9RJB | pdb_00009rjb

Human Signal Peptidase in complex with artificial Signal Peptide L11

PDB DOI: https://doi.org/10.2210/pdb9RJB/pdb
EM Map EMD-54010: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2025-06-12 Released: 2026-05-27
Deposition Author(s): Liaci, A.M., Vismpas, D., Skalidis, I., Koh, F.A., Abhay, K., Forster, G.F.
Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of the human signal peptidase complex with a signal peptide

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.

(2026) Nat Commun

DOI: https://doi.org/10.1038/s41467-026-73423-3

Macromolecule Content

Total Structure Weight: 69.94 kDa
Atom Count: 4,784
Modeled Residue Count: 589
Deposited Residue Count: 612
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal peptidase complex subunit 2	A [auth C]	177	Homo sapiens	Mutation(s): 0 Gene Names: SPCS2, KIAA0102, SPC25
UniProt & NIH Common Fund Data Resources
Find proteins for Q15005 (Homo sapiens) Explore Q15005 Go to UniProtKB: Q15005
GTEx: ENSG00000118363
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15005
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal peptidase complex catalytic subunit SEC11A	B [auth A]	177	Homo sapiens	Mutation(s): 1 Gene Names: SEC11A, SEC11L1, SPC18, SPCS4A EC: 3.4.21.89
UniProt & NIH Common Fund Data Resources
Find proteins for P67812 (Homo sapiens) Explore P67812 Go to UniProtKB: P67812
PHAROS: P67812 GTEx: ENSG00000140612
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P67812
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal peptidase complex subunit 3	C [auth D]	174	Homo sapiens	Mutation(s): 0 Gene Names: SPCS3, SPC22, UNQ1841/PRO3567
UniProt & NIH Common Fund Data Resources
Find proteins for P61009 (Homo sapiens) Explore P61009 Go to UniProtKB: P61009
PHAROS: P61009 GTEx: ENSG00000129128
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61009
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal peptidase complex subunit 1	D [auth B]	64	Homo sapiens	Mutation(s): 0 Gene Names: SPCS1, SPC12, HSPC033
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6A9 (Homo sapiens) Explore Q9Y6A9 Go to UniProtKB: Q9Y6A9
PHAROS: Q9Y6A9 GTEx: ENSG00000114902
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y6A9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Artificial Signal Peptide L11	E	20	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.1
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	OCENW.M.22.151
Netherlands Organisation for Scientific Research (NWO)	Netherlands	184.034.014