[English] 日本語
Yorodumi
- PDB-8yo8: Crystal structure of hFSP1 with both 6-OH-FAD and NAD (hFSP1-6-OH... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more