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- PDB-24ip: Cryo-EM structure of the dimeric WDR11-FAM91A1-C17orf75 complex -

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Basic information

Entry
Database: PDB / ID: 24ip
TitleCryo-EM structure of the dimeric WDR11-FAM91A1-C17orf75 complex
Components
  • Protein FAM91A1
  • Protein Njmu-R1
  • WD repeat-containing protein 11
KeywordsPROTEIN TRANSPORT / dimeric WDR11-FAM91A1-C17orf75 complex
Function / homology
Function and homology information


: / head development / regulation of smoothened signaling pathway / RHOH GTPase cycle / cilium assembly / axoneme / multicellular organism growth / centriole / sperm end piece / sperm principal piece ...: / head development / regulation of smoothened signaling pathway / RHOH GTPase cycle / cilium assembly / axoneme / multicellular organism growth / centriole / sperm end piece / sperm principal piece / trans-Golgi network / intracellular protein transport / heart development / microtubule cytoskeleton / cytoplasmic vesicle / cilium / ciliary basal body / lysosomal membrane / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein Njmu-R1 / Njmu-R1-like protein family / WD repeat-containing protein 11 / : / : / : / WDR11 first beta-propeller / WDR11 second beta-propeller / WDR11 TPR domain / FAM91, N-terminal domain ...Protein Njmu-R1 / Njmu-R1-like protein family / 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 / Protein Njmu-R1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsLiu, Z.M. / Zhang, Y.F. / Chen, Z.Y. / Chen, Z.G. / Ding, J.P.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071190 China
National Natural Science Foundation of China (NSFC)32571391 China
Ministry of Science and Technology (MoST, China)2020YFA0509000 China
Ministry of Science and Technology (MoST, China)2020YFA0803200 China
CitationJournal: Structure / Year: 2026
Title: Cryo-EM structure of the dimeric WDR11-FAM91A1-C17orf75 complex (focused on body1)
Authors: Liu, Z.M. / Zhang, Y.F. / Chen, Z.Y. / Chen, Z.G. / Ding, J.P.
History
DepositionMar 4, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: WD repeat-containing protein 11
C: Protein Njmu-R1
A: WD repeat-containing protein 11
B: Protein FAM91A1
F: Protein Njmu-R1
E: Protein FAM91A1


Theoretical massNumber of molelcules
Total (without water)559,8446
Polymers559,8446
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein WD repeat-containing protein 11 / Bromodomain and WD repeat-containing protein 2 / WD repeat-containing protein 15


Mass: 138330.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR11, BRWD2, KIAA1351, WDR15 / Production host: Homo sapiens (human) / References: UniProt: Q9BZH6
#2: Protein Protein Njmu-R1


Mass: 46157.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C17orf75 / Production host: Homo sapiens (human) / References: UniProt: Q9HAS0
#3: Protein Protein FAM91A1


Mass: 95433.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM91A1 / Production host: Homo sapiens (human) / 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: dimeric WDR11-FAM91A1-C17orf75 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS 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: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 190979 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00128803
ELECTRON MICROSCOPYf_angle_d0.38539032
ELECTRON MICROSCOPYf_dihedral_angle_d17.12210579
ELECTRON MICROSCOPYf_chiral_restr0.0384448
ELECTRON MICROSCOPYf_plane_restr0.0034970

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