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- EMDB-54011: Apo Structure of the Human Signal Peptidase -

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Basic information

Entry
Database: EMDB / ID: EMD-54011
TitleApo Structure of the Human Signal Peptidase
Map dataapo-SPC sharp map
Sample
  • Complex: Apo Structure of the Human Signal Peptidase Complex
    • Protein or peptide: Signal peptidase complex subunit 2
    • Protein or peptide: Signal peptidase complex catalytic subunit SEC11A
    • Protein or peptide: Signal peptidase complex subunit 3
    • Protein or peptide: Signal peptidase complex subunit 1
KeywordsSignal Peptidase Complex / protein biogenesis / secretory pathway / membrane thinning / MEMBRANE PROTEIN
Function / homology
Function and homology information


signal peptidase complex / Maturation of DENV proteins / signal peptidase I / signal peptidase activity / : / protein targeting to ER / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / virion assembly / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / Maturation of hRSV A proteins ...signal peptidase complex / Maturation of DENV proteins / signal peptidase I / signal peptidase activity / : / protein targeting to ER / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / virion assembly / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / Maturation of hRSV A proteins / Synthesis, secretion, and deacylation of Ghrelin / SRP-dependent cotranslational protein targeting to membrane / response to virus / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / peptidase activity / viral protein processing / serine-type endopeptidase activity / endoplasmic reticulum membrane / endoplasmic reticulum / proteolysis
Similarity search - Function
Peptidase S26B / Signal peptidase complex subunit 3 / Signal peptidase complex subunit 2 / Signal peptidase subunit / Microsomal signal peptidase 25 kDa subunit (SPC25) / Signal peptidase complex subunit 1 / Microsomal signal peptidase 12 kDa subunit (SPC12) / Peptidase S26A, signal peptidase I, conserved site / Signal peptidases I signature 3. / Peptidase S26A, signal peptidase I, serine active site ...Peptidase S26B / Signal peptidase complex subunit 3 / Signal peptidase complex subunit 2 / Signal peptidase subunit / Microsomal signal peptidase 25 kDa subunit (SPC25) / Signal peptidase complex subunit 1 / Microsomal signal peptidase 12 kDa subunit (SPC12) / Peptidase S26A, signal peptidase I, conserved site / Signal peptidases I signature 3. / Peptidase S26A, signal peptidase I, serine active site / Signal peptidases I serine active site. / Peptidase S26 / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily
Similarity search - Domain/homology
Signal peptidase complex subunit 3 / Signal peptidase complex catalytic subunit SEC11A / Signal peptidase complex subunit 2 / Signal peptidase complex subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsLiaci AM / Vismpas D / Skalidis I / Koh FA / Abhay K / Forster GF
Funding support Netherlands, 2 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)OCENW.M.22.151 Netherlands
Netherlands Organisation for Scientific Research (NWO)184.034.014 Netherlands
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis of signal peptide recognition by the signal peptidase complex.
Authors: A Manuel Liaci / Dimitrios Vismpas / Lisbeth R Kjølbye / Ioannis Skalidis / Gilberto P Pereira / Adrian Fujiet Koh / Mariska Gröllers-Mulderij / Abhay Kotecha / Paulo C T Souza / Friedrich Förster /
Abstract: The signal peptidase complex (SPC) is responsible for cleaving signal peptides (SPs) from approximately 10% of the human proteome. SPs are characterized by a tripartite structure, consisting of an N- ...The signal peptidase complex (SPC) is responsible for cleaving signal peptides (SPs) from approximately 10% of the human proteome. SPs are characterized by a tripartite structure, consisting of an N-terminal n-region, a central helical h-region and a C-terminal c-region, each defined by rather general chemical properties rather than strict sequence conservation. Despite their sequence diversity, SPC recognizes and processes SPs with exquisite specificity. Here, we present a 2.6 Å cryo-EM map of the human SPC-A, one of two SPC paralogs, bound to a model SP. The c-region binds to a hydrophobic binding groove near the active site, a narrow gate marks the transition from c- to h-region, and the h-region localizes in a transmembrane (TM) window. Substrate engagement stabilizes N- and C-terminal helices of Sec11A, which frame the SP and are unresolved in the apo structure. Molecular dynamics (MD) simulations confirm a stable hydrogen-bonding network at the c-region and indicate dynamic interactions within a thinned lipid environment at the TM window. AlphaFold modeling supports this binding mode across physiological SPs. Collectively, our structural and computational analyses explain how the SPC achieves its specificity by combining the selectivity of the luminal binding groove and of the transmembrane window.
History
DepositionJun 12, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54011.png

Downloads & links

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Map

FileDownload / File: emd_54011.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationapo-SPC sharp map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 420 pix.
= 283.08 Å		0.67 Å/pix.
x 420 pix.
= 283.08 Å		0.67 Å/pix.
x 420 pix.
= 283.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.674 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-1.2157686 - 1.992135
Average (Standard dev.)0.0011439208 (±0.030989403)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 283.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54011_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: apo-SPC half-map A

Fileemd_54011_half_map_1.map
Annotationapo-SPC half-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: apo-SPC half-map B

Fileemd_54011_half_map_2.map
Annotationapo-SPC half-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Apo Structure of the Human Signal Peptidase Complex

EntireName: Apo Structure of the Human Signal Peptidase Complex
Components
  • Complex: Apo Structure of the Human Signal Peptidase Complex
    • Protein or peptide: Signal peptidase complex subunit 2
    • Protein or peptide: Signal peptidase complex catalytic subunit SEC11A
    • Protein or peptide: Signal peptidase complex subunit 3
    • Protein or peptide: Signal peptidase complex subunit 1

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Supramolecule #1: Apo Structure of the Human Signal Peptidase Complex

SupramoleculeName: Apo Structure of the Human Signal Peptidase Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3, #1, #4, #2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.34 KDa

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Macromolecule #1: Signal peptidase complex catalytic subunit SEC11A

MacromoleculeName: Signal peptidase complex catalytic subunit SEC11A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: signal peptidase I
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.394979 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SLDFLDDVRR MNKRQLYYQV LNFGMIVSSA LMIWKGLMVI TGSESPIVVV LSGAMEPAFH RGDLLFLTNR VEDPIRVGEI VVFRIEGRE IPIVHRVLKI HEKQNGHIKF LTKGDNNAVD DRGLYKQGQH WLEKKDVVGR ARGFVPYIGI VTILMNDYPK F KYAVLFLL GLFVLVHRE

UniProtKB: Signal peptidase complex catalytic subunit SEC11A

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Macromolecule #2: Signal peptidase complex subunit 1

MacromoleculeName: Signal peptidase complex subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.386763 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GQKLAEQMFQ GIILFSAIVG FIYGYVAEQF GWTVYIVMAG FAFSCLLTLP PWPIYRRHPL KWLP

UniProtKB: Signal peptidase complex subunit 1

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Macromolecule #3: Signal peptidase complex subunit 2

MacromoleculeName: Signal peptidase complex subunit 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.338516 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DPVKIDKWDG SAVKNSLDDS AKKVLLEKYK YVENFGLIDG RLTICTISCF FAIVALIWDY MHPFPESKPV LALCVISYFV MMGILTIYT SYKEKSIFLV AHRKDPTGMD PDDIWQLSSS LKRFDDKYTL KLTFISGRTK QQREAEFTKS IAKFFDHSGT L VMDAYEPE ISRLHDSLA

UniProtKB: Signal peptidase complex subunit 2

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Macromolecule #4: Signal peptidase complex subunit 3

MacromoleculeName: Signal peptidase complex subunit 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.611531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MNTVLSRANS LFAFSLSVMA ALTFGCFITT AFKDRSVPVR LHVSRIMLKN VEDFTGPRER SDLGFITFDI TADLENIFDW NVKQLFLYL SAEYSTKNNA LNQVVLWDKI VLRGDNPKLL LKDMKTKYFF FDDGNGLKGN RNVTLTLSWN VVPNAGILPL V TGSGHVSV PFPDTY

UniProtKB: Signal peptidase complex subunit 3

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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

Concentration4 mg/mL
BufferpH: 7.8
Component:
ConcentrationNameFormula
10.0 mMHEPES
85.0 mMsodium chlorideNaCl
0.0174 %DDM CHS
1.0 mMEDTA

Details: addition of 1.5 mM fluorinated, fos-choline (FFosC, Anatrace) directly before vitrification
GridModel: Quantifoil Active R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 6537 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2457714
CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 516615
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1) / Software - details: ab initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1) / Software - details: homogeneous refinement
Final 3D classificationNumber classes: 2 / Avg.num./class: 50 / Software - Name: cryoSPARC (ver. 3.3.1) / Software - details: non uniform refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7p2p


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: PDB
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9rjc:
Apo Structure of the Human Signal Peptidase

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