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- EMDB-67657: The cryo-EM map of p24 complex at pH 7.5 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-67657
TitleThe cryo-EM map of p24 complex at pH 7.5
Map data
Sample
  • Complex: Structure of the GPI-AP transporter
    • Protein or peptide: Transmembrane emp24 domain-containing protein 9
    • Protein or peptide: Transmembrane emp24 domain-containing protein 2
    • Protein or peptide: Transmembrane emp24 domain-containing protein 5
    • Protein or peptide: Transmembrane emp24 domain-containing protein 10
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsMembrane protein / GPI-AP / Transporter
Function / homology
Function and homology information


: / regulation of cargo loading into COPII-coated vesicle / COPI-coated vesicle budding / protein localization to ERGIC / cytosol to ERGIC protein transport / maternal placenta development / COPI-coated vesicle membrane / COPI coating of Golgi vesicle / vesicle cargo loading / positive regulation of organelle organization ...: / regulation of cargo loading into COPII-coated vesicle / COPI-coated vesicle budding / protein localization to ERGIC / cytosol to ERGIC protein transport / maternal placenta development / COPI-coated vesicle membrane / COPI coating of Golgi vesicle / vesicle cargo loading / positive regulation of organelle organization / smoothened binding / COPI-coated vesicle / gamma-secretase complex / WNT ligand biogenesis and trafficking / zymogen granule membrane / regulation of amyloid-beta formation / labyrinthine layer blood vessel development / regulated exocytosis / Golgi ribbon formation / Pre-NOTCH Processing in Golgi / COPII vesicle coat assembly / embryonic morphogenesis / positive regulation of interleukin-1 production / negative regulation of GTPase activity / trans-Golgi network transport vesicle / cis-Golgi network / Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / frizzled binding / COPII-mediated vesicle transport / syntaxin binding / Golgi cisterna membrane / COPI-dependent Golgi-to-ER retrograde traffic / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Golgi organization / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum exit site / transmembrane protein transporter activity / endoplasmic reticulum to Golgi vesicle-mediated transport / transport vesicle / COPI-mediated anterograde transport / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / protein localization to plasma membrane / positive regulation of protein secretion / ER to Golgi transport vesicle membrane / intracellular protein transport / melanosome / synaptic vesicle / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Transmembrane emp24 domain-containing protein / emp24/gp25L/p24 family/GOLD / emp24/gp25L/p24 family/GOLD / GOLD domain superfamily / GOLD domain / GOLD domain profile.
Similarity search - Domain/homology
Transmembrane emp24 domain-containing protein 10 / Transmembrane emp24 domain-containing protein 2 / Transmembrane emp24 domain-containing protein 9 / Transmembrane emp24 domain-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHua ZK / Zhang D / Zhang M / Yu HJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of the GPI-AP transporter in pH 7.5
Authors: Hua ZK / Zhang D / Zhang M / Yu HJ
History
DepositionDec 11, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67657.png

Downloads & links

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Map

FileDownload / File: emd_67657.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.54 Å/pix.
x 448 pix.
= 241.92 Å		0.54 Å/pix.
x 448 pix.
= 241.92 Å		0.54 Å/pix.
x 448 pix.
= 241.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.54 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0493
Minimum - Maximum-0.29017198 - 0.41621476
Average (Standard dev.)0.00015085975 (±0.006270163)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 241.92001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_67657_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_67657_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 : Structure of the GPI-AP transporter

EntireName: Structure of the GPI-AP transporter
Components
  • Complex: Structure of the GPI-AP transporter
    • Protein or peptide: Transmembrane emp24 domain-containing protein 9
    • Protein or peptide: Transmembrane emp24 domain-containing protein 2
    • Protein or peptide: Transmembrane emp24 domain-containing protein 5
    • Protein or peptide: Transmembrane emp24 domain-containing protein 10
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Structure of the GPI-AP transporter

SupramoleculeName: Structure of the GPI-AP transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transmembrane emp24 domain-containing protein 9

MacromoleculeName: Transmembrane emp24 domain-containing protein 9 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.353512 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LYFHIGETEK KCFIEEIPDE TMVIGNYRTQ LYDKQREEYQ PATPGLGMFV EVKDPEDKVI LARQYGSEGR FTFTSHTPGE HQICLHSNS TKFSLFAGGM LRVHLDIQVG EHANDYAEIA AKDKLSELQL RVRQLVEQVE QIQKEQNYQR WREERFRQTS E STNQRVLW ...String:
LYFHIGETEK KCFIEEIPDE TMVIGNYRTQ LYDKQREEYQ PATPGLGMFV EVKDPEDKVI LARQYGSEGR FTFTSHTPGE HQICLHSNS TKFSLFAGGM LRVHLDIQVG EHANDYAEIA AKDKLSELQL RVRQLVEQVE QIQKEQNYQR WREERFRQTS E STNQRVLW WSILQTLILV AIGVWQMRHL KSFFEAKKLV

UniProtKB: Transmembrane emp24 domain-containing protein 9

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Macromolecule #2: Transmembrane emp24 domain-containing protein 2

MacromoleculeName: Transmembrane emp24 domain-containing protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.805738 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
YFVSIDAHAE ECFFERVTSG TKMGLIFEVA EGGFLDIDVE ITGPDNKGIY KGDRESSGKY TFAAHMDGTY KFCFSNRMST MTPKIVMFT IDIGEAPKGQ DMETEAHQNK LEEMINELAV AMTAVKHEQE YMEVRERIHR AINDNTNSRV VLWSFFEALV L VAMTLGQI YYLKRFFEVR RVV

UniProtKB: Transmembrane emp24 domain-containing protein 2

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Macromolecule #3: Transmembrane emp24 domain-containing protein 5

MacromoleculeName: Transmembrane emp24 domain-containing protein 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.276381 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FTPSLDSDFT FTLPAGQKEC FYQPMPLKAS LEIEYQVLDG AGLDIDFHLA SPEGKTLVFE QRKSDGVHTV ETEVGDYMFC FDNTFSTIS EKVIFFELIL DNMGEQAQEQ EDWKKYITGT DILDMKLEDI LESINSIKSR LSKSGHIQTL LRAFEARDRN I QESNFDRV ...String:
FTPSLDSDFT FTLPAGQKEC FYQPMPLKAS LEIEYQVLDG AGLDIDFHLA SPEGKTLVFE QRKSDGVHTV ETEVGDYMFC FDNTFSTIS EKVIFFELIL DNMGEQAQEQ EDWKKYITGT DILDMKLEDI LESINSIKSR LSKSGHIQTL LRAFEARDRN I QESNFDRV NFWSMVNLVV MVVVSAIQVY MLKSLFEDKR KSRT

UniProtKB: Transmembrane emp24 domain-containing protein 5

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Macromolecule #4: Transmembrane emp24 domain-containing protein 10

MacromoleculeName: Transmembrane emp24 domain-containing protein 10 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.782986 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ISFHLPINSR KCLREEIHKD LLVTGAYEIS DQSGGAGGLR SHLKITDSAG HILYSKEDAT KGKFAFTTED YDMFEVCFES KGTGRIPDQ LVILDMKHGV EAKNYEEIAK VEKLKPLEVE LRRLEDLSES IVNDFAYMKK REEEMRDTNE STNTRVLYFS I FSMFCLIG LATWQVFYLR RFFKAKKLIE

UniProtKB: Transmembrane emp24 domain-containing protein 10

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
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: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 449242
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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