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- PDB-9k92: Cryo-EM structure of human signal peptide peptidase like 2A (SPPL2a) -

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Basic information

Entry
Database: PDB / ID: 9k92
TitleCryo-EM structure of human signal peptide peptidase like 2A (SPPL2a)
ComponentsSignal peptide peptidase-like 2A
KeywordsMEMBRANE PROTEIN / Intramembrane protease / signal peptide peptidase
Function / homology
Function and homology information


aspartic endopeptidase activity, intramembrane cleaving / membrane protein proteolysis / membrane protein intracellular domain proteolysis / Golgi-associated vesicle membrane / regulation of tumor necrosis factor-mediated signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / cytoplasmic side of endoplasmic reticulum membrane / membrane protein ectodomain proteolysis / regulation of immune response / lumenal side of endoplasmic reticulum membrane ...aspartic endopeptidase activity, intramembrane cleaving / membrane protein proteolysis / membrane protein intracellular domain proteolysis / Golgi-associated vesicle membrane / regulation of tumor necrosis factor-mediated signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / cytoplasmic side of endoplasmic reticulum membrane / membrane protein ectodomain proteolysis / regulation of immune response / lumenal side of endoplasmic reticulum membrane / Regulation of TNFR1 signaling / late endosome membrane / late endosome / lysosomal membrane / intracellular membrane-bounded organelle / protein homodimerization activity / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Peptidase A22B, signal peptide peptidase / Signal peptide peptidase / Presenilin/signal peptide peptidase / Presenilin, signal peptide peptidase, family / PA domain superfamily / PA domain / PA domain
Similarity search - Domain/homology
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Signal peptide peptidase-like 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhou, R. / Huang, G. / Guo, X. / Wang, J. / Ge, X. / Shi, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2020YFA0509300 China
CitationJournal: To Be Published
Title: Structural insights into human signal peptide peptidase
Authors: Zhou, R. / Huang, G. / Guo, X. / Wang, J. / Ge, X. / Shi, Y.
History
DepositionOct 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 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

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Assembly

Deposited unit
A: Signal peptide peptidase-like 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9802
Polymers58,1901
Non-polymers7901
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 Signal peptide peptidase-like 2A / SPP-like 2A / SPPL2a / Intramembrane protease 3 / IMP-3 / Presenilin-like protein 2


Mass: 58189.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPPL2A, IMP3, PSL2, PSEC0147
Production host: Insect expression vector pBlueBachsGCA1 (others)
References: UniProt: Q8TCT8, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#2: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY
Has protein modificationN

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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: human signal peptide peptidase like 2A (SPPL2a) / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Insect expression vector pBlueBachsGCA1 (others)
Buffer solutionpH: 7.4
SpecimenConc.: 10 mg/ml / Embedding 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: 1800 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
8PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 345338 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0032274
ELECTRON MICROSCOPYf_angle_d0.513090
ELECTRON MICROSCOPYf_dihedral_angle_d5.699318
ELECTRON MICROSCOPYf_chiral_restr0.037378
ELECTRON MICROSCOPYf_plane_restr0.003353

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