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- EMDB-65260: Cryo-EM structure of Elapor1WT in tetrameric form -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-65260
TitleCryo-EM structure of Elapor1WT in tetrameric form
Map data
Sample
  • Complex: Tetrameric Elapor1 bound to copper
    • Protein or peptide: Endosome/lysosome-associated apoptosis and autophagy regulator 1
    • Protein or peptide: Endosome/lysosome-associated apoptosis and autophagy regulator 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: COPPER (II) ION
KeywordsTethering factor / MEMBRANE PROTEIN
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
Endosome/lysosome-associated apoptosis and autophagy regulator 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMa J / Zheng S
Funding support China, 1 items
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, 2025-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65260.png

Downloads & links

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Map

FileDownload / File: emd_65260.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 350 pix.
= 380.45 Å		1.09 Å/pix.
x 350 pix.
= 380.45 Å		1.09 Å/pix.
x 350 pix.
= 380.45 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-2.3542829 - 3.194511
Average (Standard dev.)-0.001126053 (±0.055588584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 380.45 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65260_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_65260_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 : Tetrameric Elapor1 bound to copper

EntireName: Tetrameric Elapor1 bound to copper
Components
  • Complex: Tetrameric Elapor1 bound to copper
    • Protein or peptide: Endosome/lysosome-associated apoptosis and autophagy regulator 1
    • Protein or peptide: Endosome/lysosome-associated apoptosis and autophagy regulator 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: COPPER (II) ION

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Supramolecule #1: Tetrameric Elapor1 bound to copper

SupramoleculeName: Tetrameric Elapor1 bound to copper / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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

MacromoleculeName: Endosome/lysosome-associated apoptosis and autophagy regulator 1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 108.851289 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKGS HHHHHHSGTG PELHACKESE YHFEYTACDS TGSRWRVAVP HSPGLCTSLP DPVKGTECSF SCNAGEFLDM KDQSCKPCA EGRYSLGTGI RFDEWDELPH GFASLSANLE VDDSISESTE NCTSSKWVPR GDYIASNTDE CTATLMYAVN L KQSGTVNF ...String:
DYKDDDDKGS HHHHHHSGTG PELHACKESE YHFEYTACDS TGSRWRVAVP HSPGLCTSLP DPVKGTECSF SCNAGEFLDM KDQSCKPCA EGRYSLGTGI RFDEWDELPH GFASLSANLE VDDSISESTE NCTSSKWVPR GDYIASNTDE CTATLMYAVN L KQSGTVNF EYYYPDSSII FEFFVQNDQC QPSADDSRWM KTTEKGWEFH SVELNRGNNV LYWRTTAFSV WSKVSKPVLV RN IAITGVA YTSECFPCKP GTYAAKQGSP FCKLCPANYY SNKGETSCHP CDADKYSEKG SSTCKVRPAC TDKDYFYTHT ACD AQGETQ LMYKWAIPKI CGEDLEGAVK LPASGVKTRC PPCNPGFFKT DNSTCEPCPY GSYSNGSDCT HCPAGTEPAV GFEY KWWNT LPSNMETTVL SGINFEYKGL TGWEVAGDHI YTAVGASDND FMILTLVVPG FRPPQSVVAD TENKEVARIT FVFET ICSV NCELYFMVGM NSRTNTPVET WKGTKGKQSY TYTIEENATV SFTWAFQRTT LHETGRKYTN DVAKIYSINV TNVMGG VAS YCRPCALEAS DLGSSCTSCP AGHYINRDSG TCHLCPSNTI LKAHQPYGAQ ACVPCGPGTK NNKIHSLCYN DCTFSRN TP SRIFNYNFSA LAGTVSLAGV PSFTSKGLKY FHHFTLSLCG NQGKKMAVCT DNVTDLRIPD GEAGFSKSVT AYVCQVVI I PSEVMGYKAG VSSQPVSLAD RLVGVSTDMT LEGIVSPVEL FHPETSGIPD IVFFFRSNDV TQSCSSGRST TIRLRCNPM KAAPGTLRLP SMCSDGTCDG CNFHFLWESV AACPLCSASD YHTFVSSCVA GIQKTTYMWR EPKLCSGGIS LPEQRVTICK TIDFWLKVG ISAGTCTAIL LTVLTCYFWK KNQKLEYKYS KLVMNATLKD CDLPAADSCA IMEGEDVEDD FIFTSKKSLF G KIKSFTSK RTPDGFDSVP LKTSSGGPDM DM

UniProtKB: Endosome/lysosome-associated apoptosis and autophagy regulator 1

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Macromolecule #2: Endosome/lysosome-associated apoptosis and autophagy regulator 1

MacromoleculeName: Endosome/lysosome-associated apoptosis and autophagy regulator 1
type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 110.543531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTIIALSYI FCLVFADYKD DDDKGSHHHH HHSGMELHAC KESEYHFEYT ACDSTGSRWR VAVPHSPGLC TSLPDPVKGT ECSFSCNAG EFLDMKDQSC KPCAEGRYSL GTGIRFDEWD ELPHGFASLS ANLEVDDSIS ESTENCTSSK WVPRGDYIAS N TDECTATL ...String:
MKTIIALSYI FCLVFADYKD DDDKGSHHHH HHSGMELHAC KESEYHFEYT ACDSTGSRWR VAVPHSPGLC TSLPDPVKGT ECSFSCNAG EFLDMKDQSC KPCAEGRYSL GTGIRFDEWD ELPHGFASLS ANLEVDDSIS ESTENCTSSK WVPRGDYIAS N TDECTATL MYAVNLKQSG TVNFEYYYPD SSIIFEFFVQ NDQCQPSADD SRWMKTTEKG WEFHSVELNR GNNVLYWRTT AF SVWSKVS KPVLVRNIAI TGVAYTSECF PCKPGTYAAK QGSPFCKLCP ANYYSNKGET SCHPCDADKY SEKGSSTCKV RPA CTDKDY FYTHTACDAQ GETQLMYKWA IPKICGEDLE GAVKLPASGV KTRCPPCNPG FFKTDNSTCE PCPYGSYSNG SDCT HCPAG TEPAVGFEYK WWNTLPSNME TTVLSGINFE YKGLTGWEVA GDHIYTAVGA SDNDFMILTL VVPGFRPPQS VVADT ENKE VARITFVFET ICSVNCELYF MVGMNSRTNT PVETWKGTKG KQSYTYTIEE NATVSFTWAF QRTTLHETGR KYTNDV AKI YSINVTNVMG GVASYCRPCA LEASDLGSSC TSCPAGHYIN RDSGTCHLCP SNTILKAHQP YGAQACVPCG PGTKNNK IH SLCYNDCTFS RNTPSRIFNY NFSALAGTVS LAGVPSFTSK GLKYFHHFTL SLCGNQGKKM AVCTDNVTDL RIPDGEAG F SKSVTAYVCQ VVIIPSEVMG YKAGVSSQPV SLADRLVGVS TDMTLEGIVS PVELFHPETS GIPDIVFFFR SNDVTQSCS SGRSTTIRLR CNPMKAAPGT LRLPSMCSDG TCDGCNFHFL WESVAACPLC SASDYHTFVS SCVAGIQKTT YMWREPKLCS GGISLPEQR VTICKTIDFW LKVGISAGTC TAILLTVLTC YFWKKNQKLE YKYSKLVMNA TLKDCDLPAA DSCAIMEGED V EDDFIFTS KKSLFGKIKS FTSKRTPDGF DSVPLKTSSG GPDMDM

UniProtKB: Endosome/lysosome-associated apoptosis and autophagy regulator 1

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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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: 7.4
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 929496
CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 291029
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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