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- EMDB-39949: Cryo-EM structure of WDR11-dm-FAM91A1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-39949
TitleCryo-EM structure of WDR11-dm-FAM91A1 complex
Map data
Sample
  • Complex: Cryo-EM structure of WDR11-dm-FAM91A1 complex
    • Protein or peptide: Protein FAM91A1
  • Protein or peptide: WD repeat-containing protein 11 dm
KeywordsCryo-EM / Vesicle Trafficking / Neural Development / PROTEIN TRANSPORT
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 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
DepositionApr 30, 2024-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39949.png

Downloads & links

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Map

FileDownload / File: emd_39949.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.038
Minimum - Maximum-0.06149222 - 0.113032945
Average (Standard dev.)0.00006758538 (±0.0053193728)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 244.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39949_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_39949_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 : Cryo-EM structure of WDR11-dm-FAM91A1 complex

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

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

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

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Macromolecule #1: Protein FAM91A1

MacromoleculeName: Protein FAM91A1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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

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Macromolecule #2: WD repeat-containing protein 11 dm

MacromoleculeName: WD repeat-containing protein 11 dm / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MLPYTVNFKV SARTLTGALN AHNKAAVDWG WQGLIAYGCH SLVVVIDSIT AQTLQVLEKH KADVVKVKWA RENYHHNIGS PYCLRLASAD VNGKIIVWDV AAGVAQCEIQ EHAKPIQDVQ WLWNQDASRD LLLAIHPPNY IVLWNADTGT KLWKKSYADN ILSFSFDPFD ...String:
MLPYTVNFKV SARTLTGALN AHNKAAVDWG WQGLIAYGCH SLVVVIDSIT AQTLQVLEKH KADVVKVKWA RENYHHNIGS PYCLRLASAD VNGKIIVWDV AAGVAQCEIQ EHAKPIQDVQ WLWNQDASRD LLLAIHPPNY IVLWNADTGT KLWKKSYADN ILSFSFDPFD PSHLTLLTSE GIVFISDFSP SKPPSGPGKK VYISSPHSSP AHNKLATATG AKKALNKVKI LITQEKPSAE FITLNDCLQL AYLPSKRNHM LLLYPREILI LDLEVNQTVG VIAIERTGVP FLQVIPCFQR DGLFCLHENG CITLRVRRSY NNIFTTSNEE PDPDPVQELT YDLRSQCDAI RVTKTVRPFS MVCCPVNENA AALVVSDGRV MIWELKSAVC NRNSRNSSSG VSPLYSPVSF CGIPVGVLQN KLPDLSLDNM IGQSAIAGEE HPRGSILREV HLKFLLTGLL SGLPAPQFAI RMCPPLTTKN IKMYQPLLAV GTSNGSVLVY HLTSGLLHKE LSIHSCEVKG IEWTSLTSFL SFATSTPNNM GLVRNELQLV DLPTGRSIAF RGERGNDESA IEMIKVSHLK QYLAVVFRDK PLELWDVRTC TLLREMSKNF PTITALEWSP SHNLKSLRKK QLATREAMAR QTVVSDTELS IVESSVISLL QEAESKSELS QNISAREHFV FTDIDGQVYH LTVEGNSVKD SARIPPDGSM GSITCIAWKG DTLVLGDMDG NLNFWDLKGR VSRGIPTHRS WVRKIRFAPG KGNQKLIAMY NDGAEVWDTK EVQMVSSLRS GRNVTFRILD VDWCTSDKVI LASDDGCIRV LEMSMKSACF RMDEQELTEP VWCPYLLVPR ASLALKAFLL HQPWNGQYSL DISHVDYPEN EEIKNLLQEQ LNSLSNDIKK LLLDPEFTLL QRCLLVSRLY GDESELHFWT VAAHYLHSLS QEKSASTTAP KEAAPRDKLS NPLDICYDVL CENAYFQKFQ LERVNLQEVK RSTYDHTRKC TDQLLLLGQT DRAVQLLLET SADNQHGGSG GSGGSTVTSS GPSQSTIKLV ATNMIANGKL AEGVQLLCLI DKAADACRYL QTYGEWNRAA WLAKVRLNPE ECADVLRRWV DHLCSPQVNQ KSKALLVLLS LGCFFSVAET LHSMRYFDRA ALFVEACLKY GAFEVTEDTE KLITAIYADY ARSLKNLGFK QGAVLFASKA GAAGKDLLNE LESPKEEPIE E

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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: 58.47 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.992 µm / Nominal defocus min: 0.2 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: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35118
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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