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- EMDB-13171: Human Signal Peptidase Complex Paralog A (SPC-A) -

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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
KeywordsEndoplasmic Reticulum / Signal peptide / Serine protease / Membrane complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


signal peptidase complex / signal peptidase I / signal peptide processing / protein targeting to ER / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / virion assembly / Maturation of hRSV A proteins / SRP-dependent cotranslational protein targeting to membrane / Synthesis, secretion, and deacylation of Ghrelin / response to virus ...signal peptidase complex / signal peptidase I / signal peptide processing / protein targeting to ER / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / virion assembly / Maturation of hRSV A proteins / SRP-dependent cotranslational protein targeting to membrane / Synthesis, secretion, and deacylation of Ghrelin / 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: 4.9 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-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0135
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0135
  • Imaged by UCSF Chimera
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  • 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

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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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 200 pix.
= 162. Å		0.81 Å/pix.
x 200 pix.
= 162. Å		0.81 Å/pix.
x 200 pix.
= 162. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
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

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Supplemental data

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Mask #1

Fileemd_13171_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_13171_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_13171_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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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

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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

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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

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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

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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

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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

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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: 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

UniProtKB: Signal peptidase complex catalytic subunit SEC11A

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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

UniProtKB: Signal peptidase complex subunit 3

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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 / 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

UniProtKB: Signal peptidase complex subunit 2

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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

UniProtKB: Signal peptidase complex subunit 1

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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 #1

Preparation ID1
Concentration0.5 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
10.0 mMHEPESHEPES
85.0 mMNaClsodium chloride
1.0 mMEDTAethylenediaminetetraacetic 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)

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Sample preparation #2

Preparation ID2
Concentration4 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
10.0 mMHEPESHEPES
85.0 mMNaClsodium chloride
1.0 mMEDTAethylenediaminetetraacetic 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)

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
TemperatureMin: 93.0 K / Max: 93.0 K
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
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
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 FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Image recording ID1
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.
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
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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