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- PDB-21gl: The atomic coordinate of p24 complex at pH 6.8 -

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Basic information

Entry
Database: PDB / ID: 21gl
TitleThe atomic coordinate of p24 complex at pH 6.8
Components
  • Transmembrane emp24 domain-containing protein 10
  • Transmembrane emp24 domain-containing protein 2
  • Transmembrane emp24 domain-containing protein 5
  • Transmembrane emp24 domain-containing protein 9
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsHua, Z.K. / Zhang, D. / Zhang, M. / Yu, H.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of the GPI-AP transporter in pH 6.8
Authors: Hua, Z.K. / Zhang, D. / Zhang, M. / Yu, H.J.
History
DepositionDec 11, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 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

Downloads & links

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Assembly

Deposited unit
A: Transmembrane emp24 domain-containing protein 9
B: Transmembrane emp24 domain-containing protein 2
C: Transmembrane emp24 domain-containing protein 5
D: Transmembrane emp24 domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4405
Polymers89,2194
Non-polymers2211
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 Transmembrane emp24 domain-containing protein 9 / GMP25 / Glycoprotein 25L2 / p24 family protein alpha-2 / p24alpha2 / p25


Mass: 23353.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMED9, GP25L2 / Production host: Homo sapiens (human) / References: UniProt: Q9BVK6
#2: Protein Transmembrane emp24 domain-containing protein 2 / Membrane protein p24A / p24 / p24 family protein beta-1 / p24beta1


Mass: 20805.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMED2, RNP24 / Production host: Homo sapiens (human) / References: UniProt: Q15363
#3: Protein Transmembrane emp24 domain-containing protein 5 / p24 family protein gamma-2 / p24gamma2 / p28


Mass: 23276.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMED5, CGI-100, UNQ397/PRO733 / Production host: Homo sapiens (human) / References: UniProt: Q9Y3A6
#4: Protein Transmembrane emp24 domain-containing protein 10 / Protein TMED10 / 21 kDa transmembrane-trafficking protein / S31I125 / S31III125 / Tmp-21-I / ...Protein TMED10 / 21 kDa transmembrane-trafficking protein / S31I125 / S31III125 / Tmp-21-I / Transmembrane protein Tmp21 / p23 / p24 family protein delta-1 / p24delta1 / p24delta


Mass: 21782.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMED10, TMP21 / Production host: Homo sapiens (human) / References: UniProt: P49755
#5: 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.: 1 / 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
Has ligand of interestN
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: Structure of the GPI-AP transporter / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 6.8
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 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
13cry3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 598141 / Symmetry type: POINT
RefinementHighest resolution: 3.25 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035700
ELECTRON MICROSCOPYf_angle_d0.4717689
ELECTRON MICROSCOPYf_dihedral_angle_d4.293769
ELECTRON MICROSCOPYf_chiral_restr0.039865
ELECTRON MICROSCOPYf_plane_restr0.003999

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