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- PDB-9rjb: Human Signal Peptidase in complex with artificial Signal Peptide L11 -

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Basic information

Entry
Database: PDB / ID: 9rjb
TitleHuman Signal Peptidase in complex with artificial Signal Peptide L11
Components
  • Artificial Signal Peptide L11
  • Signal peptidase complex catalytic subunit SEC11A
  • Signal peptidase complex subunit 1
  • Signal peptidase complex subunit 2
  • Signal peptidase complex subunit 3
KeywordsMEMBRANE PROTEIN / Signal Peptidase Complex / Signal Peptide / protein biogenesis / secretory pathway / membrane thinning
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsLiaci, A.M. / Vismpas, D. / Skalidis, I. / Koh, F.A. / Abhay, K. / Forster, G.F.
Funding support Netherlands, 2items
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, A.M. / Vismpas, D. / Kjolbye, L.R. / Skalidis, I. / Periera, G.P. / Koh, A.F. / Grollers-Mulderij, M. / Kotecha, A. / Souza, P.C.T. / Forster, F.G.
History
DepositionJun 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 27, 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
C: Signal peptidase complex subunit 2
A: Signal peptidase complex catalytic subunit SEC11A
D: Signal peptidase complex subunit 3
B: Signal peptidase complex subunit 1
E: Artificial Signal Peptide L11


Theoretical massNumber of molelcules
Total (without water)69,9395
Polymers69,9395
Non-polymers00
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 Signal peptidase complex subunit 2 / Microsomal signal peptidase 25 kDa subunit / SPase 25 kDa subunit


Mass: 20338.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPCS2, KIAA0102, SPC25 / Production host: Homo sapiens (human) / References: UniProt: Q15005
#2: Protein Signal peptidase complex catalytic subunit SEC11A / Endopeptidase SP18 / Microsomal signal peptidase 18 kDa subunit / SPase 18 kDa subunit / SEC11 ...Endopeptidase SP18 / Microsomal signal peptidase 18 kDa subunit / SPase 18 kDa subunit / SEC11 homolog A / SEC11-like protein 1 / SPC18


Mass: 20394.979 Da / Num. of mol.: 1 / Mutation: S56A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC11A, SEC11L1, SPC18, SPCS4A / Production host: Homo sapiens (human) / References: UniProt: P67812, signal peptidase I
#3: Protein Signal peptidase complex subunit 3 / Microsomal signal peptidase 22/23 kDa subunit / SPC22/23 / SPase 22/23 kDa subunit


Mass: 19611.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPCS3, SPC22, UNQ1841/PRO3567 / Production host: Homo sapiens (human) / References: UniProt: P61009
#4: Protein Signal peptidase complex subunit 1 / Microsomal signal peptidase 12 kDa subunit / SPase 12 kDa subunit


Mass: 7386.763 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPCS1, SPC12, HSPC033 / Production host: Homo sapiens (human) / References: UniProt: Q9Y6A9
#5: Protein/peptide Artificial Signal Peptide L11


Mass: 2206.878 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: Signal peptidase complex with a signal peptide / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.09604 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK 293
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPES1
285 mMsodium chlorideNaCl1
30.0174 %DDM CHS1
41 mMEDTA1
SpecimenConc.: 7.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil Active R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

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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: 1200 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10119

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC3.3.1particle selection
2EPU3.1image acquisition
4cryoSPARC3.3.1CTF correction
7Coot0.9.8.3model fitting
9cryoSPARC3.3.1initial Euler assignmentab initio
10cryoSPARC3.3.1final Euler assignmenthomogeneous refinement
11cryoSPARC3.3.1classificationnon uniform refinement
12cryoSPARC3.3.13D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3214405
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 443525 / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 7P2P

7p2p


Accession code: 7P2P / Details: PDB / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0014958
ELECTRON MICROSCOPYf_angle_d0.3756705
ELECTRON MICROSCOPYf_dihedral_angle_d2.85639
ELECTRON MICROSCOPYf_chiral_restr0.038764
ELECTRON MICROSCOPYf_plane_restr0.003825

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