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- PDB-8wik: Crystal structure of human FSP1 -

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Basic information

Entry
Database: PDB / ID: 8wik
TitleCrystal structure of human FSP1
ComponentsFerroptosis suppressor protein 1
KeywordsOXIDOREDUCTASE / FSP1 / Ferroptosis / FAD / NADH / inhibitor
Function / homology
Function and homology information


electron-transferring-flavoprotein dehydrogenase activity / ubiquinone metabolic process / negative regulation of ferroptosis / 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 / cellular detoxification / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / apoptotic mitochondrial changes / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release ...electron-transferring-flavoprotein dehydrogenase activity / ubiquinone metabolic process / negative regulation of ferroptosis / 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 / cellular detoxification / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / apoptotic mitochondrial changes / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / lipid droplet / flavin adenine dinucleotide binding / mitochondrial outer membrane / positive regulation of apoptotic process / mitochondrion / DNA binding / extracellular space / 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
AuthorsFeng, S. / Huang, X. / Tang, D. / Qi, S.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82304600 China
National Natural Science Foundation of China (NSFC)32201025 China
National Natural Science Foundation of China (NSFC)32071214 China
CitationJournal: MedComm (2020) / Year: 2024
Title: The crystal structure of human ferroptosis suppressive protein 1 in complex with flavin adenine dinucleotide and nicotinamide adenine nucleotide.
Authors: Feng, S. / Huang, X. / Tang, D. / Liu, X. / Ouyang, L. / Yang, D. / Wang, K. / Liao, B. / Qi, S.
History
DepositionSep 24, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 8, 2024Provider: 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)42,0393
Polymers40,5741
Non-polymers1,4652
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-8 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.875, 56.875, 505.105
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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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: 40573.598 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: Spodoptera frugiperda (fall armyworm)
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: HEPES , MgCl2, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 291 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 34829 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 24.58 Å2 / CC1/2: 0.969 / CC star: 0.992 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.04 / Rrim(I) all: 0.125 / Χ2: 0.959 / Net I/σ(I): 4.6 / Num. measured all: 339711
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2-2.079.21.62133530.530.8320.5591.7180.906100
2.07-2.159.91.21533580.7210.9150.4051.2820.92100
2.15-2.2510.10.86233850.8410.9560.2820.9080.954100
2.25-2.379.90.6134130.9080.9760.2020.6430.976100
2.37-2.5210.40.42433660.9560.9890.1370.4460.99399.9
2.52-2.719.80.27634450.9760.9940.0920.2911.001100
2.71-2.99100.18834640.9880.9970.0620.1981.01699.8
2.99-3.4210.10.1234770.9930.9980.0390.1261.04899.9
3.42-4.319.50.0935990.9950.9990.0310.0960.992100
4.31-508.80.07239690.9890.9970.0260.0760.77299.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→35.26 Å / SU ML: 0.2611 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0098
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2627 2717 6.48 %
Rwork0.2245 39225 -
obs0.227 34829 68.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.59 Å2
Refinement stepCycle: LAST / Resolution: 2→35.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 0 98 197 3083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762941
X-RAY DIFFRACTIONf_angle_d0.94343994
X-RAY DIFFRACTIONf_chiral_restr0.0571462
X-RAY DIFFRACTIONf_plane_restr0.009505
X-RAY DIFFRACTIONf_dihedral_angle_d9.2836474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.36380.3099545X-RAY DIFFRACTION17.81
2.04-2.080.2851480.3092700X-RAY DIFFRACTION23.53
2.08-2.120.3269620.2983898X-RAY DIFFRACTION29.05
2.12-2.170.3291820.30661198X-RAY DIFFRACTION40.25
2.17-2.220.32731060.29421524X-RAY DIFFRACTION50.15
2.22-2.270.36231130.29691653X-RAY DIFFRACTION53.74
2.27-2.330.33961130.29181645X-RAY DIFFRACTION55.34
2.33-2.40.30081180.28871758X-RAY DIFFRACTION57.53
2.4-2.480.34051290.2841867X-RAY DIFFRACTION60.74
2.48-2.570.35231340.2681955X-RAY DIFFRACTION65.3
2.57-2.670.31991510.27712184X-RAY DIFFRACTION72.2
2.67-2.790.31281850.26672627X-RAY DIFFRACTION87.19
2.79-2.940.29722050.26032858X-RAY DIFFRACTION94.3
2.94-3.120.27151990.23512975X-RAY DIFFRACTION97.51
3.12-3.360.30872100.22452998X-RAY DIFFRACTION98.28
3.36-3.70.25532010.20412914X-RAY DIFFRACTION97.37
3.7-4.240.25482060.17912923X-RAY DIFFRACTION96.6
4.24-5.330.18012130.16772959X-RAY DIFFRACTION97.57
5.34-35.260.1992040.2093044X-RAY DIFFRACTION99.66
Refinement TLS params.Method: refined / Origin x: 16.4241703844 Å / Origin y: -9.36275331131 Å / Origin z: -18.5992812359 Å
111213212223313233
T0.295370245462 Å2-0.0570098145349 Å2-0.0758739527061 Å2-0.231417311777 Å20.1163749507 Å2--0.268602987422 Å2
L1.06348773037 °2-0.142224938428 °20.396194918724 °2-3.23959488252 °2-2.18326953324 °2--2.93905181403 °2
S0.113517177928 Å °-0.0448439625863 Å °-0.193768577349 Å °0.264921657363 Å °0.039217252203 Å °0.223428559998 Å °-0.0259450812868 Å °-0.113803166447 Å °-0.144094604126 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 10 through 402)

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