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- PDB-8yo8: Crystal structure of hFSP1 with both 6-OH-FAD and NAD (hFSP1-6-OH... -

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Basic information

Entry
Database: PDB / ID: 8yo8
TitleCrystal structure of hFSP1 with both 6-OH-FAD and NAD (hFSP1-6-OH-FAD-NAD)
ComponentsFerroptosis suppressor protein 1
KeywordsOXIDOREDUCTASE / Flavoprotein / 6-OH-FAD / Redox
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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Ferroptosis suppressor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 12, 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)41,5964
Polymers40,0351
Non-polymers1,5613
Water3,693205
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)83,1928
Polymers80,0702
Non-polymers3,1226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6810 Å2
ΔGint-54 kcal/mol
Surface area28910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.162, 60.162, 195.256
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-548-

HOH

21A-688-

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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
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: 2→32.54 Å / Num. obs: 28766 / % possible obs: 84.01 % / Redundancy: 19.2 % / Biso Wilson estimate: 24.41 Å2 / Rpim(I) all: 0.03 / Net I/σ(I): 17.2
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 2813 / Rpim(I) all: 0.425

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
PHENIX1.19.2_4158phasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→32.54 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2225 1233 5.12 %
Rwork0.1858 --
obs0.1877 24080 84.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→32.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2752 0 103 205 3060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.878
X-RAY DIFFRACTIONf_dihedral_angle_d14.6211092
X-RAY DIFFRACTIONf_chiral_restr0.054465
X-RAY DIFFRACTIONf_plane_restr0.006496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.080.2213730.21911035X-RAY DIFFRACTION36
2.08-2.170.2669770.21031479X-RAY DIFFRACTION50
2.17-2.290.2283930.21932082X-RAY DIFFRACTION70
2.29-2.430.26621740.21522892X-RAY DIFFRACTION98
2.43-2.620.23181470.21673030X-RAY DIFFRACTION100
2.62-2.880.27261340.20633036X-RAY DIFFRACTION100
2.88-3.30.24491640.19473008X-RAY DIFFRACTION100
3.3-4.160.1961990.1643045X-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)
11.14990.71260.5821.97791.16271.80310.07420.029-0.12560.41790.202-0.4190.18930.5747-0.18390.16720.0029-0.03660.2659-0.06640.21732.682621.261224.1694
21.75661.09680.23792.71530.85451.7666-0.02890.1648-0.24870.01120.1279-0.35320.16630.6339-0.23670.12680.07590.04870.2645-0.01970.255529.169210.936.2588
31.20830.26930.03342.08530.58752.05140.0806-0.1713-0.27620.3584-0.05970.2350.592-0.14380.05660.28-0.00370.04860.1184-0.01710.248411.8955-0.28159.4819
40.92380.14760.19871.65590.84462.07930.0952-0.1021-0.33860.7657-0.0516-0.37320.43560.0984-0.2530.49280.0964-0.05760.1419-0.02820.314225.4396-2.997312.1703
50.72050.72860.19131.46170.9871.55010.2059-0.3633-0.18210.9028-0.135-0.01210.7813-0.1765-0.09491.2001-0.3139-0.11780.2278-0.15290.078624.066912.601236.8137
61.09640.78461.21852.64882.29833.1520.2359-0.41590.26360.6845-0.33080.22870.1953-0.15020.12110.3235-0.13840.08230.3168-0.09010.192121.539624.218934.1111
70.77490.62780.24251.61211.11421.40760.3419-0.39340.18560.6128-0.26790.1950.2697-0.140.23210.3222-0.03760.10190.2967-0.09770.22828.152716.599622.7012
84.12312.81540.29684.31090.86831.87950.0095-0.03870.5236-0.1152-0.10540.1778-0.39520.08990.09960.15410.02330.05390.1186-0.00870.156619.324925.354413.1118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 113 )
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 141 )
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 214 )
4X-RAY DIFFRACTION4chain 'A' and (resid 215 through 256 )
5X-RAY DIFFRACTION5chain 'A' and (resid 257 through 294 )
6X-RAY DIFFRACTION6chain 'A' and (resid 295 through 313 )
7X-RAY DIFFRACTION7chain 'A' and (resid 314 through 354 )
8X-RAY DIFFRACTION8chain 'A' and (resid 355 through 373 )

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