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- EMDB-9537: Complex structure of the fission yeast SREBP-SCAP binding domains -

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Basic information

Entry
Database: EMDB / ID: EMD-9537
TitleComplex structure of the fission yeast SREBP-SCAP binding domains
Map data
Sample
  • Complex: Complex structure of the fission yeast SREBP-SCAP binding domains
    • Protein or peptide: Sterol regulatory element-binding protein cleavage-activating protein
    • Protein or peptide: Sterol regulatory element-binding protein cleavage-activating protein
    • Protein or peptide: Sterol regulatory element-binding protein 1
Keywordsprotein complex / PROTEIN TRANSPORT
Function / homology
Function and homology information


regulation of ergosterol biosynthetic process / positive regulation of ergosterol biosynthetic process / SREBP-SCAP complex / regulation of cholesterol biosynthetic process / sterol binding / SREBP signaling pathway / DNA-binding transcription activator activity / steroid metabolic process / cytoplasmic side of endoplasmic reticulum membrane / DNA-binding transcription activator activity, RNA polymerase II-specific ...regulation of ergosterol biosynthetic process / positive regulation of ergosterol biosynthetic process / SREBP-SCAP complex / regulation of cholesterol biosynthetic process / sterol binding / SREBP signaling pathway / DNA-binding transcription activator activity / steroid metabolic process / cytoplasmic side of endoplasmic reticulum membrane / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to hypoxia / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Golgi membrane / endoplasmic reticulum membrane / chromatin / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Sterol regulatory element-binding protein 1, C-terminal / Domain of unknown function (DUF2014) / : / Sterol regulatory element-binding protein cleavage-activating protein / : / Sterol-sensing domain of SREBP cleavage-activation / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / Helix-loop-helix DNA-binding domain / helix loop helix domain ...Sterol regulatory element-binding protein 1, C-terminal / Domain of unknown function (DUF2014) / : / Sterol regulatory element-binding protein cleavage-activating protein / : / Sterol-sensing domain of SREBP cleavage-activation / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / Helix-loop-helix DNA-binding domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Sterol regulatory element-binding protein cleavage-activating protein / Sterol regulatory element-binding protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast) / Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsGong X / Qian HW
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2015CB9101012014, ZX09507003006 China
National Natural Science Foundation of Chinaproject 31321062 and 81590761 China
CitationJournal: Cell Res / Year: 2016
Title: Complex structure of the fission yeast SREBP-SCAP binding domains reveals an oligomeric organization.
Authors: Xin Gong / Hongwu Qian / Wei Shao / Jingxian Li / Jianping Wu / Jun-Jie Liu / Wenqi Li / Hong-Wei Wang / Peter Espenshade / Nieng Yan /
Abstract: Sterol regulatory element-binding protein (SREBP) transcription factors are master regulators of cellular lipid homeostasis in mammals and oxygen-responsive regulators of hypoxic adaptation in fungi. ...Sterol regulatory element-binding protein (SREBP) transcription factors are master regulators of cellular lipid homeostasis in mammals and oxygen-responsive regulators of hypoxic adaptation in fungi. SREBP C-terminus binds to the WD40 domain of SREBP cleavage-activating protein (SCAP), which confers sterol regulation by controlling the ER-to-Golgi transport of the SREBP-SCAP complex and access to the activating proteases in the Golgi. Here, we biochemically and structurally show that the carboxyl terminal domains (CTD) of Sre1 and Scp1, the fission yeast SREBP and SCAP, form a functional 4:4 oligomer and Sre1-CTD forms a dimer of dimers. The crystal structure of Sre1-CTD at 3.5 Å and cryo-EM structure of the complex at 5.4 Å together with in vitro biochemical evidence elucidate three distinct regions in Sre1-CTD required for Scp1 binding, Sre1-CTD dimerization and tetrameric formation. Finally, these structurally identified domains are validated in a cellular context, demonstrating that the proper 4:4 oligomeric complex formation is required for Sre1 activation.
History
DepositionSep 5, 2016-
Header (metadata) releaseDec 14, 2016-
Map releaseDec 14, 2016-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
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  • Surface view with fitted model
  • Atomic models: PDB-5grs
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9537.png

Downloads & links

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Map

FileDownload / File: emd_9537.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 200 pix.
= 264. Å		1.32 Å/pix.
x 200 pix.
= 264. Å		1.32 Å/pix.
x 200 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.028372295 - 0.07998708
Average (Standard dev.)0.00033701854 (±0.0048510367)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z264.000264.000264.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0280.0800.000

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Supplemental data

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Sample components

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Entire : Complex structure of the fission yeast SREBP-SCAP binding domains

EntireName: Complex structure of the fission yeast SREBP-SCAP binding domains
Components
  • Complex: Complex structure of the fission yeast SREBP-SCAP binding domains
    • Protein or peptide: Sterol regulatory element-binding protein cleavage-activating protein
    • Protein or peptide: Sterol regulatory element-binding protein cleavage-activating protein
    • Protein or peptide: Sterol regulatory element-binding protein 1

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Supramolecule #1: Complex structure of the fission yeast SREBP-SCAP binding domains

SupramoleculeName: Complex structure of the fission yeast SREBP-SCAP binding domains
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast)

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Macromolecule #1: Sterol regulatory element-binding protein cleavage-activating protein

MacromoleculeName: Sterol regulatory element-binding protein cleavage-activating protein
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843
Molecular weightTheoretical: 44.95675 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGWSDHDELS TDTTLHEEKF RIEPVPVHHQ LDILKIAVSE NYKTFASVGL DRCLVVWDLR QWCTKLVLSK EQMPRTLKAI ALDPQGNYV SLFSKDTLFI LNVESPSLML QHSYHCKPNS KLNVFWMPGT HKDDEWKNFE LVVVESSGEI QVFSLTIEIE G ADIALVEK ...String:
MGWSDHDELS TDTTLHEEKF RIEPVPVHHQ LDILKIAVSE NYKTFASVGL DRCLVVWDLR QWCTKLVLSK EQMPRTLKAI ALDPQGNYV SLFSKDTLFI LNVESPSLML QHSYHCKPNS KLNVFWMPGT HKDDEWKNFE LVVVESSGEI QVFSLTIEIE G ADIALVEK FQLSSPIIKS ISIVSPTANR IACLTESGEV TVYSKKGPVW SPKILSQNKN YLTETKKDIY GIAMADILFL AR DSGVDMI DLKNDELLHS FTLPPIKVNT FSVGVSNSRF VNGQFRVSSI SFCFTHAVTE KVLYYYYGNE SNESYIILNK WDQ QPNLVD VHDPDNSLAS LTFDELQENI HEVEDASESV MSSDGLYIFG MRRKSSSGIS PTADEKNEDN GFTLRNRKLR

UniProtKB: Sterol regulatory element-binding protein cleavage-activating protein

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Macromolecule #2: Sterol regulatory element-binding protein cleavage-activating protein

MacromoleculeName: Sterol regulatory element-binding protein cleavage-activating protein
type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843
Molecular weightTheoretical: 11.868574 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AHMNTHSGGE TQVWEVWMYS QSEKKHRSKS LKMYNSLIIA DPGPSLAVSD RCVAIVLGNY VALVGYGSEI FRDFYQIRNS DEMDRILRR KRKNLQRKRS GTIG

UniProtKB: Sterol regulatory element-binding protein cleavage-activating protein

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Macromolecule #3: Sterol regulatory element-binding protein 1

MacromoleculeName: Sterol regulatory element-binding protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843
Molecular weightTheoretical: 30.318842 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AHMQHSKSSV HAELRELPES TANLIENSHA DDVFSPNMVE RLWVLAKSTR DSAQMSDSII SSLSDVLVLS PLEVLASWYA ADLLDALLM ESLSRKVEIS EIEEIISLCP KNSSIIRHAL LAKLVLFPEN TADSLNEVLA AYKNTLDLCS QDKRKQSSVL K INLSKLFT ...String:
AHMQHSKSSV HAELRELPES TANLIENSHA DDVFSPNMVE RLWVLAKSTR DSAQMSDSII SSLSDVLVLS PLEVLASWYA ADLLDALLM ESLSRKVEIS EIEEIISLCP KNSSIIRHAL LAKLVLFPEN TADSLNEVLA AYKNTLDLCS QDKRKQSSVL K INLSKLFT LHSCLSLALQ RLGYGDVSKR MYQEIFVPDS DADITPLSFI ISWTALNTFA PICTSPKEND VVEKMAMYVR TA IGTLKIQ DLKLSRKLIN SCIDIGSRLQ EDLGY

UniProtKB: Sterol regulatory element-binding protein 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

Concentration20 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 157243
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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