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- PDB-8xfb: Cryo-EM structure of partial dimeric WDR11-FAM91A1 complex -

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Basic information

Entry
Database: PDB / ID: 8xfb
TitleCryo-EM structure of partial dimeric WDR11-FAM91A1 complex
Components
  • Protein FAM91A1
  • WD repeat-containing protein 11
KeywordsPROTEIN TRANSPORT / Cryo-EM / Vesicle Trafficking / Neural Development
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsJia, G.W. / Deng, Q.H. / Su, Z.M. / Jia, D.
Funding support China, 6items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update
Revision 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: WD repeat-containing protein 11
A: Protein FAM91A1
B: WD repeat-containing protein 11


Theoretical massNumber of molelcules
Total (without water)368,9403
Polymers368,9403
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein WD repeat-containing protein 11


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
#2: Protein Protein FAM91A1


Mass: 95253.234 Da / Num. of mol.: 1
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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of partial dimeric WDR11-FAM91A1 complex
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 52 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35698 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212081
ELECTRON MICROSCOPYf_angle_d0.46916387
ELECTRON MICROSCOPYf_dihedral_angle_d3.1021595
ELECTRON MICROSCOPYf_chiral_restr0.0391889
ELECTRON MICROSCOPYf_plane_restr0.0062070

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