+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4759 | |||||||||
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Title | Cryo-EM structure of the Human BRISC-SHMT2 complex | |||||||||
Map data | C1 reconstruction. Filtererd by local resolution in Relion. | |||||||||
Sample |
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Keywords | Complex / Deubiquitylation / Ubiquitin / Immune signalling / signaling protein | |||||||||
Function / homology | Function and homology information peroxisome targeting sequence binding / BRISC complex / L-allo-threonine aldolase activity / regulation of mitochondrial translation / BRCA1-A complex / attachment of spindle microtubules to kinetochore / L-serine metabolic process / nuclear ubiquitin ligase complex / glycine metabolic process / L-serine biosynthetic process ...peroxisome targeting sequence binding / BRISC complex / L-allo-threonine aldolase activity / regulation of mitochondrial translation / BRCA1-A complex / attachment of spindle microtubules to kinetochore / L-serine metabolic process / nuclear ubiquitin ligase complex / glycine metabolic process / L-serine biosynthetic process / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / Metabolism of folate and pterines / L-serine catabolic process / regulation of DNA damage checkpoint / regulation of oxidative phosphorylation / tetrahydrofolate metabolic process / response to type I interferon / mitotic G2/M transition checkpoint / tumor necrosis factor receptor binding / metal-dependent deubiquitinase activity / protein K63-linked deubiquitination / DNA repair-dependent chromatin remodeling / tetrahydrofolate interconversion / K63-linked deubiquitinase activity / regulation of aerobic respiration / positive regulation of NLRP3 inflammasome complex assembly / response to ionizing radiation / cobalt ion binding / mitochondrial nucleoid / mitotic G2 DNA damage checkpoint signaling / response to X-ray / RHOG GTPase cycle / mitotic spindle assembly / folic acid metabolic process / polyubiquitin modification-dependent protein binding / regulation of DNA repair / enzyme regulator activity / ubiquitin ligase complex / Mitochondrial protein degradation / positive regulation of DNA repair / chromosome segregation / response to ischemia / cellular response to ionizing radiation / Nonhomologous End-Joining (NHEJ) / protein tetramerization / G2/M DNA damage checkpoint / Metalloprotease DUBs / spindle pole / metallopeptidase activity / microtubule cytoskeleton / double-strand break repair / pyridoxal phosphate binding / one-carbon metabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / mitotic cell cycle / Processing of DNA double-strand break ends / microtubule binding / protein homotetramerization / microtubule / cysteine-type deubiquitinase activity / mitochondrial inner membrane / mitochondrial matrix / cell division / apoptotic process / DNA damage response / chromatin binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / signal transduction / mitochondrion / proteolysis / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Walden M / Hesketh E | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nature / Year: 2019 Title: Metabolic control of BRISC-SHMT2 assembly regulates immune signalling. Authors: Miriam Walden / Lei Tian / Rebecca L Ross / Upasana M Sykora / Dominic P Byrne / Emma L Hesketh / Safi K Masandi / Joel Cassel / Rachel George / James R Ault / Farid El Oualid / Krzysztof ...Authors: Miriam Walden / Lei Tian / Rebecca L Ross / Upasana M Sykora / Dominic P Byrne / Emma L Hesketh / Safi K Masandi / Joel Cassel / Rachel George / James R Ault / Farid El Oualid / Krzysztof Pawłowski / Joseph M Salvino / Patrick A Eyers / Neil A Ranson / Francesco Del Galdo / Roger A Greenberg / Elton Zeqiraj / Abstract: Serine hydroxymethyltransferase 2 (SHMT2) regulates one-carbon transfer reactions that are essential for amino acid and nucleotide metabolism, and uses pyridoxal-5'-phosphate (PLP) as a cofactor. ...Serine hydroxymethyltransferase 2 (SHMT2) regulates one-carbon transfer reactions that are essential for amino acid and nucleotide metabolism, and uses pyridoxal-5'-phosphate (PLP) as a cofactor. Apo SHMT2 exists as a dimer with unknown functions, whereas PLP binding stabilizes the active tetrameric state. SHMT2 also promotes inflammatory cytokine signalling by interacting with the deubiquitylating BRCC36 isopeptidase complex (BRISC), although it is unclear whether this function relates to metabolism. Here we present the cryo-electron microscopy structure of the human BRISC-SHMT2 complex at a resolution of 3.8 Å. BRISC is a U-shaped dimer of four subunits, and SHMT2 sterically blocks the BRCC36 active site and inhibits deubiquitylase activity. Only the inactive SHMT2 dimer-and not the active PLP-bound tetramer-binds and inhibits BRISC. Mutations in BRISC that disrupt SHMT2 binding impair type I interferon signalling in response to inflammatory stimuli. Intracellular levels of PLP regulate the interaction between BRISC and SHMT2, as well as inflammatory cytokine responses. These data reveal a mechanism in which metabolites regulate deubiquitylase activity and inflammatory signalling. | |||||||||
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_4759.map.gz | 96.1 MB | EMDB map data format | |
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Header (meta data) | emd-4759-v30.xml emd-4759.xml | 24.2 KB 24.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4759_fsc.xml | 12.5 KB | Display | FSC data file |
Images | emd_4759.png | 39.5 KB | ||
Filedesc metadata | emd-4759.cif.gz | 7.3 KB | ||
Others | emd_4759_half_map_1.map.gz emd_4759_half_map_2.map.gz | 129.2 MB 129.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4759 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4759 | HTTPS FTP |
-Validation report
Summary document | emd_4759_validation.pdf.gz | 633 KB | Display | EMDB validaton report |
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Full document | emd_4759_full_validation.pdf.gz | 632.6 KB | Display | |
Data in XML | emd_4759_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | emd_4759_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4759 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4759 | HTTPS FTP |
-Related structure data
Related structure data | 6r8fMC 4760C 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_4759.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | C1 reconstruction. Filtererd by local resolution in Relion. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0651 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: C1 refinement half map 2.
File | emd_4759_half_map_1.map | ||||||||||||
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Annotation | C1 refinement half map 2. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: C1 refinement half map 1.
File | emd_4759_half_map_2.map | ||||||||||||
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Annotation | C1 refinement half map 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : BRISC-SHMT2
Entire | Name: BRISC-SHMT2 |
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Components |
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-Supramolecule #1: BRISC-SHMT2
Supramolecule | Name: BRISC-SHMT2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Molecular weight | Theoretical: 388.47 kDa/nm |
-Supramolecule #2: MERIT40 (BRISC and BRCA1-A complex member 1)
Supramolecule | Name: MERIT40 (BRISC and BRCA1-A complex member 1) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2, #4 Details: MERIT40 also expressed along with other macromolecules, but no model is built into the low resolution density. |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Serine hydroxymethyltransferase, mitochondrial
Supramolecule | Name: Serine hydroxymethyltransferase, mitochondrial / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Lys-63-specific deubiquitinase BRCC36
Macromolecule | Name: Lys-63-specific deubiquitinase BRCC36 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO EC number: Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 36.119918 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MAVQVVQAVQ AVHLESDAFL VCLNHALSTE KEEVMGLCIG ELNDDTRSDS KFAYTGTEMR TVAEKVDAVR IVHIHSVIIL RRSDKRKDR VEISPEQLSA ASTEAERLAE LTGRPMRVVG WYHSHPHITV WPSHVDVRTQ AMYQMMDQGF VGLIFSCFIE D KNTKTGRV ...String: MAVQVVQAVQ AVHLESDAFL VCLNHALSTE KEEVMGLCIG ELNDDTRSDS KFAYTGTEMR TVAEKVDAVR IVHIHSVIIL RRSDKRKDR VEISPEQLSA ASTEAERLAE LTGRPMRVVG WYHSHPHITV WPSHVDVRTQ AMYQMMDQGF VGLIFSCFIE D KNTKTGRV LYTCFQSIQA QKSSESLHGP RDFWSSSQHI SIEGQKEEER YERIEIPIHI VPHVTIGKVC LESAVELPKI LC QEEQDAY RRIHSLTHLD SVTKIHNGSV FTKNLCSQMS AVSGPLLQWL EDRLEQNQQH LQELQQEKEE LMQELSSLE UniProtKB: Lys-63-specific deubiquitinase BRCC36 |
-Macromolecule #2: BRISC complex subunit Abraxas 2
Macromolecule | Name: BRISC complex subunit Abraxas 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 31.033945 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MAASISGYTF SAVCFHSANS NADHEGFLLG EVRQEETFSI SDSQISNTEF LQVIEIHNHQ PCSKLFSFYD YASKVNEESL DRILKDRRK KVIGWYRFRR NTQQQMSYRE QVLHKQLTRI LGVPDLVFLL FSFISTANNS THALEYVLFR PNRRYNQRIS L AIPNLGNT ...String: MAASISGYTF SAVCFHSANS NADHEGFLLG EVRQEETFSI SDSQISNTEF LQVIEIHNHQ PCSKLFSFYD YASKVNEESL DRILKDRRK KVIGWYRFRR NTQQQMSYRE QVLHKQLTRI LGVPDLVFLL FSFISTANNS THALEYVLFR PNRRYNQRIS L AIPNLGNT SQQEYKVSSV PNTSQSYAKV IKEHGTDFFD KDGVMKDIRA IYQVYNALQE KVQAVCADVE KSERVVESCQ AE VNKLRRQ ITQRKNEKEQ ERRLQQAVLS UniProtKB: BRISC complex subunit Abraxas 2 |
-Macromolecule #3: Serine hydroxymethyltransferase, mitochondrial
Macromolecule | Name: Serine hydroxymethyltransferase, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: glycine hydroxymethyltransferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 56.097902 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MLYFSLFWAA RPLQRCGQLV RMAIRAQHSN AAQTQTGEAN RGWTGQESLS DSDPEMWELL QREKDRQCRG LELIASENFC SRAALEALG SCLNNKYSEG YPGKRYYGGA EVVDEIELLC QRRALEAFDL DPAQWGVNVQ PYSGSPANLA VYTALLQPHD R IMGLDLPD ...String: MLYFSLFWAA RPLQRCGQLV RMAIRAQHSN AAQTQTGEAN RGWTGQESLS DSDPEMWELL QREKDRQCRG LELIASENFC SRAALEALG SCLNNKYSEG YPGKRYYGGA EVVDEIELLC QRRALEAFDL DPAQWGVNVQ PYSGSPANLA VYTALLQPHD R IMGLDLPD GGHLTHGYMS DVKRISATSI FFESMPYKLN PKTGLIDYNQ LALTARLFRP RLIIAGTSAY ARLIDYARMR EV CDEVKAH LLADMAHISG LVAAKVIPSP FKHADIVTTT THKTLRGTRS GLIFYRKGVK AVDPKTGREI PYTFEDRINF AVF PSLQGG PHNHAIAAVA VALKQACTPM FREYSLQVLK NARAMADALL ERGYSLVSGG TDNHLVLVDL RPKGLDGARA ERVL ELVSI TANKNTCPGD RSAITPGGLR LGAPALTSRQ FREDDFRRVV DFIDEGVNIG LEVKSKTAKL QDFKSFLLKD SETSQ RLAN LRQRVEQFAR AFPMPGFDEH UniProtKB: Serine hydroxymethyltransferase, mitochondrial |
-Macromolecule #4: BRISC and BRCA1-A complex member 2,BRCC45 (BRE, BRISC and BRCA1-A...
Macromolecule | Name: BRISC and BRCA1-A complex member 2,BRCC45 (BRE, BRISC and BRCA1-A complex member 2) type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 22.026717 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: GAMSPEVALN RISPMLSPFI SSVVRNGKVG LDATNCLRIT DLKSGCTSLT PGPNCDRFKL HIPYAGETLK WDIIFNAQYP ELPPDFIFG EDAEFLPDPS ALQNLASWNP SNPECLLLVV KELVQQYHQF QCSRLR(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK) ...String: GAMSPEVALN RISPMLSPFI SSVVRNGKVG LDATNCLRIT DLKSGCTSLT PGPNCDRFKL HIPYAGETLK WDIIFNAQYP ELPPDFIFG EDAEFLPDPS ALQNLASWNP SNPECLLLVV KELVQQYHQF QCSRLR(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) UniProtKB: BRISC and BRCA1-A complex member 2 |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.051 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K | ||||||||||||
Details | Specimen contained BRCC36, ABRAXAS2, BRCC45, MERIT40 and SHMT2 macromolecules |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 3 / Number real images: 7494 / Average exposure time: 2.0 sec. / Average electron dose: 1.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -1.6 µm / Nominal defocus min: -3.1 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |