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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 / 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 ...signal peptidase complex / 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: Structure of the human signal peptidase complex with a signal peptide
Authors: Liaci AM / Vismpas D / Kjolbye LR / Skalidis I / Periera GP / Koh AF / Grollers-Mulderij M / Kotecha A / Souza PCT / Forster FG
History
DepositionJun 12, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 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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