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- PDB-8yoq: Crystal structure of hFSP1 with both 6-OH-FAD and NADP (hFSP1-6-O... -

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Basic information

Entry
Database: PDB / ID: 8yoq
TitleCrystal structure of hFSP1 with both 6-OH-FAD and NADP (hFSP1-6-OH-FAD-NADP)
ComponentsFerroptosis suppressor protein 1
KeywordsOXIDOREDUCTASE / Flavoprotein / 6-OH-FAD / Redox / NADP
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 / cytoplasm / cytosol
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 / Chem-NDP / Ferroptosis suppressor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsLan, H.Y. / Gao, Y. / Hong, T. / Zhao, Z.Z. / Chang, Z.H. / Wang, Y.F. / Wang, F.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071269 China
National Natural Science Foundation of China (NSFC)31770827 China
CitationJournal: Cell Discov / Year: 2024
Title: Structural insight into 6-OH-FAD-dependent activation of hFSP1 for ferroptosis suppression.
Authors: Lan, H. / Gao, Y. / Hong, T. / Chang, Z. / Zhao, Z. / Wang, Y. / Wang, F.
History
DepositionMar 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferroptosis suppressor protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6784
Polymers40,0351
Non-polymers1,6433
Water5,585310
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ferroptosis suppressor protein 1
hetero molecules

A: Ferroptosis suppressor protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3568
Polymers80,0702
Non-polymers3,2866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6870 Å2
ΔGint-51 kcal/mol
Surface area28480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.302, 60.302, 194.721
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-534-

HOH

21A-746-

HOH

31A-781-

HOH

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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: 40035.066 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.1 M Sodium chloride, 0.12 M Lithium sulfate, 0.1 M Sodium HEPES, 16.5% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.78→46.021 Å / Num. obs: 40126 / % possible obs: 94.33 % / Redundancy: 18.9 % / Biso Wilson estimate: 17.5 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.069 / Rrim(I) all: 0.301 / Net I/σ(I): 19.6
Reflection shellResolution: 1.8→1.806 Å / Num. unique obs: 3915 / CC1/2: 0.704

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8YOX

8yox


Resolution: 1.79→32.45 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2187 1963 5.2 %
Rwork0.1944 --
obs0.1957 37747 94.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→32.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 0 107 310 3151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.927
X-RAY DIFFRACTIONf_dihedral_angle_d13.6051050
X-RAY DIFFRACTIONf_chiral_restr0.055461
X-RAY DIFFRACTIONf_plane_restr0.006495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.2359890.211383X-RAY DIFFRACTION52
1.83-1.880.27311090.24121909X-RAY DIFFRACTION72
1.88-1.940.3051400.25322541X-RAY DIFFRACTION96
1.94-20.26631520.22912657X-RAY DIFFRACTION100
2-2.070.23921280.2242693X-RAY DIFFRACTION100
2.07-2.150.24641600.212668X-RAY DIFFRACTION100
2.15-2.250.25261450.21462659X-RAY DIFFRACTION100
2.25-2.370.25221400.20332686X-RAY DIFFRACTION100
2.37-2.520.22141530.2042708X-RAY DIFFRACTION100
2.52-2.710.23531650.19192679X-RAY DIFFRACTION100
2.71-2.980.20351250.19952745X-RAY DIFFRACTION100
2.98-3.420.22331580.18432726X-RAY DIFFRACTION100
3.42-4.30.1721420.16652802X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0083-0.0314-0.01970.1158-0.02780.02470.04330.02620.03190.06320.04560.1172-0.0373-0.1794-00.1058-0.01830.00750.14220.04730.1198-29.7051-16.77518.0635
20.0231-0.003-0.01390.01240.00350.01830.0650.00070.07250.0529-0.0562-0.064-0.1154-0.0353-0.00060.1553-0.0063-0.02180.05410.00560.1471-10.22261.690111.3047
30.1719-0.05350.04180.0248-0.00090.01830.113-0.06690.10010.2263-0.18020.03980.0088-0.0405-0.1360.3884-0.06150.0290.01560.0850.0577-24.9103-4.366823.5976
40.0739-0.11340.04370.2151-0.0760.05820.1132-0.0273-0.09320.046-0.0871-0.17650.11460.0220.02520.139-0.0561-0.08890.14020.05860.0962-13.9859-20.41722.7135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 164 )
2X-RAY DIFFRACTION2chain 'A' and (resid 165 through 214 )
3X-RAY DIFFRACTION3chain 'A' and (resid 215 through 294 )
4X-RAY DIFFRACTION4chain 'A' and (resid 295 through 373 )

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