[English] 日本語
Yorodumi
- EMDB-13171: Human Signal Peptidase Complex Paralog A (SPC-A) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13171
TitleHuman Signal Peptidase Complex Paralog A (SPC-A)
Map dataAmphipol has been largely masked out
Sample
  • Complex: Signal peptidase complex paralog A (SPC-A)
    • Complex: Signal peptidase complex catalytic subunit A (SEC11A)
      • Protein or peptide: Signal peptidase complex catalytic subunit SEC11A
    • Complex: Signal peptidase complex subunit 3 (SPC22/23)
      • Protein or peptide: Signal peptidase complex subunit 3
    • Complex: Signal peptidase complex subunit 2 (SPC25)
      • Protein or peptide: Signal peptidase complex subunit 2
    • Complex: Signal peptidase complex subunit 1 (SPC12)
      • Protein or peptide: Signal peptidase complex subunit 1
Function / homology
Function and homology information


signal peptidase complex / signal peptidase I / : / signal peptide processing / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / protein targeting to ER / virion assembly / SRP-dependent cotranslational protein targeting to membrane / Synthesis, secretion, and deacylation of Ghrelin / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) ...signal peptidase complex / signal peptidase I / : / signal peptide processing / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / protein targeting to ER / virion assembly / SRP-dependent cotranslational protein targeting to membrane / Synthesis, secretion, and deacylation of Ghrelin / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / peptidase activity / membrane => GO:0016020 / viral protein processing / serine-type endopeptidase activity / endoplasmic reticulum membrane / endoplasmic reticulum / proteolysis
Similarity search - Function
Signal peptidase complex catalytic subunit SEC11A / 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 / Signal peptidase complex subunit Spc1 / Microsomal signal peptidase 12 kDa subunit (SPC12) / Peptidase S26A, signal peptidase I, conserved site ...Signal peptidase complex catalytic subunit SEC11A / 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 / Signal peptidase complex subunit Spc1 / 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: 4.9 Å
AuthorsLiaci AM / Foerster F
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)724425 Netherlands
Citation
Journal: Mol Cell / Year: 2021
Title: Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage.
Authors: A Manuel Liaci / Barbara Steigenberger / Paulo Cesar Telles de Souza / Sem Tamara / Mariska Gröllers-Mulderij / Patrick Ogrissek / Siewert J Marrink / Richard A Scheltema / Friedrich Förster /
Abstract: The signal peptidase complex (SPC) is an essential membrane complex in the endoplasmic reticulum (ER), where it removes signal peptides (SPs) from a large variety of secretory pre-proteins with ...The signal peptidase complex (SPC) is an essential membrane complex in the endoplasmic reticulum (ER), where it removes signal peptides (SPs) from a large variety of secretory pre-proteins with exquisite specificity. Although the determinants of this process have been established empirically, the molecular details of SP recognition and removal remain elusive. Here, we show that the human SPC exists in two functional paralogs with distinct proteolytic subunits. We determined the atomic structures of both paralogs using electron cryo-microscopy and structural proteomics. The active site is formed by a catalytic triad and abuts the ER membrane, where a transmembrane window collectively formed by all subunits locally thins the bilayer. Molecular dynamics simulations indicate that this unique architecture generates specificity for SPs based on the length of their hydrophobic segments.
#1: Journal: BioRxiv / Year: 2020
Title: Structure of the Human Signal Peptidase Complex Reveals the Determinants for Signal Peptide Cleavage
Authors: Liaci AM / Steigenberger B / Tamara S / Telles de Souza PC / Grollers-Mulderij M / Ogrissek P / Marrik SJ / Scheltema RA / Foerster F
History
DepositionJul 6, 2021-
Header (metadata) releaseOct 6, 2021-
Map releaseOct 6, 2021-
UpdateDec 21, 2022-
Current statusDec 21, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0135
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0135
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7p2p
  • Surface level: 0.0135
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13171.png

Downloads & links

-
Map

FileDownload / File: emd_13171.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAmphipol has been largely masked out
Voxel sizeX=Y=Z: 0.81 Å
Density
Contour LevelBy AUTHOR: 0.0135 / Movie #1: 0.0135
Minimum - Maximum-0.019206602 - 0.03816892
Average (Standard dev.)0.00028426043 (±0.0019296525)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 162.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.810.810.81
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z162.000162.000162.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0190.0380.000

-
Supplemental data

-
Mask #1

Fileemd_13171_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_13171_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_13171_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Signal peptidase complex paralog A (SPC-A)

EntireName: Signal peptidase complex paralog A (SPC-A)
Components
  • Complex: Signal peptidase complex paralog A (SPC-A)
    • Complex: Signal peptidase complex catalytic subunit A (SEC11A)
      • Protein or peptide: Signal peptidase complex catalytic subunit SEC11A
    • Complex: Signal peptidase complex subunit 3 (SPC22/23)
      • Protein or peptide: Signal peptidase complex subunit 3
    • Complex: Signal peptidase complex subunit 2 (SPC25)
      • Protein or peptide: Signal peptidase complex subunit 2
    • Complex: Signal peptidase complex subunit 1 (SPC12)
      • Protein or peptide: Signal peptidase complex subunit 1

-
Supramolecule #1: Signal peptidase complex paralog A (SPC-A)

SupramoleculeName: Signal peptidase complex paralog A (SPC-A) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human) / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum
Molecular weightTheoretical: 20.3 KDa

-
Supramolecule #2: Signal peptidase complex catalytic subunit A (SEC11A)

SupramoleculeName: Signal peptidase complex catalytic subunit A (SEC11A) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human) / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

-
Supramolecule #3: Signal peptidase complex subunit 3 (SPC22/23)

SupramoleculeName: Signal peptidase complex subunit 3 (SPC22/23) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human) / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

-
Supramolecule #4: Signal peptidase complex subunit 2 (SPC25)

SupramoleculeName: Signal peptidase complex subunit 2 (SPC25) / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human) / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

-
Supramolecule #5: Signal peptidase complex subunit 1 (SPC12)

SupramoleculeName: Signal peptidase complex subunit 1 (SPC12) / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human) / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum

-
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: 22.376088 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PMLSLDFLDD VRRMNKRQLY YQVLNFGMIV SSALMIWKGL MVITGSESPI VVVLSGSMEP AFHRGDLLFL TNRVEDPIRV GEIVVFRIE GREIPIVHRV LKIHEKQNGH IKFLTKGDNN AVDDRGLYKQ GQHWLEKKDV VGRARGFVPY IGIVTILMND Y PKFKYAVL ...String:
PMLSLDFLDD VRRMNKRQLY YQVLNFGMIV SSALMIWKGL MVITGSESPI VVVLSGSMEP AFHRGDLLFL TNRVEDPIRV GEIVVFRIE GREIPIVHRV LKIHEKQNGH IKFLTKGDNN AVDDRGLYKQ GQHWLEKKDV VGRARGFVPY IGIVTILMND Y PKFKYAVL FLLGLFVLVH REGGSPGGSG GGSAENLYFQ

-
Macromolecule #2: Signal peptidase complex subunit 3

MacromoleculeName: Signal peptidase complex subunit 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.348457 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PMNTVLSRAN SLFAFSLSVM AALTFGCFIT TAFKDRSVPV RLHVSRIMLK NVEDFTGPRE RSDLGFITFD ITADLENIFD WNVKQLFLY LSAEYSTKNN ALNQVVLWDK IVLRGDNPKL LLKDMKTKYF FFDDGNGLKG NRNVTLTLSW NVVPNAGILP L VTGSGHVS ...String:
PMNTVLSRAN SLFAFSLSVM AALTFGCFIT TAFKDRSVPV RLHVSRIMLK NVEDFTGPRE RSDLGFITFD ITADLENIFD WNVKQLFLY LSAEYSTKNN ALNQVVLWDK IVLRGDNPKL LLKDMKTKYF FFDDGNGLKG NRNVTLTLSW NVVPNAGILP L VTGSGHVS VPFPDTYEIT KSYGSGEGRG SLLTCGDVEE NPG

-
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 / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.215236 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAAAVQGGR SGGSGGCSGA GGASNCGTGS GRSGLLDKWK IDDKPVKIDK WDGSAVKNSL DDSAKKVLLE KYKYVENFGL IDGRLTICT ISCFFAIVAL IWDYMHPFPE SKPVLALCVI SYFVMMGILT IYTSYKEKSI FLVAHRKDPT GMDPDDIWQL S SSLKRFDD ...String:
MAAAAVQGGR SGGSGGCSGA GGASNCGTGS GRSGLLDKWK IDDKPVKIDK WDGSAVKNSL DDSAKKVLLE KYKYVENFGL IDGRLTICT ISCFFAIVAL IWDYMHPFPE SKPVLALCVI SYFVMMGILT IYTSYKEKSI FLVAHRKDPT GMDPDDIWQL S SSLKRFDD KYTLKLTFIS GRTKQQREAE FTKSIAKFFD HSGTLVMDAY EPEISRLHDS LAIERKIKGS GQCTNYALLK LA GDVESNP G

-
Macromolecule #4: Signal peptidase complex subunit 1

MacromoleculeName: Signal peptidase complex subunit 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.488445 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
PMARGGDTGC TGPSETSASG AAAIALPGLE GPATDAQCQT LPLTVLKSRS PSPRSLPPAL SCPPPQPAML EHLSSLPTQM DYKGQKLAE QMFQGIILFS AIVGFIYGYV AEQFGWTVYI VMAGFAFSCL LTLPPWPIYR RHPLKWLPVQ ESSTDDKKPG E RKIKRHAK NNGSGATNFS LLKQAGDVEE NPG

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation #1

Preparation ID1
Concentration0.5 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
10.0 mMHEPESHEPES
85.0 mMNaClSodium chloridesodium chloride
1.0 mMEDTAEthylenediaminetetraacetic acidethylenediaminetetraacetic acid
1.0 mMDTTdithiothreitol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Film type ID: 1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 4s with blot force 0 before plunging..
Detailsgrid condition 1 (frozen without fluorinated fos-choline-8)

-
Sample preparation #2

Preparation ID2
Concentration4 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
10.0 mMHEPESHEPES
85.0 mMNaClSodium chloridesodium chloride
1.0 mMEDTAEthylenediaminetetraacetic acidethylenediaminetetraacetic acid
1.0 mMDTTdithiothreitol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Film type ID: 1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 4s with blot force 0 before plunging..
Detailsgrid condition 2 (frozen with 1.5 mM fluorinated fos-choline-8)

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Calibrated defocus max: 4.8 µm / Calibrated defocus min: 0.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 93.0 K / Max: 93.0 K
Details200 kV Talos Arctica at Utrecht University, the Netherlands. Same settings were used for both grid conditions.
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: COUNTING / #0 - Number grids imaged: 1 / #0 - Number real images: 5203 / #0 - Average exposure time: 9.0 sec. / #0 - Average electron dose: 63.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Detector mode: COUNTING / #1 - Digitization - Dimensions - Width: 3838 pixel / #1 - Digitization - Dimensions - Height: 3710 pixel / #1 - Number grids imaged: 1 / #1 - Number real images: 2083 / #1 - Average exposure time: 10.2 sec. / #1 - Average electron dose: 63.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1015857
Startup modelType of model: INSILICO MODEL
In silico model: Starting models were generated using trRosetta with (SEC11A) or without (SPC12, SPC22/23, SPC25) available homology templates.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 29508
Image recording ID1
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7p2p:
Human Signal Peptidase Complex Paralog A (SPC-A)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more