[English] 日本語
Yorodumi
- EMDB-12932: Mouse RNF213, with mixed nucleotides bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12932
TitleMouse RNF213, with mixed nucleotides bound
Map datafull non-sharpened map
Sample
  • Complex: RNF213 incubated with ATPgS
    • Protein or peptide: E3 ubiquitin-protein ligase RNF213
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Function / homology
Function and homology information


lipid ubiquitination / lipid droplet formation / negative regulation of non-canonical Wnt signaling pathway / xenophagy / Antigen processing: Ubiquitination & Proteasome degradation / Transferases; Acyltransferases; Aminoacyltransferases / sprouting angiogenesis / immune system process / protein K63-linked ubiquitination / regulation of lipid metabolic process ...lipid ubiquitination / lipid droplet formation / negative regulation of non-canonical Wnt signaling pathway / xenophagy / Antigen processing: Ubiquitination & Proteasome degradation / Transferases; Acyltransferases; Aminoacyltransferases / sprouting angiogenesis / immune system process / protein K63-linked ubiquitination / regulation of lipid metabolic process / protein autoubiquitination / lipid droplet / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / angiogenesis / protein ubiquitination / defense response to bacterium / nucleolus / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase RNF213 / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. ...E3 ubiquitin-protein ligase RNF213 / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF213
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsAhel J / Clausen T
Funding support Austria, United Kingdom, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)694978 Austria
Austrian Research Promotion Agency852936 Austria
Medical Research Council (MRC, United Kingdom)MC_UU_12016/8 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/ P003982/1 United Kingdom
CitationJournal: To Be Published
Title: E3 ubiquitin ligase RNF213 employs a non-canonical zinc finger active site and is allosterically regulated by ATP
Authors: Ahel J / Fletcher AJ / Grabarczyk D / Roitinger E / Deszcz L / Lehner A / Virdee S / Clausen T
History
DepositionMay 11, 2021-
Header (metadata) releaseJun 1, 2022-
Map releaseJun 1, 2022-
UpdateJun 1, 2022-
Current statusJun 1, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_12932.png

Downloads & links

-
Map

FileDownload / File: emd_12932.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull non-sharpened map
Voxel sizeX=Y=Z: 1.053 Å
Density
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.009532791 - 0.033896964
Average (Standard dev.)7.5062817e-06 (±0.0011747222)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 370.656 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_12932_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_12932_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: full sharpened map

Fileemd_12932_additional_1.map
Annotationfull sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: sharpened focused map, focused on AAA core

Fileemd_12932_additional_2.map
Annotationsharpened focused map, focused on AAA core
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: non-sharpened focused map, focused on AAA core

Fileemd_12932_additional_3.map
Annotationnon-sharpened focused map, focused on AAA core
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: non-sharpened focused half map 1, focused on AAA cpre

Fileemd_12932_additional_4.map
Annotationnon-sharpened focused half map 1, focused on AAA cpre
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: non-sharpened focused half map 2, focused on AAA cpre

Fileemd_12932_additional_5.map
Annotationnon-sharpened focused half map 2, focused on AAA cpre
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: full non-sharpened map, half volume 2

Fileemd_12932_half_map_1.map
Annotationfull non-sharpened map, half volume 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: full non-sharpened map, half volume 1

Fileemd_12932_half_map_2.map
Annotationfull non-sharpened map, half volume 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : RNF213 incubated with ATPgS

EntireName: RNF213 incubated with ATPgS
Components
  • Complex: RNF213 incubated with ATPgS
    • Protein or peptide: E3 ubiquitin-protein ligase RNF213
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

-
Supramolecule #1: RNF213 incubated with ATPgS

SupramoleculeName: RNF213 incubated with ATPgS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 580 KDa

-
Macromolecule #1: E3 ubiquitin-protein ligase RNF213

MacromoleculeName: E3 ubiquitin-protein ligase RNF213 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 552.623375 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASWSHPQFE KGSTSAFNPR DTVTVYFHAI VSRHFGFNPE EHKVYVRGGE GLGQKGWTDA CEMYCTQDLH DLGSLVEGKM DIPRQSLDK PIPYKYVIHR GGSSKDTVEY EFIYEQAQKK GEHVNRCLRV VSTSLGNGDW HQYDDIICMR STGFFQQAKN R ILDSTRKE ...String:
MASWSHPQFE KGSTSAFNPR DTVTVYFHAI VSRHFGFNPE EHKVYVRGGE GLGQKGWTDA CEMYCTQDLH DLGSLVEGKM DIPRQSLDK PIPYKYVIHR GGSSKDTVEY EFIYEQAQKK GEHVNRCLRV VSTSLGNGDW HQYDDIICMR STGFFQQAKN R ILDSTRKE LLKGKKQAAV VMLDRIFSVL QPWSDINLQS FMTQFLQFYS VVREPMIHDG RARKWTSLQY EEKEVWTNLW EH VKKQMAP FLEGKSGESL PADCPVRSKL TLGLSILFMV EAAEFTVPKK DLDSLCYLLI PSAGSPEALH SDLSPVLRIR QRW RIYLTN LCLRCIDERC DRWLGILPLL HTCMQKSPPK KNSKSQPEDT WAGLEGISFS EFRDKAPTRS QPLQFMQSKM ALLR VDEYL FRSWLSVVPL ESLSSYLENS IDYLSDVPVR VLDCLQGISY RLPGLRKISN QNMKKDVENV FKMLMHLVDI YQHRI FGEN LLQIYLTECL TLHETVCNIT ANHQFFEIPA LSAELICKLL ELSPPGHTDE GLPEKSYEDL VTSTLQEALA TTRNWL RSL FKSRMLSISS AYVRLTYSEE MAVWRRLVEI GFPEKHGWKG SLLGDMEGRL KQEPPRLQIS FFCSSQCRDG GLHDSVS RS FEKCVIEAVS SACQSQTSVL EGLSCQDLQK FGTLLSAVIT KSWPVHNGEP VFDVDEIFKY LLKWPDVRQL FELCGTNE K IIDNITEEGR QLMATAESVF QKVAGELENG TIVVGQLELI LEHQSQFLDI WNLNRRRLPS QEKACDVRSL LKRRRDDLL FLKQEKRYVE SLLRQLGRVK HLVQVDFGNI EIIHSQDLSN KKLNEAVIKL PNSSSYKRET HYCLSPDIRE MASKLDSLKD SHIFQDFWQ ETAESLNTLD KDPRELKVSL PEVLEYLYNP CYDNFYTLYE NLKSGKITFA EVDAIFKDFV DKYDELKNDL K FMCTMNPQ DQKGWISERV GQIKEYHTLH QAVSSAKVIL QVRRALGVTG DFSVLNPLLN FADSFEDFGN EKLDQISPQF IK AKQLLQD ISEPRQRCLE ELARQTELVA WLHKALEDIN ELKVFVDLAS ISAGENDIDV DRVACFHDAV QGYASLLYKM DER TNFSDF MNHLQELWRA LDNDQHLPDK LKDSARNLEW LKTVKESHGS VELSSLSLAT AINSRGVYVI EAPKDGQKIS PDTV LRLLL PDGHGYPEAL RTYSTEELKE LLNKLMLMSG KKDHNSNTEV EKFSEVFSNM QRLVHVFIKL HCAGNMLFRT WTAKV YCCP DGGIFMNFGL ELLSQLTEKG DVIQLLGALC RQMEDFLDNW KTVVAQKRAE HFYLNFYTAE QLVYLSSELR KPRPSE AAL MMLSFIKGKC TVQDLVQATS ACESKADRYC LREVMKKLPQ QLLSEPSLMG KLQVIMMQSL VYMSAFLPHC LDLDALG RC LAHLATMGGT PVERPLPKGL QAGQPNLILC GHSEVLPAAL AIYMQAPRQP LPTFDEVLLC TPATTIEEVE LLLRRCLT S GSQGHKVYSL LFADQLSYEV GCQAEEFFQS LCTRAHREDY QLVILCDAAR EHCYIPSTFS QYKVPLVPQA PLPNIQAYL QSHYQVPKRL LSAATVFRDG LCVGIVTSER AGVGKSLYVN TLHTKLKAKL RDETVPLKII RLTEPHLDEN QVLSALLPFL KEKYQKMPV IFHIDISTSV QTGIPIFLFK LLILQYLMDI NGKIWRRSPG HLYLVEIPQG LSVQPKRSSK LNARAPLFKF L DLFPKVTC RPPKEVIDME LTPERSHTDP AMDPVEFCSE AFQRPYQYLK RFHQQQNLDT FQYEKGSVEG SPEECLQHFL IY CGLINPS WSELRNFAWF LNCQLKDCEA SIFCKSAFTG DTLRGFKNFV VTFMILMARD FATPTLHTSD QSPGRQSVTI GEV VEEDLA PFSLRKRWES EPHPYVFFNG DHMTMTFIGF HLETNNNGYV DAINPSNGKV IKKDVMTKEL FDGLRLQRVP FNID FDNLP RYEKLERLCL ALGIEWPIDP DETYELTTDN MLKILAIEMR FRCGIPVIIM GETGCGKTRL IKFLSDLKRG SVEAE TMKL VKVHGGTTPS MIYSKVKEAE RTAFSNKAQH KLDTILFFDE ANTTEAVSCI KEILCDRTVD GEHLHEDSGL HIIAAC NPY RKHSQEMILR LESAGLGYRV SAEETADRLG SIPLRQLVYR VHALPPSLIP LVWDFGQLND SAEKLYIQQI VQRLVDS VS VNPSETCVIA DVLSASQMFM RKRENECGFV SLRDVERCVK VFRWFHDHSD MLLKELDKFL HESSDSTHTF ERDPVLWS L VMAIGVCYHA SLEEKASYRT AIARCFPKPY NSSRAILDEV THVQDLFLRG APIRTNIARN LALKENVFMM VICIELKIP LFLVGKPGSS KSLAKIIVAD AMQGQAAFSE LFRCLKQVHL VSFQCSPHST PQGIISTFKQ CARFQQGKDL GQYVSVVVLD EVGLAEDSP KMPLKTLHPL LEDGCIEDDP APYKKVGFVG ISNWALDPAK MNRGIFVSRG SPNEKELIES AEGICSSDRL V QDKIRGYF APFAKAYETV CQKQDKEFFG LRDYYSLIKM VFAKAKASKR GLSPQDITHA VLRNFSGKDN IQALSIFTAS LP EARYKEE VSTVELIKQN IYPGPQASSR GLDGAESRYL LVLTRNYVAL QILQQTFFEG QQPEIIFGSS FPQDQEYTQI CRN INRVKI CMETGKMVVL LNLQNLYESL YDALNQYYVY LGGQKYVDLG LGTHRVKCRV HTAFRLIVIE EKDVVYKQFP VPLI NRLEK HYLDMNTVLQ PWQKSIVQEL QQWAHEFADV KADQFIARHK YSPADVFIGY HSDACASVVL QAVERQGCRD LTEEL YRKV SEEARSILLD CATPDAVVRL SGSSLGSFTA KQLSQEYYYA QQHNSFVDFL QAHLRMTHHE CRAVFTEITT FSRLLT GND CDVLASELRG LASKPVVLSL QQYDTEYSFL KDVRSWLTNP GKRKVLVIQA DFDDGTRSAQ LVASAKYTAI NEINKTQ GT KDFVFVYFVT KLSRMGSGTS YVGFHGGLWR SVHIDDLRRS TIMASDVTKL QNVTISQLFK PEDKPEQEEM EIETSQSK E LAEEQMEVED SEEMKKASDP RSCDCSQFLD TTRLVQSCVQ GAVGMLRDQN ESCARNMRRV TILLDLLNED NTRNASFLR ESKMRLHVLL NKQEENQVRS LKEWVTREAA NQDALQEAGT FRHTLWKRVQ DVVTPILASM IAHIDRDGNL ELLAQPDSPA WVQDLWMFI YSDIKFLNIS LVLNNTRSNS EMSFILVQSH MNLLKDAYNA VPFSWRIRDY LEELWVQAQY ITDTEGLSKK F VEIFQKTP LGVFLAQFPV AQQQKLLQSY LKDFLLLTMK VSSREELMFL QMALWSCLRE LQEASGTPDE TYKFPLSLPW VH LAFQHFR TRLQNFSRIL TIHPQVLSSL SQAAEKHSLA GCEMTLDAFA AMACAEMLKG DLLKPSPKAW LQLVKNLSTP LEL VCSEGY LCDSGSMTRS VIQEVRALWN RIFSIALFVE HVLLGTESHI PELSPLVTTY VSLLDKCLEE DSNLKTCRPF VAVM TTLCD CKDKASKKFS RFGIQPCFIC HGDAQDPVCL PCDHVYCLRC IQTWLIPGQM MCPYCLTDLP DKFSPTVSQD HRKAI EKHA QFRHMCNSFF VDLVSTMCFK DNTPPEKSVI DTLLSLLFVQ KELLRDASQK HREHTKSLSP FDDVVDQTPV IRSVLL KLL LKYSFHEVKD YIQNYLTQLE KKAFLTEDKT ELYLLFISCL EDSVHQKTSA GCRNLEQVLR EEGHFLRTYS PGLQGQE PV RIASVEYLQE VARVRLCLDL AADFLSELQE GSELAEDKRR FLKHVEEFCT RVNNDWHRVY LVRKLSSQRG MEFVQSFS K QGHPCQWVFP RKVIAQQKDH VSLMDRYLVH GNEYKAVRDA TAKAVLECKT LDIGNALMAC RSPKPQQTAY LLLALYTEV AALYRSPNGS LHPEAKQLEA VNKFIKESKI LSDPNIRCFA RSLVDNTLPL LKIRSANSIL KGTVTEMAVH VATILLCGHN QILKPLRNL AFYPVNMANA FLPTMPEDLL VHARTWRGLE NVTWYTCPRG HPCSVGECGR PMQESTCLDC GLPVGGLNHT P HEGFSAIR NNEDRTQTGH VLGSPQSSGV AEVSDRGQSP VVFILTRLLT HLAMLVGATH NPQALTVIIK PWVQDPQGFL QQ HIQRDLE QLTKMLGRSA DETIHVVHLI LSSLLRVQSH GVLNFNAELS TKGCRNNWEK HFETLLLREL KHLDKNLPAI NAL ISQDER ISSNPVTKII YGDPATFLPH LPQKSIIHCS KIWSCRRKIT VEYLQHIVEQ KNGKETVPVL WHFLQKEAEL RLVK FLPEI LALQRDLVKQ FQNVSRVEYS SIRGFIHSHS SDGLRKLLHD RITIFLSTWN ALRRSLETNG EIKLPKDYCC SDLDL DAEF EVILPRRQGL GLCGTALVSY LISLHNNMVY TVQKFSNEDN SYSVDISEVA DLHVISYEVE RDLNPLILSN CQYQVQ QGG ETSQEFDLEK IQRQISSRFL QGKPRLTLKG IPTLVYRRDW NYEHLFMDIK NKMAQSSLPN LAISTISGQL QSYSDAC EA LSIIEITLGF LSTAGGDPGM DLNVYIEEVL RMCDQTAQVL KAFSRCQLRH IIALWQFLSA HKSEQRLRLN KELFREID V QYKEELSTQH QRLLGTFLNE AGLDAFLLEL HEMIVLKLKG PRAANSFNPN WSLKDTLVSY METKDSDILS EVESQFPEE ILMSSCISVW KIAATRKWDR QSRGGGHHHH HHHHHH

-
Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

-
Macromolecule #6: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 1 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.2
Component:
ConcentrationFormula
200.0 mMKCl
25.0 mMHEPES
0.25 mMTCEP
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Instrument: LEICA PLUNGER

-
Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -2.5 µm / Nominal defocus min: -1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #0 - Number grids imaged: 1 / #0 - Number real images: 3055 / #0 - Average exposure time: 2.0 sec. / #0 - Average electron dose: 45.0 e/Å2 / #0 - Details: grid tilted 30 degrees 1 image per "hole" / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 QUANTUM (4k x 4k) / #1 - Detector mode: COUNTING / #1 - Digitization - Dimensions - Width: 3838 pixel / #1 - Digitization - Dimensions - Height: 3710 pixel / #1 - Digitization - Frames/image: 1-40 / #1 - Number grids imaged: 1 / #1 - Number real images: 5950 / #1 - Average exposure time: 10.0 sec. / #1 - Average electron dose: 40.5 e/Å2 / #1 - Details: non-tilted dataset 10 images per "hole"
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: EMDB MAP
EMDB ID:

10429

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 336000
Image recording ID1
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6tax


Chain - Chain ID: A
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7oim:
Mouse RNF213, with mixed nucleotides bound

+
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