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- PDB-6h3c: Cryo-EM structure of the BRISC complex bound to SHMT2 -

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Basic information

Entry
Database: PDB / ID: 6h3c
TitleCryo-EM structure of the BRISC complex bound to SHMT2
Components
  • (BRISC and BRCA1-A complex member ...) x 2
  • BRISC complex subunit Abraxas 2
  • Lys-63-specific deubiquitinase BRCC36
  • Serine hydroxymethyltransferase, mitochondrial
KeywordsSIGNALING PROTEIN / Deubiquitinase complex / DUB / Lysine-63 linkage specific / BRCC36-containing / BRCA1A binding
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 / Metabolism of folate and pterines / regulation of oxidative phosphorylation / regulation of DNA damage checkpoint / 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 / tetrahydrofolate interconversion / K63-linked deubiquitinase activity / hematopoietic stem cell proliferation / regulation of aerobic respiration / response to ionizing radiation / amino acid binding / DNA repair-dependent chromatin remodeling / positive regulation of NLRP3 inflammasome complex assembly / mitochondrial nucleoid / mitotic G2 DNA damage checkpoint signaling / response to X-ray / RHOG GTPase cycle / polyubiquitin modification-dependent protein binding / protein deubiquitination / mitotic spindle assembly / regulation of DNA repair / enzyme regulator activity / ubiquitin ligase complex / Mitochondrial protein degradation / positive regulation of DNA repair / response to ischemia / chromosome segregation / 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 / cysteine-type deubiquitinase activity / microtubule / mitochondrial inner membrane / nuclear body / mitochondrial matrix / cell division / DNA damage response / chromatin binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / apoptotic process / signal transduction / mitochondrion / proteolysis / extracellular exosome / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
BRISC and BRCA1-A complex member 1 / 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 ...BRISC and BRCA1-A complex member 1 / 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. / von Willebrand factor A-like domain superfamily / 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 1 / BRISC and BRCA1-A complex member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsBunker, R.D. / Rabl, J. / Thoma, N.H.
CitationJournal: Mol Cell / Year: 2019
Title: Structural Basis of BRCC36 Function in DNA Repair and Immune Regulation.
Authors: Julius Rabl / Richard D Bunker / Andreas D Schenk / Simone Cavadini / Mark E Gill / Wassim Abdulrahman / Amparo Andrés-Pons / Martijn S Luijsterburg / Adel F M Ibrahim / Emma Branigan / ...Authors: Julius Rabl / Richard D Bunker / Andreas D Schenk / Simone Cavadini / Mark E Gill / Wassim Abdulrahman / Amparo Andrés-Pons / Martijn S Luijsterburg / Adel F M Ibrahim / Emma Branigan / Jacob D Aguirre / Aimee H Marceau / Claire Guérillon / Tewis Bouwmeester / Ulrich Hassiepen / Antoine H F M Peters / Martin Renatus / Laurent Gelman / Seth M Rubin / Niels Mailand / Haico van Attikum / Ronald T Hay / Nicolas H Thomä /
Abstract: In mammals, ∼100 deubiquitinases act on ∼20,000 intracellular ubiquitination sites. Deubiquitinases are commonly regarded as constitutively active, with limited regulatory and targeting capacity. ...In mammals, ∼100 deubiquitinases act on ∼20,000 intracellular ubiquitination sites. Deubiquitinases are commonly regarded as constitutively active, with limited regulatory and targeting capacity. The BRCA1-A and BRISC complexes serve in DNA double-strand break repair and immune signaling and contain the lysine-63 linkage-specific BRCC36 subunit that is functionalized by scaffold subunits ABRAXAS and ABRO1, respectively. The molecular basis underlying BRCA1-A and BRISC function is currently unknown. Here we show that in the BRCA1-A complex structure, ABRAXAS integrates the DNA repair protein RAP80 and provides a high-affinity binding site that sequesters the tumor suppressor BRCA1 away from the break site. In the BRISC structure, ABRO1 binds SHMT2α, a metabolic enzyme enabling cancer growth in hypoxic environments, which we find prevents BRCC36 from binding and cleaving ubiquitin chains. Our work explains modularity in the BRCC36 DUB family, with different adaptor subunits conferring diversified targeting and regulatory functions.
History
DepositionJul 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Category: em_imaging_optics / struct_conn
Item: _em_imaging_optics.phase_plate / _em_imaging_optics.sph_aberration_corrector ..._em_imaging_optics.phase_plate / _em_imaging_optics.sph_aberration_corrector / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
A: BRISC complex subunit Abraxas 2
B: Lys-63-specific deubiquitinase BRCC36
C: BRISC and BRCA1-A complex member 2
D: BRISC and BRCA1-A complex member 1
F: BRISC complex subunit Abraxas 2
G: Lys-63-specific deubiquitinase BRCC36
H: BRISC and BRCA1-A complex member 2
I: BRISC and BRCA1-A complex member 1
E: Serine hydroxymethyltransferase, mitochondrial
J: Serine hydroxymethyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)458,07712
Polymers457,94610
Non-polymers1312
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, Assembly can be purified by glycerol gradient centrifugation or size exclusion chromatography. Affinity between BRISC and SHMT2 was determined by biolayer interferometry (Kd ~46 nM).
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area43420 Å2
ΔGint-322 kcal/mol
Surface area129910 Å2
MethodPISA

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Components

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Protein , 3 types, 6 molecules AFBGEJ

#1: Protein BRISC complex subunit Abraxas 2 / Abraxas brother protein 1 / Protein FAM175B


Mass: 49256.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABRAXAS2, ABRO1, FAM175B, KIAA0157 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15018
#2: Protein Lys-63-specific deubiquitinase BRCC36 / BRCA1-A complex subunit BRCC36 / BRCA1/BRCA2-containing complex subunit 3 / BRCA1/BRCA2-containing ...BRCA1-A complex subunit BRCC36 / BRCA1/BRCA2-containing complex subunit 3 / BRCA1/BRCA2-containing complex subunit 36 / BRISC complex subunit BRCC36


Mass: 38417.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCC3, BRCC36, C6.1A, CXorf53 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P46736, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#5: Protein Serine hydroxymethyltransferase, mitochondrial / SHMT / Glycine hydroxymethyltransferase / Serine methylase


Mass: 56144.711 Da / Num. of mol.: 2 / Mutation: A264T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHMT2 / Plasmid: p28a-LIC
Details (production host): SGC Clone Accession: SHMT2:APC005_8-E02:C16046 (undocumented point mutation A285T (A264T for isoform 3))
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P34897, glycine hydroxymethyltransferase

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BRISC and BRCA1-A complex member ... , 2 types, 4 molecules CHDI

#3: Protein BRISC and BRCA1-A complex member 2 / BRCA1-A complex subunit BRE / BRCA1/BRCA2-containing complex subunit 45 / Brain and reproductive ...BRCA1-A complex subunit BRE / BRCA1/BRCA2-containing complex subunit 45 / Brain and reproductive organ-expressed protein


Mass: 45890.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BABAM2, BRCC45, BRE / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NXR7
#4: Protein BRISC and BRCA1-A complex member 1 / Mediator of RAP80 interactions and targeting subunit of 40 kDa / New component of the BRCA1-A complex


Mass: 39263.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BABAM1, C19orf62, MERIT40, NBA1, HSPC142 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NWV8

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Non-polymers , 2 types, 4 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1BRISC complex bound to SHMT2 alphaCOMPLEX#1-#50MULTIPLE SOURCES
2BRISC complexCOMPLEX#1-#41RECOMBINANT
3SHMT2 alphaCOMPLEX#51RECOMBINANT
Molecular weightValue: 0.438 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainPlasmid
22Trichoplusia ni (cabbage looper)7111High FivepFastBac
33Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPES1
2150 mMsodium chlorideNaCl1
30.2 mMTCEP1
SpecimenConc.: 0.44 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was purified by gel filtration over a Superose 6 column.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 277 K
Details: A 4 ul sample was applied to the grid and a protocol consisting of 30 s pre-blot incubation, 2 s blotting and no post-blot incubation was utilized for vitrification.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Calibrated magnification: 58140 X / Calibrated defocus min: 500 nm / Calibrated defocus max: 5000 nm / Cs: 0 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 7 sec. / Electron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1822
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV / Spherical aberration corrector: CEOS Cs-corrector
Image scansSampling size: 5 µm / Width: 3710 / Height: 3838 / Movie frames/image: 40 / Used frames/image: 4-20

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Processing

EM software
IDNameVersionCategoryDetails
1Gautomatch0.53particle selection
2EPU1.1.0.30image acquisitionCryoFLARE was used for automation of the drift correction, particle picking and CTF determination during data aquisition
4RELION2.1CTF correction
7Coot0.8.9model fitting
8Rosetta2018.09.60072model fitting
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
12RELION2.1classification
13RELION2.13D reconstruction
20Rosetta2018.09.60072model refinement
21PHENIX1.15-3459model refinement
Image processingDetails: Drift correction was performed using Motioncor2. CTF was fitted using GCTF CryoFLARE was used for automation.
CTF correctionDetails: CTF was determined using GCTF. CTF was corrected within RELION.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 332598 / Details: Particles were auto-picked.
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35595 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 117 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient and
Details: Initial fitting with done using COOT, Rosetta was used for amino acid sequence threading and flexible fitting. COOT and ISOLDE were used for local rebuilding. Phenix was used for atom ...Details: Initial fitting with done using COOT, Rosetta was used for amino acid sequence threading and flexible fitting. COOT and ISOLDE were used for local rebuilding. Phenix was used for atom displacement parameter (ADP / B-factor) refinement.
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
16GVW

6gvw

6GVW1
25V7I

5v7i

A5V7I2

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