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- EMDB-0132: Cryo-EM structure of the BRISC complex bound to SHMT2 -

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Basic information

Entry
Database: EMDB / ID: EMD-0132
TitleCryo-EM structure of the BRISC complex bound to SHMT2
Map data
Sample
  • Complex: BRISC complex bound to SHMT2 alpha
    • Complex: BRISC complex
      • Protein or peptide: BRISC complex subunit Abraxas 2
      • Protein or peptide: Lys-63-specific deubiquitinase BRCC36
      • Protein or peptide: BRISC and BRCA1-A complex member 2
      • Protein or peptide: BRISC and BRCA1-A complex member 1
    • Complex: SHMT2 alpha
      • Protein or peptide: Serine hydroxymethyltransferase, mitochondrial
  • Ligand: ZINC ION
  • Ligand: water
KeywordsDeubiquitinase complex / DUB / Lysine-63 linkage specific / BRCC36-containing / BRCA1A binding / 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 / Metabolism of folate and pterines / 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 / tetrahydrofolate interconversion / DNA repair-dependent chromatin remodeling / K63-linked deubiquitinase activity / hematopoietic stem cell proliferation / regulation of aerobic respiration / positive regulation of NLRP3 inflammasome complex assembly / response to ionizing radiation / amino acid binding / mitochondrial nucleoid / mitotic G2 DNA damage checkpoint signaling / polyubiquitin modification-dependent protein binding / response to X-ray / RHOG GTPase cycle / 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 / microtubule / cysteine-type deubiquitinase activity / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSchenk AD / Julius R / Cavadini S / Thoma NH
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, 2018-
Header (metadata) releaseJul 3, 2019-
Map releaseJul 10, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00816
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.00816
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6h3c
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0132.png

Downloads & links

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Map

FileDownload / File: emd_0132.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 350 pix.
= 301. Å		0.86 Å/pix.
x 350 pix.
= 301. Å		0.86 Å/pix.
x 350 pix.
= 301. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00816 / Movie #1: 0.00816
Minimum - Maximum-0.06578454 - 0.1309982
Average (Standard dev.)0.0002689527 (±0.0028135402)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 301.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z301.000301.000301.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.0660.1310.000

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Supplemental data

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Mask #1

Fileemd_0132_msk_1.map
Projections & Slices
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Additional map: Half map 1: unfiltered and unsharpened

Fileemd_0132_additional_1.map
AnnotationHalf map 1: unfiltered and unsharpened
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Additional map: Half map 1: unfiltered and unsharpened

Fileemd_0132_additional_2.map
AnnotationHalf map 1: unfiltered and unsharpened
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Half map: Half map 1 sharpened: filtered and sharpened in...

Fileemd_0132_half_map_1.map
AnnotationHalf map 1 sharpened: filtered and sharpened in the same manner as the final combined map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: Half map 2: filtered and sharpened in the...

Fileemd_0132_half_map_2.map
AnnotationHalf map 2: filtered and sharpened in the same manner as the final combined map
Projections & Slices
AxesZYX

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Sample components

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Entire : BRISC complex bound to SHMT2 alpha

EntireName: BRISC complex bound to SHMT2 alpha
Components
  • Complex: BRISC complex bound to SHMT2 alpha
    • Complex: BRISC complex
      • Protein or peptide: BRISC complex subunit Abraxas 2
      • Protein or peptide: Lys-63-specific deubiquitinase BRCC36
      • Protein or peptide: BRISC and BRCA1-A complex member 2
      • Protein or peptide: BRISC and BRCA1-A complex member 1
    • Complex: SHMT2 alpha
      • Protein or peptide: Serine hydroxymethyltransferase, mitochondrial
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: BRISC complex bound to SHMT2 alpha

SupramoleculeName: BRISC complex bound to SHMT2 alpha / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Molecular weightTheoretical: 438 KDa

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Supramolecule #2: BRISC complex

SupramoleculeName: BRISC complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: SHMT2 alpha

SupramoleculeName: SHMT2 alpha / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: BRISC complex subunit Abraxas 2

MacromoleculeName: BRISC complex subunit Abraxas 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.256246 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHVDE NLYFQGGGRM AASISGYTFS AVCFHSANSN ADHEGFLLGE VRQEETFSIS DSQISNTEFL QVIEIHNHQP CSKLFSFYD YASKVNEESL DRILKDRRKK VIGWYRFRRN TQQQMSYREQ VLHKQLTRIL GVPDLVFLLF SFISTANNST H ALEYVLFR ...String:
MHHHHHHVDE NLYFQGGGRM AASISGYTFS AVCFHSANSN ADHEGFLLGE VRQEETFSIS DSQISNTEFL QVIEIHNHQP CSKLFSFYD YASKVNEESL DRILKDRRKK VIGWYRFRRN TQQQMSYREQ VLHKQLTRIL GVPDLVFLLF SFISTANNST H ALEYVLFR PNRRYNQRIS LAIPNLGNTS QQEYKVSSVP NTSQSYAKVI KEHGTDFFDK DGVMKDIRAI YQVYNALQEK VQ AVCADVE KSERVVESCQ AEVNKLRRQI TQRKNEKEQE RRLQQAVLSR QMPSESLDPA FSPRMPSSGF AAEGRSTLGD AEA SDPPPP YSDFHPNNQE STLSHSRMER SVFMPRPQAV GSSNYASTSA GLKYPGSGAD LPPPQRAAGD SGEDSDDSDY ENLI DPTEP SNSEYSHSKD SRPMAHPDED PRNTQTSQI

UniProtKB: BRISC complex subunit Abraxas 2

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Macromolecule #2: Lys-63-specific deubiquitinase BRCC36

MacromoleculeName: Lys-63-specific deubiquitinase BRCC36 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.417402 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHVDE NLYFQGGGRM AVQVVQAVQA VHLESDAFLV CLNHALSTEK EEVMGLCIGE LNDDTRSDSK FAYTGTEMRT VAEKVDAVR IVHIHSVIIL RRSDKRKDRV EISPEQLSAA STEAERLAEL TGRPMRVVGW YHSHPHITVW PSHVDVRTQA M YQMMDQGF ...String:
MHHHHHHVDE NLYFQGGGRM AVQVVQAVQA VHLESDAFLV CLNHALSTEK EEVMGLCIGE LNDDTRSDSK FAYTGTEMRT VAEKVDAVR IVHIHSVIIL RRSDKRKDRV EISPEQLSAA STEAERLAEL TGRPMRVVGW YHSHPHITVW PSHVDVRTQA M YQMMDQGF VGLIFSCFIE DKNTKTGRVL YTCFQSIQAQ KSSESLHGPR DFWSSSQHIS IEGQKEEERY ERIEIPIHIV PH VTIGKVC LESAVELPKI LCQEEQDAYR RIHSLTHLDS VTKIHNGSVF TKNLCSQMSA VSGPLLQWLE DRLEQNQQHL QEL QQEKEE LMQELSSLE

UniProtKB: Lys-63-specific deubiquitinase BRCC36

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Macromolecule #3: BRISC and BRCA1-A complex member 2

MacromoleculeName: BRISC and BRCA1-A complex member 2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.890949 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHVDE NLYFQGGGRM SPEVALNRIS PMLSPFISSV VRNGKVGLDA TNCLRITDLK SGCTSLTPGP NCDRFKLHIP YAGETLKWD IIFNAQYPEL PPDFIFGEDA EFLPDPSALQ NLASWNPSNP ECLLLVVKEL VQQYHQFQCS RLRESSRLMF E YQTLLEEP ...String:
MHHHHHHVDE NLYFQGGGRM SPEVALNRIS PMLSPFISSV VRNGKVGLDA TNCLRITDLK SGCTSLTPGP NCDRFKLHIP YAGETLKWD IIFNAQYPEL PPDFIFGEDA EFLPDPSALQ NLASWNPSNP ECLLLVVKEL VQQYHQFQCS RLRESSRLMF E YQTLLEEP QYGENMEIYA GKKNNWTGEF SARFLLKLPV DFSNIPTYLL KDVNEDPGED VALLSVSFED TEATQVYPKL YL SPRIEHA LGGSSALHIP AFPGGGCLID YVPQVCHLLT NKVQYVIQGY HKRREYIAAF LSHFGTGVVE YDAEGFTKLT LLL MWKDFC FLVHIDLPLF FPRDQPTLTF QSVYHFTNSG QLYSQAQKNY PYSPRWDGNE MAKRAKAYFK TFVPQFQEAA FANG KL

UniProtKB: BRISC and BRCA1-A complex member 2

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Macromolecule #4: BRISC and BRCA1-A complex member 1

MacromoleculeName: BRISC and BRCA1-A complex member 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.263824 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASWSHPQFE KVDENLYFQG GGRMEVAEPS SPTEEEEEEE EHSAEPRPRT RSNPEGAEDR AVGAQASVGS RSEGEGEAAS ADDGSLNTS GAGPKSWQVP PPAPEVQIRT PRVNCPEKVI ICLDLSEEMS LPKLESFNGS KTNALNVSQK MIEMFVRTKH K IDKSHEFA ...String:
MASWSHPQFE KVDENLYFQG GGRMEVAEPS SPTEEEEEEE EHSAEPRPRT RSNPEGAEDR AVGAQASVGS RSEGEGEAAS ADDGSLNTS GAGPKSWQVP PPAPEVQIRT PRVNCPEKVI ICLDLSEEMS LPKLESFNGS KTNALNVSQK MIEMFVRTKH K IDKSHEFA LVVVNDDTAW LSGLTSDPRE LCSCLYDLET ASCSTFNLEG LFSLIQQKTE LPVTENVQTI PPPYVVRTIL VY SRPPCQP QFSLTEPMKK MFQCPYFFFD VVYIHNGTEE KEEEMSWKDM FAFMGSLDTK GTSYKYEVAL AGPALELHNC MAK LLAHPL QRPCQSHASY SLLEEEDEAI EVEATV

UniProtKB: BRISC and BRCA1-A complex member 1

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Macromolecule #5: Serine hydroxymethyltransferase, mitochondrial

MacromoleculeName: Serine hydroxymethyltransferase, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: glycine hydroxymethyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.144711 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSG QLVRMAIRAQ HSNAAQTQTG EANRGWTGQE SLSDSDPEMW ELLQREKDRQ CRGLELIASE NFCSRAALE ALGSCLNNKY SEGYPGKRYY GGAEVVDEIE LLCQRRALEA FDLDPAQWGV NVQPYSGSPA NLAVYTALLQ P HDRIMGLD ...String:
MGSSHHHHHH SSGLVPRGSG QLVRMAIRAQ HSNAAQTQTG EANRGWTGQE SLSDSDPEMW ELLQREKDRQ CRGLELIASE NFCSRAALE ALGSCLNNKY SEGYPGKRYY GGAEVVDEIE LLCQRRALEA FDLDPAQWGV NVQPYSGSPA NLAVYTALLQ P HDRIMGLD LPDGGHLTHG YMSDVKRISA TSIFFESMPY KLNPKTGLID YNQLALTARL FRPRLIIAGT SAYARLIDYA RM REVCDEV KAHLLADMAH ISGLVAAKVI PSPFKHADIV TTTTHKTLRG TRSGLIFYRK GVKAVDPKTG REIPYTFEDR INF AVFPSL QGGPHNHAIA AVAVALKQAC TPMFREYSLQ VLKNARAMAD ALLERGYSLV SGGTDNHLVL VDLRPKGLDG ARAE RVLEL VSITANKNTC PGDRSAITPG GLRLGAPALT SRQFREDDFR RVVDFIDEGV NIGLEVKSKT AKLQDFKSFL LKDSE TSQR LANLRQRVEQ FARAFPMPGF DEH

UniProtKB: Serine hydroxymethyltransferase, mitochondrial

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.44 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
50.0 mMHEPES
150.0 mMsodium chlorideNaCl
0.2 mMTCEP
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 12 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: LEICA EM GP
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..
DetailsSample was purified by gel filtration over a Superose 6 column.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: CEOS Cs-corrector / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 4-20 / Number real images: 1822 / Average exposure time: 7.0 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 5.0 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 58140 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.0 mm / Nominal magnification: 130000
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

DetailsDrift correction was performed using Motioncor2. CTF was fitted using GCTF CryoFLARE was used for automation.
Particle selectionNumber selected: 332598 / Details: Particles were auto-picked.
Startup modelType of model: OTHER
Details: Initial model was generated without symmetry within RELION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 35595
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 14794 / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6gvw

source_name: PDB, initial_model_type: experimental model

5v7i

chain_id: A, source_name: PDB, initial_model_type: experimental model
DetailsInitial 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.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 117 / Target criteria: Correlation coefficient and
Output model

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

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