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- PDB-8yox: Crystal structure of hFSP1 with 6-OH-FAD (hFSP1-6-OH-FAD) -

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Basic information

Entry
Database: PDB / ID: 8yox
TitleCrystal structure of hFSP1 with 6-OH-FAD (hFSP1-6-OH-FAD)
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 / 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 / Ferroptosis suppressor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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 14, 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)40,9333
Polymers40,0351
Non-polymers8982
Water59433
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)81,8656
Polymers80,0702
Non-polymers1,7954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4390 Å2
ΔGint-49 kcal/mol
Surface area29220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.360, 60.360, 194.380
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

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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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 33 / 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: 51.83 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M Sodium chloride, 0.12 M Lithium sulfate, 0.1 M Sodium HEPES, 16% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.48→35.59 Å / Num. obs: 15119 / % possible obs: 98.41 % / Redundancy: 14.9 % / Biso Wilson estimate: 52.84 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.3
Reflection shellResolution: 2.48→2.54 Å / Num. unique obs: 1005 / CC1/2: 0.813

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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 / Resolution: 2.48→27.54 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0.19 / Phase error: 31.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2674 1443 5.28 %
Rwork0.191 --
obs0.1948 15068 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.48→27.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2751 0 59 33 2843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.922
X-RAY DIFFRACTIONf_dihedral_angle_d15.9791053
X-RAY DIFFRACTIONf_chiral_restr0.052452
X-RAY DIFFRACTIONf_plane_restr0.006495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.570.30571190.28292207X-RAY DIFFRACTION83
2.57-2.670.33751270.26822508X-RAY DIFFRACTION94
2.67-2.790.34151430.26222626X-RAY DIFFRACTION98
2.79-2.940.33872010.26362577X-RAY DIFFRACTION100
2.94-3.120.36861520.2662630X-RAY DIFFRACTION100
3.12-3.360.2511620.23132692X-RAY DIFFRACTION100
3.37-3.70.31481150.20342645X-RAY DIFFRACTION99
3.7-4.230.20191140.16542684X-RAY DIFFRACTION100
4.24-5.330.19581380.14552660X-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)
10.3130.1919-0.19190.135-0.05340.1989-0.17820.0411-0.01960.26160.0633-0.0179-0.03720.15390.00010.6697-0.0281-0.04450.3737-0.05390.464832.761327.044330.1768
20.2549-0.20030.31331.42060.35320.59440.05180.28670.03580.2080.1221-0.2770.03210.31520.01090.5114-0.03250.01690.3737-0.07960.47131.692616.279516.7205
30.5736-0.13830.12140.6001-0.08180.63240.01940.0201-0.08720.2104-0.03850.15120.1186-0.0915-00.6206-0.08060.05910.4273-0.05280.551311.8473-0.41959.5999
40.54440.26230.18550.45320.19340.34170.12310.0535-0.17530.8024-0.1089-0.04520.3704-0.205-0.09761.0076-0.0777-0.0090.287-0.01370.463725.11374.178423.4184
50.54-0.0240.63590.42640.02420.61390.04680.06970.1170.2594-0.13010.2865-0.1096-0.1160.00910.6332-0.07540.12860.3932-0.07240.453814.126320.514522.5354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 141 )
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 214 )
4X-RAY DIFFRACTION4chain 'A' and (resid 215 through 294 )
5X-RAY DIFFRACTION5chain 'A' and (resid 295 through 373 )

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