+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21149 | |||||||||
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Title | Cryo-EM structure of IRP2-FBXL5-SKP1 complex | |||||||||
Map data | IRP2-FBXL5-SKP1 complex | |||||||||
Sample |
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Keywords | E3 ligase / [2Fe-2S] cluster / Iron metabolism / LIGASE | |||||||||
Function / homology | Function and homology information aconitate hydratase activity / iron-responsive element binding / : / F-box domain binding / citrate metabolic process / PcG protein complex / protoporphyrinogen IX biosynthetic process / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling ...aconitate hydratase activity / iron-responsive element binding / : / F-box domain binding / citrate metabolic process / PcG protein complex / protoporphyrinogen IX biosynthetic process / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / maintenance of protein location in nucleus / intestinal absorption / erythrocyte homeostasis / SCF ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / protein monoubiquitination / Association of TriC/CCT with target proteins during biosynthesis / cullin family protein binding / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / ubiquitin ligase complex / translation repressor activity / tricarboxylic acid cycle / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / osteoclast differentiation / post-embryonic development / molecular function activator activity / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of beta-catenin by the destruction complex / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / 2 iron, 2 sulfur cluster binding / multicellular organismal-level iron ion homeostasis / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / beta-catenin binding / FCERI mediated NF-kB activation / Interleukin-1 signaling / Orc1 removal from chromatin / positive regulation of protein catabolic process / protein polyubiquitination / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / Regulation of PLK1 Activity at G2/M Transition / Circadian Clock / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / iron ion transport / 4 iron, 4 sulfur cluster binding / proteasome-mediated ubiquitin-dependent protein catabolic process / intracellular iron ion homeostasis / protein ubiquitination / chromatin remodeling / iron ion binding / protein domain specific binding / centrosome / perinuclear region of cytoplasm / mitochondrion / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Wang H / Shi H | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Mol Cell / Year: 2020 Title: FBXL5 Regulates IRP2 Stability in Iron Homeostasis via an Oxygen-Responsive [2Fe2S] Cluster. Authors: Hui Wang / Hui Shi / Malini Rajan / Elizabeth R Canarie / Seoyeon Hong / Daniele Simoneschi / Michele Pagano / Matthew F Bush / Stefan Stoll / Elizabeth A Leibold / Ning Zheng / Abstract: Cellular iron homeostasis is dominated by FBXL5-mediated degradation of iron regulatory protein 2 (IRP2), which is dependent on both iron and oxygen. However, how the physical interaction between ...Cellular iron homeostasis is dominated by FBXL5-mediated degradation of iron regulatory protein 2 (IRP2), which is dependent on both iron and oxygen. However, how the physical interaction between FBXL5 and IRP2 is regulated remains elusive. Here, we show that the C-terminal substrate-binding domain of FBXL5 harbors a [2Fe2S] cluster in the oxidized state. A cryoelectron microscopy (cryo-EM) structure of the IRP2-FBXL5-SKP1 complex reveals that the cluster organizes the FBXL5 C-terminal loop responsible for recruiting IRP2. Interestingly, IRP2 binding to FBXL5 hinges on the oxidized state of the [2Fe2S] cluster maintained by ambient oxygen, which could explain hypoxia-induced IRP2 stabilization. Steric incompatibility also allows FBXL5 to physically dislodge IRP2 from iron-responsive element RNA to facilitate its turnover. Taken together, our studies have identified an iron-sulfur cluster within FBXL5, which promotes IRP2 polyubiquitination and degradation in response to both iron and oxygen concentrations. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21149.map.gz | 8.2 MB | EMDB map data format | |
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Header (meta data) | emd-21149-v30.xml emd-21149.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | emd_21149.png | 53.3 KB | ||
Filedesc metadata | emd-21149.cif.gz | 6.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21149 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21149 | HTTPS FTP |
-Related structure data
Related structure data | 6vcdMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21149.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | IRP2-FBXL5-SKP1 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.056 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : IRP2-FBLX5-SKP1 complex
Entire | Name: IRP2-FBLX5-SKP1 complex |
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Components |
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-Supramolecule #1: IRP2-FBLX5-SKP1 complex
Supramolecule | Name: IRP2-FBLX5-SKP1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Iron-responsive element binding protein 2, isoform CRA_a
Macromolecule | Name: Iron-responsive element binding protein 2, isoform CRA_a type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 105.165328 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MDAPKAGYAF EYLIETLNDS SHKKFFDVSK LGTKYDVLPY SIRVLLEAAV RNCDGFLMKK EDVMNILDWK TKQSNVEVPF FPARVLLQD FTGIPAMVDF AAMREAVKTL GGDPEKVHPA CPTDLTVDHS LQIDFSKCAI QNAPNPGGGD LQKAGKLSPL K VQPKKLPC ...String: MDAPKAGYAF EYLIETLNDS SHKKFFDVSK LGTKYDVLPY SIRVLLEAAV RNCDGFLMKK EDVMNILDWK TKQSNVEVPF FPARVLLQD FTGIPAMVDF AAMREAVKTL GGDPEKVHPA CPTDLTVDHS LQIDFSKCAI QNAPNPGGGD LQKAGKLSPL K VQPKKLPC RGQTTCRGSC DSGELGRNSG TFSSQIENTP ILCPFHLQPV PEPETVLKNQ EVEFGRNRER LQFFKWSSRV FK NVAVIPP GTGMAHQINL EYLSRVVFEE KDLLFPDSVV GTDSHITMVN GLGILGWGVG GIETEAVMLG LPVSLTLPEV VGC ELTGSS NPFVTSIDVV LGITKHLRQV GVAGKFVEFF GSGVSQLSIV DRTTIANMCP EYGAILSFFP VDNVTLKHLE HTGF SKAKL ESMETYLKAV KLFRNDQNSS GEPEYSQVIQ INLNSIVPSV SGPKRPQDRV AVTDMKSDFQ ACLNEKVGFK GFQIA AEKQ KDIVSIHYEG SEYKLSHGSV VIAAVISCTN NCNPSVMLAA GLLAKKAVEA GLRVKPYIRT SLSPGSGMVT HYLSSS GVL PYLSKLGFEI VGYGCSTCVG NTAPLSDAVL NAVKQGDLVT CGILSGNKNF EGRLCDCVRA NYLASPPLVV AYAIAGT VN IDFQTEPLGT DPTGKNIYLH DIWPSREEVH RVEEEHVILS MFKALKDKIE MGNKRWNSLE APDSVLFPWD LKSTYIRC P SFFDKLTKEP IALQAIENAH VLLYLGDSVT TDHISPAGSI ARNSAAAKYL TNRGLTPREF NSYGARRGND AVMTRGTFA NIKLFNKFIG KPAPKTIHFP SGQTLDVFEA AELYQKEGIP LIILAGKKYG SGNSRDWAAK GPYLLGVKAV LAESYEKIHK DHLIGIGIA PLQFLPGENA DSLGLSGRET FSLTFPEELS PGITLNIQTS TGKVFSVIAS FEDDVEITLY KHGGLLNFVA R KFS UniProtKB: Iron-responsive element-binding protein 2 |
-Macromolecule #2: F-box/LRR-repeat protein 5
Macromolecule | Name: F-box/LRR-repeat protein 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 54.832441 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: EHSTGITHLP PEVMLSIFSY LNPQELCRCS QVSMKWSQLT KTGSLWKHLY PVHWARGDWY SGPATELDTE PDDEWVKNRK DESRAFHEW DEDADIDESE ESAEESIAIS IAQMEKRLLH GLIHNVLPYV GTSVKTLVLA YSSAVSSKMV RQILELCPNL E HLDLTQTD ...String: EHSTGITHLP PEVMLSIFSY LNPQELCRCS QVSMKWSQLT KTGSLWKHLY PVHWARGDWY SGPATELDTE PDDEWVKNRK DESRAFHEW DEDADIDESE ESAEESIAIS IAQMEKRLLH GLIHNVLPYV GTSVKTLVLA YSSAVSSKMV RQILELCPNL E HLDLTQTD ISDSAFDSWS WLGCCQSLRH LDLSGCEKIT DVALEKISRA LGILTSHQSG FLKTSTSKIT STAWKNKDIT MQ STKQYAC LHDLTNKGIG EEIDNEHPWT KPVSSENFTS PYVWMLDAED LADIEDTVEW RHRNVESLCV METASNFSCS TSG CFSKDI VGLRTSVCWQ QHCASPAFAY CGHSFCCTGT ALRTMSSLPE SSAMCRKAAR TRLPRGKDLI YFGSEKSDQE TGRV LLFLS LSGCYQITDH GLRVLTLGGG LPYLEHLNLS GCLTITGAGL QDLVSACPSL NDEYFYYCDN INGPHADTAS GCQNL QCGF RACCRSGE UniProtKB: F-box/LRR-repeat protein 5 |
-Macromolecule #3: S-phase kinase-associated protein 1
Macromolecule | Name: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 18.679965 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPSIKLQSSD GEIFEVDVEI AKQSVTIKTM LEDLGMDDEG DDDPVPLPNV NAAILKKVIQ WCTHHKDDPP PPEDDENKEK RTDDIPVWD QEFLKVDQGT LFELILAANY LDIKGLLDVT CKTVANMIKG KTPEEIRKTF NIKNDFTEEE EAQVRKENQW C EEK UniProtKB: S-phase kinase-associated protein 1 |
-Macromolecule #4: FE2/S2 (INORGANIC) CLUSTER
Macromolecule | Name: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 4 / Number of copies: 1 / Formula: FES |
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Molecular weight | Theoretical: 175.82 Da |
Chemical component information | ChemComp-FES: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 73.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL / In silico model: generated by relion |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 955060 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |