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- PDB-8jsc: Structure of the FSP1 protein from Human -

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Basic information

Entry
Database: PDB / ID: 8jsc
TitleStructure of the FSP1 protein from Human
ComponentsFerroptosis suppressor protein 1
KeywordsOXIDOREDUCTASE / NADH-ubiquinone oxidoreductase / OXIDOREDUCTASE (E.C.1.-.-.-)
Function / homology
Function and homology information


electron-transferring-flavoprotein dehydrogenase activity / ubiquinone metabolic process / Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / vitamin K metabolic process / regulation of cellular response to oxidative stress / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / cellular detoxification / negative regulation of ferroptosis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / apoptotic mitochondrial changes ...electron-transferring-flavoprotein dehydrogenase activity / ubiquinone metabolic process / Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / vitamin K metabolic process / regulation of cellular response to oxidative stress / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / cellular detoxification / negative regulation of ferroptosis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / apoptotic mitochondrial changes / lipid droplet / flavin adenine dinucleotide binding / mitochondrial outer membrane / positive regulation of apoptotic process / mitochondrion / extracellular space / DNA binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Ferroptosis suppressor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsZhang, S.T. / Jia, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res. / Year: 2023
Title: FSP1 oxidizes NADPH to suppress ferroptosis.
Authors: Zhang, S. / Gou, S. / Zhang, Q. / Yong, X. / Gan, B. / Jia, D.
History
DepositionJun 19, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Ferroptosis suppressor protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9873
Polymers40,4421
Non-polymers1,5452
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-7 kcal/mol
Surface area15290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.820, 39.126, 70.345
Angle α, β, γ (deg.)90.000, 108.952, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Ferroptosis suppressor protein 1 / FSP1 / Apoptosis-inducing factor homologous mitochondrion-associated inducer of death / AMID / p53- ...FSP1 / Apoptosis-inducing factor homologous mitochondrion-associated inducer of death / AMID / p53-responsive gene 3 protein


Mass: 40442.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIFM2, AMID, PRG3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BRQ8, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#2: Chemical ChemComp-6FA / 6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE


Mass: 801.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O16P2
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Ammonium nitrate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.16→62.25 Å / Num. obs: 18472 / % possible obs: 99.4 % / Redundancy: 3.6 % / CC1/2: 0.972 / Net I/σ(I): 4.1
Reflection shellResolution: 2.16→2.27 Å / Num. unique obs: 2689 / CC1/2: 0.556

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
PDB_EXTRACTv3.27data extraction
Cootmodel building
PHENIXv1.13phasing
ADDREFdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→39.5 Å / SU ML: 0.2844 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.9055
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2267 825 4.48 %
Rwork0.1866 17575 -
obs0.1884 18340 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.72 Å2
Refinement stepCycle: LAST / Resolution: 2.16→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 102 152 3038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01172941
X-RAY DIFFRACTIONf_angle_d1.2823996
X-RAY DIFFRACTIONf_chiral_restr0.0706458
X-RAY DIFFRACTIONf_plane_restr0.0069499
X-RAY DIFFRACTIONf_dihedral_angle_d20.89951088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.290.29161660.23562864X-RAY DIFFRACTION98.09
2.29-2.470.27651400.21082871X-RAY DIFFRACTION98.59
2.47-2.720.26751210.2042934X-RAY DIFFRACTION99.45
2.72-3.110.25551330.18412944X-RAY DIFFRACTION99.61
3.11-3.920.1941220.16912967X-RAY DIFFRACTION99.17

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