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- PDB-9m3m: Structure of FSP1 in complex with FSEN1 -

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Basic information

Entry
Database: PDB / ID: 9m3m
TitleStructure of FSP1 in complex with FSEN1
ComponentsFerroptosis suppressor protein 1
KeywordsMEMBRANE PROTEIN / complex monomer inhibitor
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 / apoptotic mitochondrial changes / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release ...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 / 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 / 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: 2.01 Å
AuthorsZhang, S.T. / Jia, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Cocrystal structure reveals the mechanism of FSP1 inhibition by FSEN1.
Authors: Zhang, S. / Megarioti, A.H. / Hendricks, J.M. / Zhou, J. / Sun, Q. / Jia, D. / Olzmann, J.A.
History
DepositionMar 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: 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)42,6034
Polymers40,5741
Non-polymers2,0293
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-7 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.539, 38.946, 70.097
Angle α, β, γ (deg.)90.000, 107.893, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-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: 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: Escherichia coli (E. coli)
References: UniProt: Q9BRQ8, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#2: 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
#3: Chemical ChemComp-6FA / 6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE


Mass: 801.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O16P2
#4: Chemical ChemComp-A1EMU / 3-(4-bromophenyl)-6-[[4-(4-methoxyphenyl)piperazin-1-yl]methyl]-[1,3]thiazolo[2,3-c][1,2,4]triazole


Mass: 484.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22BrN5OS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium citrate tribasic dihydrate, pH5.5,22% polyethylene glycol 1000

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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: Jul 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.01→66.71 Å / Num. obs: 22805 / % possible obs: 99.9 % / Redundancy: 3.3 % / CC1/2: 0.994 / Net I/σ(I): 7.6
Reflection shellResolution: 2.01→2.12 Å / Num. unique obs: 3291 / CC1/2: 0.453

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Cootmodel building
PHENIXphasing
ADDREFdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→62.37 Å / SU ML: 0.3193 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.6426
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2472 1088 4.78 %
Rwork0.2172 21661 -
obs0.2186 22749 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.92 Å2
Refinement stepCycle: LAST / Resolution: 2.01→62.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 132 176 3092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312975
X-RAY DIFFRACTIONf_angle_d0.77984044
X-RAY DIFFRACTIONf_chiral_restr0.0617458
X-RAY DIFFRACTIONf_plane_restr0.0074502
X-RAY DIFFRACTIONf_dihedral_angle_d20.69051098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.10.37391650.33552608X-RAY DIFFRACTION98.58
2.1-2.210.32281300.28752664X-RAY DIFFRACTION99.71
2.21-2.350.28351250.27392729X-RAY DIFFRACTION99.89
2.35-2.530.31411510.25942663X-RAY DIFFRACTION99.86
2.53-2.790.271220.23082730X-RAY DIFFRACTION99.93
2.79-3.190.25581310.22252721X-RAY DIFFRACTION100
3.19-4.020.21021220.18462739X-RAY DIFFRACTION100
4.02-62.370.18671420.1722807X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: 13.9674925344 Å / Origin y: -1.82644912997 Å / Origin z: 12.6761878162 Å
111213212223313233
T0.192053771985 Å2-0.00539048989554 Å2-0.0232269151129 Å2-0.187157111727 Å20.0187083045453 Å2--0.207575031729 Å2
L1.28258310203 °20.557137884117 °2-0.312762194579 °2-2.4800868137 °20.375050620366 °2--1.52432047114 °2
S0.0802731998327 Å °-0.14150459123 Å °0.0784172241975 Å °0.423553456051 Å °0.0359881534604 Å °0.0463008991607 Å °0.142323385015 Å °0.0102216639548 Å °-0.118383266442 Å °
Refinement TLS groupSelection details: all

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