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- EMDB-62186: Cryo-EM structure of human signal peptide peptidase like 2A (SPPL... -

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Basic information

Entry
Database: EMDB / ID: EMD-62186
TitleCryo-EM structure of human signal peptide peptidase like 2A (SPPL2a) in complex with L685,458
Map data
Sample
  • Organelle or cellular component: human signal peptide peptidase like 2A (SPPL2a) in complex with L685,458
    • Protein or peptide: Signal peptide peptidase-like 2A
  • Ligand: ~{tert}-butyl ~{N}-[(2~{S},3~{R},5~{R})-6-[[(2~{S})-1-[[(2~{S})-1-azanyl-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-3-oxidanyl-6-oxidanylidene-1-phenyl-5-(phenylmethyl)hexan-2-yl]carbamate
KeywordsIntramembrane protease / signal peptide peptidase / MEMBRANE PROTEIN
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
Signal peptide peptidase-like 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZhou R / Huang G / Guo X / Wang J / Ge X / Shi Y
Funding support China, 1 items
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, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62186.png

Downloads & links

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Map

FileDownload / File: emd_62186.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 192 pix.
= 207.84 Å		1.08 Å/pix.
x 192 pix.
= 207.84 Å		1.08 Å/pix.
x 192 pix.
= 207.84 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.665
Minimum - Maximum-5.2591643 - 7.1996436
Average (Standard dev.)0.0031851162 (±0.13145465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 207.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62186_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_62186_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : human signal peptide peptidase like 2A (SPPL2a) in complex with L...

EntireName: human signal peptide peptidase like 2A (SPPL2a) in complex with L685,458
Components
  • Organelle or cellular component: human signal peptide peptidase like 2A (SPPL2a) in complex with L685,458
    • Protein or peptide: Signal peptide peptidase-like 2A
  • Ligand: ~{tert}-butyl ~{N}-[(2~{S},3~{R},5~{R})-6-[[(2~{S})-1-[[(2~{S})-1-azanyl-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-3-oxidanyl-6-oxidanylidene-1-phenyl-5-(phenylmethyl)hexan-2-yl]carbamate

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Supramolecule #1: human signal peptide peptidase like 2A (SPPL2a) in complex with L...

SupramoleculeName: human signal peptide peptidase like 2A (SPPL2a) in complex with L685,458
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Signal peptide peptidase-like 2A

MacromoleculeName: Signal peptide peptidase-like 2A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.189816 KDa
Recombinant expressionOrganism: Insect expression vector pBlueBachsGCA1 (others)
SequenceString: MGPQRRLSPA GAALLWGFLL QLTAAQEAIL HASGNGTTKD YCMLYNPYWT ALPSTLENAT SISLMNLTST PLCNLSDIPP VGIKSKAVV VPWGSCHFLE KARIAQKGGA EAMLVVNNSV LFPPSGNRSE FPDVKILIAF ISYKDFRDMN QTLGDNITVK M YSPSWPNF ...String:
MGPQRRLSPA GAALLWGFLL QLTAAQEAIL HASGNGTTKD YCMLYNPYWT ALPSTLENAT SISLMNLTST PLCNLSDIPP VGIKSKAVV VPWGSCHFLE KARIAQKGGA EAMLVVNNSV LFPPSGNRSE FPDVKILIAF ISYKDFRDMN QTLGDNITVK M YSPSWPNF DYTMVVIFVI AVFTVALGGY WSGLVELENL KAVTTEDREM RKKKEEYLTF SPLTVVIFVV ICCVMMVLLY FF YKWLVYV MIAIFCIASA MSLYNCLAAL IHKIPYGQCT IACRGKNMEV RLIFLSGLCI AVAVVWAVFR NEDRWAWILQ DIL GIAFCL NLIKTLKLPN FKSCVILLGL LLLYDVFFVF ITPFITKNGE SIMVELAAGP FGNNEKLPVV IRVPKLIYFS VMSV CLMPV SILGFGDIIV PGLLIAYCRR FDVQTGSSYI YYVSSTVAYA IGMILTFVVL VLMKKGQPAL LYLVPCTLIT ASVVA WRRK EMKKFWKGNS YQMMDHLDCA TNEENPVISG EQIVQQ

UniProtKB: Signal peptide peptidase-like 2A

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Macromolecule #2: ~{tert}-butyl ~{N}-[(2~{S},3~{R},5~{R})-6-[[(2~{S})-1-[[(2~{S})-1...

MacromoleculeName: ~{tert}-butyl ~{N}-[(2~{S},3~{R},5~{R})-6-[[(2~{S})-1-[[(2~{S})-1-azanyl-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-3-oxidanyl-6-oxidanylidene-1- ...Name: ~{tert}-butyl ~{N}-[(2~{S},3~{R},5~{R})-6-[[(2~{S})-1-[[(2~{S})-1-azanyl-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-3-oxidanyl-6-oxidanylidene-1-phenyl-5-(phenylmethyl)hexan-2-yl]carbamate
type: ligand / ID: 2 / Number of copies: 1 / Formula: FTO
Molecular weightTheoretical: 672.853 Da
Chemical component information

ChemComp-FTO:
~{tert}-butyl ~{N}-[(2~{S},3~{R},5~{R})-6-[[(2~{S})-1-[[(2~{S})-1-azanyl-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-3-oxidanyl-6-oxidanylidene-1-phenyl-5-(phenylmethyl)hexan-2-yl]carbamate

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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

Concentration10 mg/mL
BufferpH: 7.4
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: 1.8 µm / Nominal defocus min: 1.5 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 116016
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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