[English] 日本語
Yorodumi
- PDB-5grs: Complex structure of the fission yeast SREBP-SCAP binding domains -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5grs
TitleComplex structure of the fission yeast SREBP-SCAP binding domains
Components
  • (Sterol regulatory element-binding protein cleavage-activating protein) x 2
  • Sterol regulatory element-binding protein 1
KeywordsPROTEIN TRANSPORT / protein complex
Function / homology
Function and homology information


positive regulation of ergosterol biosynthetic process / regulation of ergosterol biosynthetic process / SREBP-SCAP complex / regulation of cholesterol biosynthetic process / SREBP signaling pathway / sterol binding / negative regulation of cellular response to hypoxia / steroid metabolic process / cytoplasmic side of endoplasmic reticulum membrane / cellular response to hypoxia ...positive regulation of ergosterol biosynthetic process / regulation of ergosterol biosynthetic process / SREBP-SCAP complex / regulation of cholesterol biosynthetic process / SREBP signaling pathway / sterol binding / negative regulation of cellular response to hypoxia / steroid metabolic process / cytoplasmic side of endoplasmic reticulum membrane / cellular response to hypoxia / DNA-binding transcription activator activity, RNA polymerase II-specific / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Golgi membrane / chromatin / endoplasmic reticulum membrane / 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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) 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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / 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 (fission yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsGong, X. / Qian, H.W. / Wu, J.P. / Yan, N.
Funding support China, 2items
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
DepositionAug 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Other / Category: atom_sites / cell / em_image_scans
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9537
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sterol regulatory element-binding protein cleavage-activating protein
I: Sterol regulatory element-binding protein cleavage-activating protein
B: Sterol regulatory element-binding protein cleavage-activating protein
J: Sterol regulatory element-binding protein cleavage-activating protein
C: Sterol regulatory element-binding protein cleavage-activating protein
K: Sterol regulatory element-binding protein cleavage-activating protein
D: Sterol regulatory element-binding protein cleavage-activating protein
L: Sterol regulatory element-binding protein cleavage-activating protein
E: Sterol regulatory element-binding protein 1
F: Sterol regulatory element-binding protein 1
G: Sterol regulatory element-binding protein 1
H: Sterol regulatory element-binding protein 1


Theoretical massNumber of molelcules
Total (without water)348,57712
Polymers348,57712
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area31390 Å2
ΔGint-180 kcal/mol
Surface area122760 Å2

-
Components

#1: Protein
Sterol regulatory element-binding protein cleavage-activating protein / SREBP cleavage-activating protein


Mass: 44956.750 Da / Num. of mol.: 4 / Fragment: UNP residues 567-961 / Mutation: C671S, C873S, C901S, C920S, C941S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: scp1, SPBC3B9.15c / Production host: Escherichia coli (E. coli) / References: UniProt: O43043
#2: Protein
Sterol regulatory element-binding protein cleavage-activating protein / SREBP cleavage-activating protein


Mass: 11868.574 Da / Num. of mol.: 4 / Fragment: UNP residues 986-1085 / Mutation: C1010S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: scp1, SPBC3B9.15c / Production host: Escherichia coli (E. coli) / References: UniProt: O43043
#3: Protein
Sterol regulatory element-binding protein 1


Mass: 30318.842 Da / Num. of mol.: 4 / Fragment: UNP residues 628-896 / Mutation: C644S, C672S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: sre1, SPBC19C2.09 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UUD1

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Complex structure of the fission yeast SREBP-SCAP binding domains
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast)
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pET15b, pETDuet-1
Buffer solutionpH: 8
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 157243 / Symmetry type: POINT

+
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