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- PDB-9vqm: Cryo-EM structure of Elapor1WT in tetrameric form -

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Basic information

Entry
Database: PDB / ID: 9vqm
TitleCryo-EM structure of Elapor1WT in tetrameric form
Components(Endosome/lysosome-associated apoptosis and autophagy regulator 1) x 2
KeywordsMEMBRANE PROTEIN / Tethering factor
Function / homology
Function and homology information


positive regulation of autophagosome assembly / autophagosome assembly / cellular response to starvation / trans-Golgi network / late endosome / lysosome / plasma membrane
Similarity search - Function
EIG121-like / : / : / : / : / : / ELAPOR1-like, galactose binding domain / ELAPOR1-like, galactose-binding domain / ELAPOR1-like, mannose 6-phosphate receptor homology domain / ELAPOR1-like, C-terminal domain ...EIG121-like / : / : / : / : / : / ELAPOR1-like, galactose binding domain / ELAPOR1-like, galactose-binding domain / ELAPOR1-like, mannose 6-phosphate receptor homology domain / ELAPOR1-like, C-terminal domain / ELAPOR1-like, TNF receptor-like / Mannose-6-phosphate receptor binding domain superfamily / MRH domain / MRH domain profile. / Putative ephrin-receptor like / Growth factor receptor cysteine-rich domain superfamily
Similarity search - Domain/homology
COPPER (II) ION / Endosome/lysosome-associated apoptosis and autophagy regulator 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMa, J. / Zheng, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: ELAPOR1 is A Copper-Dependent Tethering Factor Driving Proacrosomal Vesicle Fusion in Acrosome Biogenesis
Authors: Shao, T. / Ma, J.
History
DepositionJul 5, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endosome/lysosome-associated apoptosis and autophagy regulator 1
B: Endosome/lysosome-associated apoptosis and autophagy regulator 1
C: Endosome/lysosome-associated apoptosis and autophagy regulator 1
D: Endosome/lysosome-associated apoptosis and autophagy regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)444,60022
Polymers440,4824
Non-polymers4,11818
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Endosome/lysosome-associated apoptosis and autophagy regulator 1


Mass: 108851.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Elapor1, 5330417C22Rik / Production host: Homo sapiens (human) / References: UniProt: A0A0A0MQC6
#2: Protein Endosome/lysosome-associated apoptosis and autophagy regulator 1


Mass: 110543.531 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Elapor1, 5330417C22Rik / Production host: Homo sapiens (human) / References: UniProt: A0A0A0MQC6
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Tetrameric Elapor1 bound to copper / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13Coot3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 929496
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 291029 / Symmetry type: POINT

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