[English] 日本語
Yorodumi
- EMDB-0132: Cryo-EM structure of the BRISC complex bound to SHMT2 -

+
Open data


ID or keywords:

Loading...

-
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
Function / homology
Function and homology information


: / : / peroxisome targeting sequence binding / BRISC complex / L-allo-threonine aldolase activity / regulation of mitochondrial translation / BRCA1-A complex / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process ...: / : / peroxisome targeting sequence binding / BRISC complex / L-allo-threonine aldolase activity / regulation of mitochondrial translation / BRCA1-A complex / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / 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 / metal-dependent deubiquitinase activity / tetrahydrofolate metabolic process / response to type I interferon / mitotic G2/M transition checkpoint / tumor necrosis factor receptor binding / protein K63-linked deubiquitination / tetrahydrofolate interconversion / K63-linked deubiquitinase activity / regulation of aerobic respiration / response to ionizing radiation / folic acid metabolic process / mitochondrial nucleoid / protein deubiquitination / mitotic G2 DNA damage checkpoint signaling / polyubiquitin modification-dependent protein binding / RHOG GTPase cycle / response to X-ray / mitotic spindle assembly / regulation of DNA repair / protein autoubiquitination / enzyme regulator activity / ubiquitin ligase complex / positive regulation of DNA repair / mRNA regulatory element binding translation repressor activity / chromosome segregation / response to ischemia / cellular response to ionizing radiation / Nonhomologous End-Joining (NHEJ) / protein tetramerization / mRNA 5'-UTR binding / G2/M DNA damage checkpoint / Metalloprotease DUBs / spindle pole / metallopeptidase activity / microtubule cytoskeleton / double-strand break repair / pyridoxal phosphate binding / one-carbon metabolic process / mitotic cell cycle / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / Processing of DNA double-strand break ends / microtubule binding / protein homotetramerization / mitochondrial inner membrane / cysteine-type deubiquitinase activity / microtubule / nuclear body / mitochondrial matrix / cell division / apoptotic process / DNA damage response / chromatin binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / signal transduction / protein homodimerization activity / mitochondrion / extracellular exosome / zinc ion binding / nucleoplasm / metal ion binding / nucleus / 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 / Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment 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 / 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-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

-
Structure visualization

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

emd_0132.png

Downloads & links

-
Map

FileDownload / File: emd_0132.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.86 Å
Density
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

-
Supplemental data

-
Mask #1

Fileemd_0132_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Half map 1: unfiltered and unsharpened

Fileemd_0132_additional_1.map
AnnotationHalf map 1: unfiltered and unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Half map 1: unfiltered and unsharpened

Fileemd_0132_additional_2.map
AnnotationHalf map 1: unfiltered and unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
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

+
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 weightExperimental: 438 KDa

+
Supramolecule #2: BRISC complex

SupramoleculeName: BRISC complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant strain: High Five / Recombinant plasmid: pFastBac

+
Supramolecule #3: SHMT2 alpha

SupramoleculeName: SHMT2 alpha / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

+
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

+
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

+
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

+
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

+
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

+
Macromolecule #6: ZINC ION

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

+
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 / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.44 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
50.0 mMHEPES
150.0 mMsodium chlorideNaClSodium chloride
0.2 mMTCEP
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / 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.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
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 FIELDBright-field microscopy / Cs: 0.0 mm / Nominal magnification: 130000
Specialist opticsSpherical aberration corrector: CEOS Cs-corrector / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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 - Sampling interval: 5.0 µm / Digitization - Frames/image: 4-20 / Number real images: 1822 / Average exposure time: 7.0 sec. / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 332598 / Details: Particles were auto-picked.
CTF correctionSoftware - Name: RELION (ver. 2.1)
Details: CTF was determined using GCTF. CTF was corrected within RELION.
Startup modelType of model: OTHER
Details: Initial model was generated without symmetry within RELION
Initial 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)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
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
DetailsDrift correction was performed using Motioncor2. CTF was fitted using GCTF CryoFLARE was used for automation.
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

6gvw


5v7i

chain_id: A
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more