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- EMDB-4759: Cryo-EM structure of the Human BRISC-SHMT2 complex -

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Entry
Database: EMDB / ID: EMD-4759
TitleCryo-EM structure of the Human BRISC-SHMT2 complex
Map dataC1 reconstruction. Filtererd by local resolution in Relion.
Sample
  • Complex: BRISC-SHMT2
    • Complex: MERIT40 (BRISC and BRCA1-A complex member 1)
      • Protein or peptide: Lys-63-specific deubiquitinase BRCC36
      • Protein or peptide: BRISC complex subunit Abraxas 2
      • Protein or peptide: BRISC and BRCA1-A complex member 2,BRCC45 (BRE, BRISC and BRCA1-A complex member 2)
    • Complex: Serine hydroxymethyltransferase, mitochondrial
      • Protein or peptide: Serine hydroxymethyltransferase, mitochondrial
  • Ligand: ZINC ION
KeywordsComplex / 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 / glycine metabolic process / attachment of spindle microtubules to kinetochore / L-serine metabolic process / regulation of oxidative phosphorylation / nuclear ubiquitin ligase complex ...peroxisome targeting sequence binding / BRISC complex / L-allo-threonine aldolase activity / regulation of mitochondrial translation / BRCA1-A complex / glycine metabolic process / attachment of spindle microtubules to kinetochore / L-serine metabolic process / regulation of oxidative phosphorylation / nuclear ubiquitin ligase complex / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / Metabolism of folate and pterines / tetrahydrofolate metabolic process / regulation of DNA damage checkpoint / response to type I interferon / mitotic G2/M transition checkpoint / tumor necrosis factor receptor binding / metal-dependent deubiquitinase activity / protein K63-linked deubiquitination / tetrahydrofolate interconversion / regulation of aerobic respiration / K63-linked deubiquitinase activity / response to ionizing radiation / amino acid binding / DNA repair-dependent chromatin remodeling / positive regulation of NLRP3 inflammasome complex assembly / mitotic G2 DNA damage checkpoint signaling / mitochondrial nucleoid / RHOG GTPase cycle / polyubiquitin modification-dependent protein binding / protein deubiquitination / mitotic spindle assembly / response to X-ray / ubiquitin ligase complex / regulation of DNA repair / enzyme regulator activity / Mitochondrial protein degradation / one-carbon metabolic process / positive regulation of DNA repair / response to ischemia / cellular response to ionizing radiation / chromosome segregation / Nonhomologous End-Joining (NHEJ) / protein tetramerization / G2/M DNA damage checkpoint / Metalloprotease DUBs / spindle pole / metallopeptidase activity / pyridoxal phosphate binding / double-strand break repair / mitotic cell cycle / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / microtubule cytoskeleton / Processing of DNA double-strand break ends / microtubule binding / protein homotetramerization / microtubule / cysteine-type deubiquitinase activity / mitochondrial inner membrane / ciliary basal body / mitochondrial matrix / cell division / apoptotic process / positive regulation of cell population proliferation / DNA damage response / chromatin binding / negative regulation of apoptotic process / signal transduction / mitochondrion / proteolysis / extracellular exosome / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
FAM175 family, BRISC complex, Abro1 subunit / BRCA1-A complex subunit BRE / Brain and reproductive organ-expressed protein (BRE) / Brcc36 isopeptidase / BRCC36, C-terminal helical domain / BRCC36 C-terminal helical domain / FAM175 family / BRCA1-A complex subunit Abraxas 1 MPN domain / Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. ...FAM175 family, BRISC complex, Abro1 subunit / BRCA1-A complex subunit BRE / Brain and reproductive organ-expressed protein (BRE) / Brcc36 isopeptidase / BRCC36, C-terminal helical domain / BRCC36 C-terminal helical domain / FAM175 family / BRCA1-A complex subunit Abraxas 1 MPN domain / Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / : / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Serine hydroxymethyltransferase, mitochondrial / Lys-63-specific deubiquitinase BRCC36 / BRISC complex subunit Abraxas 2 / BRISC and BRCA1-A complex member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWalden M / Hesketh E
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust200523/Z/16/Z United Kingdom
CitationJournal: 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
DepositionApr 1, 2019-
Header (metadata) releaseJun 5, 2019-
Map releaseJun 5, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6r8f
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4759.png

Downloads & links

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Map

FileDownload / File: emd_4759.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC1 reconstruction. Filtererd by local resolution in Relion.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 350 pix.
= 372.785 Å		1.07 Å/pix.
x 350 pix.
= 372.785 Å		1.07 Å/pix.
x 350 pix.
= 372.785 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0651 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055 / Movie #1: 0.055
Minimum - Maximum-0.4546444 - 0.69702744
Average (Standard dev.)-0.000067516135 (±0.011205023)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 372.78497 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06511.06511.0651
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z372.785372.785372.785
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.4550.697-0.000

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Supplemental data

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Half map: C1 refinement half map 2.

Fileemd_4759_half_map_1.map
AnnotationC1 refinement half map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: C1 refinement half map 1.

Fileemd_4759_half_map_2.map
AnnotationC1 refinement half map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BRISC-SHMT2

EntireName: BRISC-SHMT2
Components
  • Complex: BRISC-SHMT2
    • Complex: MERIT40 (BRISC and BRCA1-A complex member 1)
      • Protein or peptide: Lys-63-specific deubiquitinase BRCC36
      • Protein or peptide: BRISC complex subunit Abraxas 2
      • Protein or peptide: BRISC and BRCA1-A complex member 2,BRCC45 (BRE, BRISC and BRCA1-A complex member 2)
    • Complex: Serine hydroxymethyltransferase, mitochondrial
      • Protein or peptide: Serine hydroxymethyltransferase, mitochondrial
  • Ligand: ZINC ION

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Supramolecule #1: BRISC-SHMT2

SupramoleculeName: BRISC-SHMT2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 388.47 kDa/nm

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Supramolecule #2: MERIT40 (BRISC and BRCA1-A complex member 1)

SupramoleculeName: 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.
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Serine hydroxymethyltransferase, mitochondrial

SupramoleculeName: Serine hydroxymethyltransferase, mitochondrial / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Lys-63-specific deubiquitinase BRCC36

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.119918 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #2: BRISC complex subunit Abraxas 2

MacromoleculeName: BRISC complex subunit Abraxas 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.033945 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #3: Serine hydroxymethyltransferase, mitochondrial

MacromoleculeName: Serine hydroxymethyltransferase, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: glycine hydroxymethyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.097902 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #4: BRISC and BRCA1-A complex member 2,BRCC45 (BRE, BRISC and BRCA1-A...

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.026717 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.051 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
25.0 mMHEPES
150.0 mMNaCl
1.0 mMTCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K
DetailsSpecimen contained BRCC36, ABRAXAS2, BRCC45, MERIT40 and SHMT2 macromolecules

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Details: Model generated in RELION using SGD from particles from 2D classification.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 403499
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 8 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5cw3

source_name: PDB, initial_model_type: experimental model

6dk3

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-6r8f:
Cryo-EM structure of the Human BRISC-SHMT2 complex

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