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- EMDB-58396: S1P complex with SPRING -

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Basic information

Entry
Database: EMDB / ID: EMD-58396
TitleS1P complex with SPRING
Map dataunfortunately this is currently the highest resolution we could achieve and it has to be uploaded to get grant extension
Sample
  • Complex: S1P complex with SPRING
    • Protein or peptide: Site-one protease
    • Protein or peptide: SPRING
Keywordsprotease / Site-one protease / glycoprotein processing / SPRING / S1P / SIGNALING PROTEIN
Function / homology
Function and homology information


site-1 protease / CREB3 factors activate genes / positive regulation of SREBP signaling pathway / ATF6-mediated unfolded protein response / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / regulation of cholesterol biosynthetic process / Assembly of active LPL and LIPC lipase complexes / membrane protein intracellular domain proteolysis / regulation of vesicle-mediated transport ...site-1 protease / CREB3 factors activate genes / positive regulation of SREBP signaling pathway / ATF6-mediated unfolded protein response / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / regulation of cholesterol biosynthetic process / Assembly of active LPL and LIPC lipase complexes / membrane protein intracellular domain proteolysis / regulation of vesicle-mediated transport / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Golgi stack / lysosome organization / mitotic G2 DNA damage checkpoint signaling / cholesterol metabolic process / endoplasmic reticulum unfolded protein response / response to endoplasmic reticulum stress / Post-translational protein phosphorylation / protein maturation / protein processing / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / protein import into nucleus / endoplasmic reticulum lumen / serine-type endopeptidase activity / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / mitochondrion / proteolysis
Similarity search - Function
SREBP regulating gene protein / SREBP regulating gene protein / Site-1 peptidase catalytic domain / : / : / : / Membrane-bound Site-1 Protease Family N-terminal domain / MBTPS1, fourth GATase-like domain / MBTPS1, third Ig-like domain / Peptidase S8, subtilisin, His-active site ...SREBP regulating gene protein / SREBP regulating gene protein / Site-1 peptidase catalytic domain / : / : / : / Membrane-bound Site-1 Protease Family N-terminal domain / MBTPS1, fourth GATase-like domain / MBTPS1, third Ig-like domain / Peptidase S8, subtilisin, His-active site / : / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
Membrane-bound transcription factor site-1 protease / SREBP regulating gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.18 Å
AuthorsMurina V / Knecht W
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Commission101191811European Union
CitationJournal: To Be Published
Title: S1P complex with SPRING
Authors: Murina V / Knecht W
History
DepositionJun 3, 2026-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58396.png

Downloads & links

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Map

FileDownload / File: emd_58396.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunfortunately this is currently the highest resolution we could achieve and it has to be uploaded to get grant extension
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 216 pix.
= 203.04 Å		0.94 Å/pix.
x 216 pix.
= 203.04 Å		0.94 Å/pix.
x 216 pix.
= 203.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.1099622 - 4.9129252
Average (Standard dev.)-0.000025824971 (±0.090404816)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 203.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_58396_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_58396_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : S1P complex with SPRING

EntireName: S1P complex with SPRING
Components
  • Complex: S1P complex with SPRING
    • Protein or peptide: Site-one protease
    • Protein or peptide: SPRING

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Supramolecule #1: S1P complex with SPRING

SupramoleculeName: S1P complex with SPRING / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 115 KDa

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Macromolecule #1: Site-one protease

MacromoleculeName: Site-one protease / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: RAIPRQVAQT LQADVLWQMG YTGANVRVAV FDTGLSEKHP HFKNVKERTN WTNERTLDDG LGHGTFVAGV IASMRECQGF APDAELHIFR VFTNNQVSYT SWFLDAFNYA ILKKIDVLNL SIGGPDFMDH PFVDKVWELT ANNVIMVSAI GNDGPLYGTL NNPADQMDVI ...String:
RAIPRQVAQT LQADVLWQMG YTGANVRVAV FDTGLSEKHP HFKNVKERTN WTNERTLDDG LGHGTFVAGV IASMRECQGF APDAELHIFR VFTNNQVSYT SWFLDAFNYA ILKKIDVLNL SIGGPDFMDH PFVDKVWELT ANNVIMVSAI GNDGPLYGTL NNPADQMDVI GVGGIDFEDN IARFSSRGMT TWELPGGYGR MKPDIVTYGA GVRGSGVKGG CRALSGTSVA SPVVAGAVTL LVSTVQKREL VNPASMKQAL IASARRLPGV NMFEQGHGKL DLLRAYQILN SYKPQASLSP SYIDLTECPY MWPYCSQPIY YGGMPTVVNV TILNGMGVTG RIVDKPDWQP YLPQNGDNIE VAFSYSSVLW PWSGYLAISI SVTKKAASWE GIAQGHVMIT VASPAETESK NGAEQTSTVK LPIKVKIIPT PPRSKRVLWD QYHNLRYPPG YFPRDNLRMK NDPLDWNGDH IHTNFRDMYQ HLRSMGYFVE VLGAPFTCFD ASQYGTLLMV DSEEEYFPEE IAKLRRDVDN GLSLVIFSDW YNTSVMRKVK FYDENTRQWW MPDTGGANIP ALNELLSVWN MGFSDGLYEG EFTLANHDMY YASGCSIAKF PEDGVVITQT FKDQGLEVLK QETAVVENVP ILGLYQIPAE GGGRIVLYGD SNCLDDSHRQ KDCFWLLDAL LQYTSYGVTP PSLSHSGNRQ RPPSGAGSVT PERMEGNHLH RYSKVLEAHL GDPKPRPLPA CPRLSWAKPQ PLNETAPSNL WKHQKLLSID LDKVVLPNFR SNRPQVRPLS PGESGAWDIP GGIMPGRYNQ EVDYKDDDDK GSDYKDDDDK GSDYKDDDDK

UniProtKB: Membrane-bound transcription factor site-1 protease

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Macromolecule #2: SPRING

MacromoleculeName: SPRING / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
KQEERAVRDR NLLQVHDHNQ PIPWKVQFNL GNSSRPSNQC RNSIQGKHLI TDELGYVCER KDLLVNGCCN VNVPSTKQYC CDGCWPNGCC SAYEYCVSCC LQPNKQLLLE RFLNRAAVAF QNLFMAVEDH FELCLAKCRT SSQSVQHENT YRDPIAKYCY GESPPELFPA ENLYFQGHHH HHHHHHH

UniProtKB: SREBP regulating gene protein

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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

Concentration0.5 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.18 Å / Resolution method: OTHER / Software - Name: cryoSPARC (ver. 5.0) / Number images used: 76861
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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