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- PDB-4yhc: Crystal structure of the WD40 domain of SCAP from fission yeast -

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Basic information

Entry
Database: PDB / ID: 4yhc
TitleCrystal structure of the WD40 domain of SCAP from fission yeast
ComponentsSterol regulatory element-binding protein cleavage-activating protein
KeywordsSTRUCTURAL PROTEIN / beta sheet / WD40
Function / homology
Function and homology information


positive regulation of ergosterol biosynthetic process / SREBP-SCAP complex / regulation of cholesterol biosynthetic process / sterol binding / SREBP signaling pathway / steroid metabolic process / cytoplasmic side of endoplasmic reticulum membrane / cellular response to hypoxia / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Sterol regulatory element-binding protein cleavage-activating protein / : / Sterol-sensing domain of SREBP cleavage-activation / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
CITRIC ACID / Sterol regulatory element-binding protein cleavage-activating protein
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsGong, X. / Li, J.X. / Wu, J.P. / Yan, C.Y. / Yan, N.
CitationJournal: Cell Res. / Year: 2015
Title: Structure of the WD40 domain of SCAP from fission yeast reveals the molecular basis for SREBP recognition.
Authors: Gong, X. / Li, J. / Shao, W. / Wu, J. / Qian, H. / Ren, R. / Espenshade, P. / Yan, N.
History
DepositionFeb 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 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 cleavage-activating protein
B: Sterol regulatory element-binding protein cleavage-activating protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,9654
Polymers105,5812
Non-polymers3842
Water5,531307
1
A: Sterol regulatory element-binding protein cleavage-activating protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1753
Polymers52,7901
Non-polymers3842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sterol regulatory element-binding protein cleavage-activating protein


Theoretical massNumber of molelcules
Total (without water)52,7901
Polymers52,7901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.009, 109.714, 103.454
Angle α, β, γ (deg.)90.00, 100.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 52790.445 Da / Num. of mol.: 2
Fragment: UNP residues 567-961, linker (AGS) and residues 986-1054
Mutation: C618S, C671S, C680S,C756S,C873S, C901S, C920S, C941S, 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
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

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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: 2.01 Å3/Da / Density % sol: 38.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 20% (v/v) PEG 3350, 0.2M Na3Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Apr 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→40 Å / Num. obs: 51974 / % possible obs: 99.1 % / Redundancy: 3.1 % / Net I/σ(I): 27.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→40 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2293 2657 5.11 %
Rwork0.1772 --
obs0.1798 51974 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6746 0 26 307 7079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0176929
X-RAY DIFFRACTIONf_angle_d1.8369402
X-RAY DIFFRACTIONf_dihedral_angle_d18.4852524
X-RAY DIFFRACTIONf_chiral_restr0.1471065
X-RAY DIFFRACTIONf_plane_restr0.011187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0481-2.08540.33631500.23872424X-RAY DIFFRACTION93
2.0854-2.12550.26881270.21552623X-RAY DIFFRACTION99
2.1255-2.16890.26661480.21642538X-RAY DIFFRACTION99
2.1689-2.2160.31651340.2062644X-RAY DIFFRACTION100
2.216-2.26760.28221430.21732582X-RAY DIFFRACTION99
2.2676-2.32430.22391110.19092624X-RAY DIFFRACTION100
2.3243-2.38710.28431450.19812643X-RAY DIFFRACTION100
2.3871-2.45740.26021460.19592544X-RAY DIFFRACTION100
2.4574-2.53670.27481640.22669X-RAY DIFFRACTION100
2.5367-2.62730.27451420.19332529X-RAY DIFFRACTION100
2.6273-2.73250.2781210.17582688X-RAY DIFFRACTION100
2.7325-2.85680.2251440.17152587X-RAY DIFFRACTION100
2.8568-3.00740.2251220.17742605X-RAY DIFFRACTION100
3.0074-3.19580.24171480.17522622X-RAY DIFFRACTION100
3.1958-3.44250.20431690.1632619X-RAY DIFFRACTION100
3.4425-3.78880.22051440.16542599X-RAY DIFFRACTION99
3.7888-4.33670.20481260.16342604X-RAY DIFFRACTION99
4.3367-5.46240.17471460.14392603X-RAY DIFFRACTION99
5.4624-46.16060.20611270.18642627X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 0.0007 Å / Origin y: 40.6507 Å / Origin z: 126.5499 Å
111213212223313233
T0.1639 Å20.0088 Å20.0193 Å2-0.2103 Å2-0.0025 Å2--0.2156 Å2
L0.2083 °20.1545 °20.2277 °2-0.38 °20.3105 °2--0.702 °2
S-0.0211 Å °-0.0542 Å °0.0407 Å °0.0626 Å °-0.0016 Å °0.0216 Å °0.0289 Å °0.0028 Å °0.0389 Å °
Refinement TLS groupSelection details: all

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