sample
  • Complex: Cryo-EM structure of partial dimeric WDR11-FAM91A1 complex
    • Protein or peptide: WD repeat-containing protein 11
    • Protein or peptide: Protein FAM91A1
KeywordsCryo-EM / Vesicle Trafficking / Neural Development / PROTEIN TRANSPORT
Function / homology
Function and homology information


vesicle tethering to Golgi / head development / regulation of smoothened signaling pathway / RHOH GTPase cycle / axoneme / cilium assembly / intracellular protein transport / trans-Golgi network / multicellular organism growth / heart development ...vesicle tethering to Golgi / head development / regulation of smoothened signaling pathway / RHOH GTPase cycle / axoneme / cilium assembly / intracellular protein transport / trans-Golgi network / multicellular organism growth / heart development / microtubule cytoskeleton / cytoplasmic vesicle / ciliary basal body / cilium / lysosomal membrane / intracellular membrane-bounded organelle / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
WD repeat-containing protein 11 / WDR11 first beta-propeller / WDR11 second beta-propeller / WDR11 TPR domain / FAM91, N-terminal domain / FAM91, C-terminal domain / FAM91 / FAM91 N-terminus / FAM91 C-terminus / WD40 repeat, conserved site ...WD repeat-containing protein 11 / WDR11 first beta-propeller / WDR11 second beta-propeller / WDR11 TPR domain / FAM91, N-terminal domain / FAM91, C-terminal domain / FAM91 / FAM91 N-terminus / FAM91 C-terminus / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Protein FAM91A1 / WD repeat-containing protein 11
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsJia GW / Deng QH / Su ZM / Jia D
Funding support China, 6 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303700 China
Ministry of Science and Technology (MoST, China)2022YFA1105200 China
National Natural Science Foundation of China (NSFC)92254302 China
National Natural Science Foundation of China (NSFC)32222040 China
National Natural Science Foundation of China (NSFC)32070049 China
National Natural Science Foundation of China (NSFC)32300578 China
CitationJournal: Cell / Year: 2024
Title: The WDR11 complex is a receptor for acidic-cluster-containing cargo proteins.
Authors: Huaqing Deng / Guowen Jia / Ping Li / Yingying Tang / Lin Zhao / Qin Yang / Jia Zhao / Jinrui Wang / Yingfeng Tu / Xin Yong / Sitao Zhang / Xianming Mo / Daniel D Billadeau / Zhaoming Su / Da Jia /
Abstract: Vesicle trafficking is a fundamental process that allows for the sorting and transport of specific proteins (i.e., "cargoes") to different compartments of eukaryotic cells. Cargo recognition ...Vesicle trafficking is a fundamental process that allows for the sorting and transport of specific proteins (i.e., "cargoes") to different compartments of eukaryotic cells. Cargo recognition primarily occurs through coats and the associated proteins at the donor membrane. However, it remains unclear whether cargoes can also be selected at other stages of vesicle trafficking to further enhance the fidelity of the process. The WDR11-FAM91A1 complex functions downstream of the clathrin-associated AP-1 complex to facilitate protein transport from endosomes to the TGN. Here, we report the cryo-EM structure of human WDR11-FAM91A1 complex. WDR11 directly and specifically recognizes a subset of acidic clusters, which we term super acidic clusters (SACs). WDR11 complex assembly and its binding to SAC-containing proteins are indispensable for the trafficking of SAC-containing proteins and proper neuronal development in zebrafish. Our studies thus uncover that cargo proteins could be recognized in a sequence-specific manner downstream of a protein coat.
History
DepositionDec 13, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38300.png

Downloads & links

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Map

FileDownload / File: emd_38300.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 384 pix.
= 326.4 Å		0.85 Å/pix.
x 384 pix.
= 326.4 Å		0.85 Å/pix.
x 384 pix.
= 326.4 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.0016326896 - 1.8624064
Average (Standard dev.)0.0009034493 (±0.021947056)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 326.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38300_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38300_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of partial dimeric WDR11-FAM91A1 complex

EntireName: Cryo-EM structure of partial dimeric WDR11-FAM91A1 complex
Components
  • Complex: Cryo-EM structure of partial dimeric WDR11-FAM91A1 complex
    • Protein or peptide: WD repeat-containing protein 11
    • Protein or peptide: Protein FAM91A1

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Supramolecule #1: Cryo-EM structure of partial dimeric WDR11-FAM91A1 complex

SupramoleculeName: Cryo-EM structure of partial dimeric WDR11-FAM91A1 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: WD repeat-containing protein 11

MacromoleculeName: WD repeat-containing protein 11 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 136.843406 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MLPYTVNFKV SARTLTGALN AHNKAAVDWG WQGLIAYGCH SLVVVIDSIT AQTLQVLEKH KADVVKVKWA RENYHHNIGS PYCLRLASA DVNGKIIVWD VAAGVAQCEI QEHAKPIQDV QWLWNQDASR DLLLAIHPPN YIVLWNADTG TKLWKKSYAD N ILSFSFDP ...String:
MLPYTVNFKV SARTLTGALN AHNKAAVDWG WQGLIAYGCH SLVVVIDSIT AQTLQVLEKH KADVVKVKWA RENYHHNIGS PYCLRLASA DVNGKIIVWD VAAGVAQCEI QEHAKPIQDV QWLWNQDASR DLLLAIHPPN YIVLWNADTG TKLWKKSYAD N ILSFSFDP FDPSHLTLLT SEGIVFISDF SPSKPPSGPG KKVYISSPHS SPAHNKLATA TGAKKALNKV KILITQEKPS AE FITLNDC LQLAYLPSKR NHMLLLYPRE ILILDLEVNQ TVGVIAIERT GVPFLQVIPC FQRDGLFCLH ENGCITLRVR RSY NNIFTT SNEEPDPDPV QELTYDLRSQ CDAIRVTKTV RPFSMVCCPV NENAAALVVS DGRVMIWELK SAVCNRNSRN SSSG VSPLY SPVSFCGIPV GVLQNKLPDL SLDNMIGQSA IAGEEHPRGS ILREVHLKFL LTGLLSGLPA PQFAIRMCPP LTTKN IKMY QPLLAVGTSN GSVLVYHLTS GLLHKELSIH SCEVKGIEWT SLTSFLSFAT STPNNMGLVR NELQLVDLPT GRSIAF RGE RGNDESAIEM IKVSHLKQYL AVVFRDKPLE LWDVRTCTLL REMSKNFPTI TALEWSPSHN LKSLRKKQLA TREAMAR QT VVSDTELSIV ESSVISLLQE AESKSELSQN ISAREHFVFT DIDGQVYHLT VEGNSVKDSA RIPPDGSMGS ITCIAWKG D TLVLGDMDGN LNFWDLKGRV SRGIPTHRSW VRKIRFAPGK GNQKLIAMYN DGAEVWDTKE VQMVSSLRSG RNVTFRILD VDWCTSDKVI LASDDGCIRV LEMSMKSACF RMDEQELTEP VWCPYLLVPR ASLALKAFLL HQPWNGQYSL DISHVDYPEN EEIKNLLQE QLNSLSNDIK KLLLDPEFTL LQRCLLVSRL YGDESELHFW TVAAHYLHSL SQEKSASTTA PKEAAPRDKL S NPLDICYD VLCENAYFQK FQLERVNLQE VKRSTYDHTR KCTDQLLLLG QTDRAVQLLL ETSADNQHYY CDSLKACLVT TV TSSGPSQ STIKLVATNM IANGKLAEGV QLLCLIDKAA DACRYLQTYG EWNRAAWLAK VRLNPEECAD VLRRWVDHLC SPQ VNQKSK ALLVLLSLGC FFSVAETLHS MRYFDRAALF VEACLKYGAF EVTEDTEKLI TAIYADYARS LKNLGFKQGA VLFA SKAGA AGKDLLNELE SPKEEPIEE

UniProtKB: WD repeat-containing protein 11

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Macromolecule #2: Protein FAM91A1

MacromoleculeName: Protein FAM91A1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 95.253234 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHM NIDVEFHIRH NYPWNKLPAN VRQSLGNSQR EYEKQVVLYS IRNQLRYRNN LVKHVKKDER RYYEELLKYS RDHLMLYPY HLSDIMVKGL RITPFSYYTG IMEDIMNSEK SYDSLPNFTA ADCLRLLGIG RNQYIDLMNQ CRSSKKFFRR K TARDLLPI ...String:
MHHHHHHHHM NIDVEFHIRH NYPWNKLPAN VRQSLGNSQR EYEKQVVLYS IRNQLRYRNN LVKHVKKDER RYYEELLKYS RDHLMLYPY HLSDIMVKGL RITPFSYYTG IMEDIMNSEK SYDSLPNFTA ADCLRLLGIG RNQYIDLMNQ CRSSKKFFRR K TARDLLPI KPVEIAIEAW WVVQAGYITE DDIKICTLPE KCAVDKIIDS GPQLSGSLDY NVVHSLYNKG FIYLDVPISD DS CIAVPPL EGFVMNRVQG DYFETLLYKI FVSIDEHTNV AELANVLEID LSLVKNAVSM YCRLGFAHKK GQVINLDQLH SSW KNVPSV NRLKSTLDPQ KMLLSWDGGE SRSPVQEASS ATDTDTNSQE DPADTASVSS LSLSTGHTKR IAFLFDSTLT AFLM MGNLS PNLKSHAVTM FEVGKLSDES LDSFLIELEK VQSTGEGEAQ RYFDHALTLR NTILFLRHNK DLVAQTAQPD QPNYG FPLD LLRCESLLGL DPATCSRVLN KNYTLLVSMA PLTNEIRPVS SCTPQHIGPA IPEVSSVWFK LYIYHVTGQG PPSLLL SKG TRLRKLPDIF QSYDRLLITS WGHDPGVVPT SNVLTMLNDA LTHSAVLIQG HGLHGIGETV HVPFPFDETE LQGEFTR VN MGVHKALQIL RNRVDLQHLC GYVTMLNASS QLADRKLSDA SDERGEPDLA SGSDVNGSTE SFEMVIEEAT IDSATKQT S GATTEADWVP LELCFGIPLF SSELNRKVCR KIAAHGLCRK ESLQNLLHSS RKLSLQVLNF VHSFQEGASI LDIHTEPSF SSLLSQSSCA DMGVPLPAKN LIFKDGVLSE WSGRSPSSLL IANLHLQ

UniProtKB: Protein FAM91A1

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35698
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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