+Open data
-Basic information
Entry | Database: PDB / ID: 8z9m | |||||||||||||||||||||
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Title | Cryo-EM structure of dimeric WDR11-FAM91A1 complex | |||||||||||||||||||||
Components |
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Keywords | PROTEIN TRANSPORT / Cryo-EM / Vesicle Trafficking / Neural Development | |||||||||||||||||||||
Function / homology | Function and homology information vesicle tethering to Golgi / head development / regulation of smoothened signaling pathway / axoneme / RHOH GTPase cycle / cilium assembly / ciliary basal body / intracellular protein transport / trans-Golgi network / multicellular organism growth ...vesicle tethering to Golgi / head development / regulation of smoothened signaling pathway / axoneme / RHOH GTPase cycle / cilium assembly / ciliary basal body / intracellular protein transport / trans-Golgi network / multicellular organism growth / microtubule cytoskeleton / heart development / cytoplasmic vesicle / lysosomal membrane / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||||||||
Authors | Jia, G.W. / Deng, Q.H. / Su, Z.M. / Jia, D. | |||||||||||||||||||||
Funding support | China, 6items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8z9m.cif.gz | 510.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8z9m.ent.gz | 400.8 KB | Display | PDB format |
PDBx/mmJSON format | 8z9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8z9m_validation.pdf.gz | 701.7 KB | Display | wwPDB validaton report |
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Full document | 8z9m_full_validation.pdf.gz | 716.3 KB | Display | |
Data in XML | 8z9m_validation.xml.gz | 71.5 KB | Display | |
Data in CIF | 8z9m_validation.cif.gz | 108.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/8z9m ftp://data.pdbj.org/pub/pdb/validation_reports/z9/8z9m | HTTPS FTP |
-Related structure data
Related structure data | 39863MC 8xfbC 61078 M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 95253.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FAM91A1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q658Y4 #2: Protein | Mass: 136843.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR11 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BZH6 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cryo-EM structure of dimeric WDR11-FAM91A1 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2992 nm / Nominal defocus min: 200 nm |
Image recording | Electron dose: 58.47 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 232473 / Symmetry type: POINT |