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- PDB-5gpd: Crystal structure of the binding domain of SREBP from fission yeast -

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Basic information

Entry
Database: PDB / ID: 5gpd
TitleCrystal structure of the binding domain of SREBP from fission yeast
ComponentsSterol regulatory element-binding protein 1
KeywordsDNA BINDING PROTEIN / Regulation domain
Function / homology
Function and homology information


regulation of ergosterol biosynthetic process / SREBP-SCAP complex / negative regulation of cellular response to hypoxia / SREBP signaling pathway / cytoplasmic side of endoplasmic reticulum membrane / steroid metabolic process / DNA-binding transcription activator activity, RNA polymerase II-specific / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin ...regulation of ergosterol biosynthetic process / SREBP-SCAP complex / negative regulation of cellular response to hypoxia / SREBP signaling pathway / cytoplasmic side of endoplasmic reticulum membrane / steroid metabolic process / DNA-binding transcription activator activity, RNA polymerase II-specific / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / 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) / 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.
Similarity search - Domain/homology
Sterol regulatory element-binding protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.501 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 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sterol regulatory element-binding protein 1
B: Sterol regulatory element-binding protein 1


Theoretical massNumber of molelcules
Total (without water)56,0802
Polymers56,0802
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-17 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.903, 96.903, 151.595
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Sterol regulatory element-binding protein 1


Mass: 28040.244 Da / Num. of mol.: 2 / Fragment: UNP residues 628-876 / 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 71.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M BTP (pH 7.0), 1.5M NaNO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.5→40 Å / Num. obs: 10643 / % possible obs: 98.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.5
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementResolution: 3.501→34.973 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.97
RfactorNum. reflection% reflection
Rfree0.2785 511 4.81 %
Rwork0.2653 --
obs0.2661 10632 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.501→34.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 0 0 2938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082978
X-RAY DIFFRACTIONf_angle_d1.094046
X-RAY DIFFRACTIONf_dihedral_angle_d21.8691079
X-RAY DIFFRACTIONf_chiral_restr0.058513
X-RAY DIFFRACTIONf_plane_restr0.005497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5008-3.85260.38691400.32272508X-RAY DIFFRACTION100
3.8526-4.40920.29661090.2992546X-RAY DIFFRACTION100
4.4092-5.55150.29731300.28272543X-RAY DIFFRACTION100
5.5515-34.97440.24851320.2362524X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: -15.7283 Å / Origin y: 37.4826 Å / Origin z: -11.8946 Å
111213212223313233
T0.6828 Å20.0644 Å2-0.01 Å2-0.7786 Å20.0213 Å2--0.7515 Å2
L2.0861 °21.4075 °20.8396 °2-1.5187 °21.0269 °2--1.4272 °2
S-0.0157 Å °0.0667 Å °0.0673 Å °0.2111 Å °-0.0512 Å °0.0088 Å °0.0229 Å °0.3009 Å °-0.0411 Å °
Refinement TLS groupSelection details: all

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