[English] 日本語
Yorodumi
- EMDB-52362: Structure of the double bead region of bovine collagen VI microfi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52362
TitleStructure of the double bead region of bovine collagen VI microfibrils.
Map dataEM map of collagen VI bovine microfibril bead region
Sample
  • Tissue: Collagen VI microfibrils formed from heterotrimers of col6a1, col6a2 and col6a3
    • Protein or peptide: Col6a1
    • Protein or peptide: Col6a2
    • Protein or peptide: Col6a3
KeywordsCollagen VI / Col6A1 / Col6A2 / Col6A3 / triple-helix / bovine / microfibril / ECM / extracellular / matrix / fibril / STRUCTURAL PROTEIN / PROTEIN FIBRIL
Function / homology
Function and homology information


Collagen chain trimerization / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / Assembly of collagen fibrils and other multimeric structures / Integrin cell surface interactions / ECM proteoglycans / Collagen degradation / collagen trimer / response to UV / collagen binding ...Collagen chain trimerization / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / Assembly of collagen fibrils and other multimeric structures / Integrin cell surface interactions / ECM proteoglycans / Collagen degradation / collagen trimer / response to UV / collagen binding / extracellular matrix / phosphatidylinositol 3-kinase/protein kinase B signal transduction / serine-type endopeptidase inhibitor activity / sarcolemma / : / neuron apoptotic process / cell adhesion / protein-containing complex / extracellular space / extracellular region
Similarity search - Function
: / Collagen alpha-3(VI) chain, vWA domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / von Willebrand factor type A domain / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain ...: / Collagen alpha-3(VI) chain, vWA domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / von Willebrand factor type A domain / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Collagen alpha-2(VI) chain / Collagen alpha-3(VI) chain / Collagen alpha-1(VI) chain
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.3 Å
AuthorsGodwin ARF / Baldock C / Snee MM / Roseman AM
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Collagen VI microfibril structure reveals mechanism for molecular assembly and clustering of inherited pathogenic mutations
Authors: Godwin A / Snee M / Becker M / Dajani R / Collins R / Roseman A / Baldock C
History
DepositionDec 18, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52362.png

Downloads & links

-
Map

FileDownload / File: emd_52362.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of collagen VI bovine microfibril bead region
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.94 Å/pix.
x 512 pix.
= 994.816 Å		1.94 Å/pix.
x 512 pix.
= 994.816 Å		1.94 Å/pix.
x 512 pix.
= 994.816 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.943 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.491
Minimum - Maximum-0.34350234 - 1.644745
Average (Standard dev.)-0.00092206127 (±0.038020533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 994.816 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_52362_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map of collagen VI bovine microfibril bead region

Fileemd_52362_half_map_1.map
AnnotationHalf map of collagen VI bovine microfibril bead region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map of collagen VI bovine microfibril bead region

Fileemd_52362_half_map_2.map
AnnotationHalf map of collagen VI bovine microfibril bead region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Collagen VI microfibrils formed from heterotrimers of col6a1, col...

EntireName: Collagen VI microfibrils formed from heterotrimers of col6a1, col6a2 and col6a3
Components
  • Tissue: Collagen VI microfibrils formed from heterotrimers of col6a1, col6a2 and col6a3
    • Protein or peptide: Col6a1
    • Protein or peptide: Col6a2
    • Protein or peptide: Col6a3

-
Supramolecule #1: Collagen VI microfibrils formed from heterotrimers of col6a1, col...

SupramoleculeName: Collagen VI microfibrils formed from heterotrimers of col6a1, col6a2 and col6a3
type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (domestic cattle) / Tissue: Cornea

-
Macromolecule #1: Col6a1

MacromoleculeName: Col6a1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
SequenceString: MRLPRALLPL LLQACWASAQ DDPVASRAIA FQDCPVDLFF VLDTSESVAL RLKPYGALVD KVKSFTKRF IDNLNDRYYR CDRNLVWNAG ALHYSDEVEI IRGLTRMPSG RDELKSSVDA V KYFGKGTY TDCAIKKGLE ELLVGGSHLK ENKYLVVVTD GHPLEGYKEP ...String:
MRLPRALLPL LLQACWASAQ DDPVASRAIA FQDCPVDLFF VLDTSESVAL RLKPYGALVD KVKSFTKRF IDNLNDRYYR CDRNLVWNAG ALHYSDEVEI IRGLTRMPSG RDELKSSVDA V KYFGKGTY TDCAIKKGLE ELLVGGSHLK ENKYLVVVTD GHPLEGYKEP CGGLEDAVNE AK HLGIKVF SVAITPDHLE PRLSIIATDH TYRRNFTAAD WGQSRDAEEV ISQTIDTITD MIK NNVEQV CCSFECQPAR GPPGPRGDPG YEGERGKPGL PGEKGEAGDP GRPGDLGPVG YQGM KGEKG SRGEKGSRGP KGYKGEKGKR GMDGVDGMKG ETGFPGLPGC KGSPGFDGIQ GPPGP KGDP GAFGLKGQKG EPGADGEPGR PGSTGPPGDE GEPGEPGPPG EKGEAGDEGN AGPDGA PGE RGGPGERGPR GTPGARGPRG DPGEAGPQGD QGREGPVGVP GDPGEAGPIG PKGYRGD EG PPGTEGPKGA PGPAGPPGDP GLMGERGEDG PPGNGTEGFP GFPGYPGSRG PPGINGTK G YPGLKGDEGE AGDPGEDNND IAARGAKGAK GYRGPEGPQG PPGHVGPPGP DECEILDII MKMCSCCECK CGPIDILFVL DSSESIGLQN FEIAKDFIVK VIDRLSKDEL VKFEPGQSHA GVVQYSHNQ MQEHVDLRDP NIRNAQDLKE AIKKLQWMGG GTFTGEALQY TRSRLLPPTP N NRIALVIT DGRSDTQRDT TPLSVLCGPD IQVVSVGIKD VFGLAAGSDQ LNVISCQGLA PQ GRPGISL VKENYAELLD DGFLKNITAQ ICIDKKCPDY SCPITFSSPA DITILLDGSA SVG SHNFDI TKRFAKRLAE RFLTASRTDP GQDVRVAVVQ YSGTGQQRPE RAALQFLQNY TVLA NTVDS MDFFNDATDV MDALGYVTRF YREASSNAAK KRLLLFSDGN SQGATPAAIE KAVQE AQRA GVEIFAVVVG RQVNEPHVRV LVTGKAAEYD VVFGERHLFR VPSYQALLRG VFYQTV SRK VALD

UniProtKB: Collagen alpha-1(VI) chain

-
Macromolecule #2: Col6a2

MacromoleculeName: Col6a2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
SequenceString: MLRRKGAAKM LRSPCSALLL WGLLGAVHAQ QQEVISPGPS DRNSCPEKAD CPVHVYFVLD TSESITMQS PTDSLLYHMQ QFVLQFISQL QDELYLDQVA LSWRYGGLHF SDLVEVFSPP G SDRASFTK SLQSISSFRR GTFTDCMLAN MTQEVRRHVG KGVVNFAVVI ...String:
MLRRKGAAKM LRSPCSALLL WGLLGAVHAQ QQEVISPGPS DRNSCPEKAD CPVHVYFVLD TSESITMQS PTDSLLYHMQ QFVLQFISQL QDELYLDQVA LSWRYGGLHF SDLVEVFSPP G SDRASFTK SLQSISSFRR GTFTDCMLAN MTQEVRRHVG KGVVNFAVVI TDGHVTGSPC GG IKLQAER AREEGIRLFA VPPNLKLNEQ GLRDIANTPH ELYRNNYATM RPDSTEIDQD TIN RIIKVM KHEAYGECYK VSCLEIPGPP GPKGYRGQKG AKGNMGEPGE PGQKGRQGDP GIEG PIGFP GPKGVPGFKG EKGEFGADGR KGAPGLAGKN GTDGQKGKLG RIGPPGCKGD TGDRG PDGY VGEAGSPGER GDQGSKGDPG RPGRRGPPGE NGAKGSKGYQ GNNGAPGSPG LKGAKG GPG PRGPKGEPGR RGDPGTKGGP GSDGPKGEKG DPGPEGPRGL AGEVGNKGAK ANRGLPG PR GPQGTVGEPG KQGSRGDPGD AGPRGDSGQP GPKGDPGRPG FSYPGPRGAP GDKGEPGP P GPEGGRGDFG SKGEPGRKGQ KGEPADPGPP GEPGPRGQRG APGPEGEPGP PGDPGLTEC DVMTYVRETC GCCDCEKRCG ALDVVFVIDS SESIGYTNFT LEKNFVINVV NRLGAIAKDP KSETGTRVG VVQYSHEGTF EAIQLDDERI DSLSSFKEAV KNLEWIAGGT WTPSALKFAY N KLIKESRR QKTRVFAVVI TDGRHDPRDD DLNLRALCNH EVTVTAIGIG DMFHEKHESE NL YSIACDK PQQVRNMTLF SDLVAEKFID DMEDVLCPDP QIVCPDLPCQ TELYVAQCTQ RPV DIVFLL DGSERLGEQN FHKVRRFVEE VSRRLTLARK DDDPLNARVA LLQFGGPREQ QVAF PLTSN LTVIQEALAS ARYLNSFSHV GTGIVQAINQ VVQGARAGAR RHAELSFVFL TDGVT GNDS LDEAVHSMRK QNVVPTVVAV GSDVDTDVLS KISLGDPAAV FREKDYDSLA QPGFFD RFI RWIC

UniProtKB: Collagen alpha-2(VI) chain

-
Macromolecule #3: Col6a3

MacromoleculeName: Col6a3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
SequenceString: MRKHRHLPLV AILCLFFSGF SFTRGQQQPD VKNGAAADII FLVDSSWSIG KEHFQLVREF LYDVIESLA VGDNDFRFAL VQFNGNPHTE FLFNTYRSKQ EVLSHVSNMS YIGGSNQTGK G LAYVMQNH LTEAAGSRAS DGVPQVIVVL THGHSEDGLA LPSAELKSAD ...String:
MRKHRHLPLV AILCLFFSGF SFTRGQQQPD VKNGAAADII FLVDSSWSIG KEHFQLVREF LYDVIESLA VGDNDFRFAL VQFNGNPHTE FLFNTYRSKQ EVLSHVSNMS YIGGSNQTGK G LAYVMQNH LTEAAGSRAS DGVPQVIVVL THGHSEDGLA LPSAELKSAD VNVFAIGVED AD EAALKEI ASEPLNMHVF NLENYTSLHD IVGNLVACVR SSMAPERAGG TEIPKDITAQ DSA DIIFLI DGSNNTGSVN FAVILDFLVN LLERLSIGTQ QIRVGVVQYS DEPRTMFSLN SYST KAQVL DAVKALGFIG GELANVGLAL DFVVENHFTR AGGSRAEEGV PQVLVLISAG PSSDE IRDG VVALKQASVF SFGLGAQAAS KAELQHIATN DNLVFTVPEF RSLGDVQEQL LPYIVG VAQ RHIVLQPPTI VTQVIEVNKR DIVFLVDGSS KLGLTNFNAI RDFIAKVIQR LEIRQDL IQ VAVAQYADTV RPEFYFNTYP SKREVINAVR KMKALDGSAL YTGSALDFVR NNLFTEAA G YRAAEGVPKL LVLVTGGKSL DAVSQPAQEL KRSGILAFAV GNKVADQAEL EEIAFDSSL VFTATEFRPA PLQGVLPGLL GPLRTLTGTT EVRVNKRDII FLLDGSSNVG ETNFPYVRDF VMNLVNSLD VGSDHIRVGL VQFSDTPVTE FSLNTYPTKS ELLAHLRQMQ LQGGSVLNTG A ALSYVHAN HFTEAGGSRI QDHVPQLLLL LTAGQSEDSY LQAANALARA GILTFCVGTS QA DRAELEE IAFNPGLVYL MDDFSSLPAL PQQLIQPLTT YVSGGVEEVP LAQPESKRDI LFL FDGSAN LMGQFTAARD FLYKVIDELD VKPEGTRVAV AQFSDDVKVE SRFDQHQNKP EILN LVKRM KLKTGKALNL GYALDYAQRY IFVKSAGSRI EDGVLQFLVL LVAGKSSDRV DTPAL NLKQ SGVVPFILQA KNADPAELEL IVPSPAFILV AESLPKIGDL QPQIVNLLKS VQNGAP APV SVEKDVVFLI DGSEGVRSGF PLLKEFVQRV VESLDVGPDR VRVAVVQYSD RTRPEFY LN SYMDQQSVVG AIRGLTLLGG PAPNTGAALE FVLRNILVGS AGSRIAEGVP QLLIVLTA D RSGDDVRGPS VVLRRGGAVP IGIGIGNADI TEMQTLSFVP DFAVVIPTFR QLGTIQQVI SERVTQLSRE ELSRLQASVT PLTTPVVSSK RDVVFLIDGS QSAGPEFQYI RTLIERLVDY LDVGFDTTR VAVIQFSDDP RVEFLLNVHS SKDEVQNAVR RLRPKGGRQV NVGGALEYVA R NIFKRPLG SRIEEGVPQF LVLISSGKSD DEVEDSAIEL KQFGVAPLTI ARNVDQEELV KI SLSPEYV FSVNTFRELP SLEQKLLTPL TTLTAGQIQQ LLASTRYPPP AVESDAADIV FLI DSSDGV KPDGIAHIRD FVIRIVRRLN VGPNKVRIGV LQFSNDVFPE FQLKTYKSQA SVLD AIRRL RFKGGSPLNT GKALEFVARN YFVKSAGSRI EDGVPQHLVL FLGGKSQDDI SRYSQ VIKS AGIASLGVGD RNIDRTELQT ITSDPRLVFT VREFRDLPSI EERMVNSFGS SGVTPA PPG VDTPSPSRPE KKKADIVFLL DGSINFRRDS FQEVLRFVSE IVDTVYEGGD SIQVGLV QY NSDPTDEFFL KDFPTKQQII DAINKVVYKG GRHANTKVGL EHLRRNHFVP EAGSRLDQ R VPQIAFVITG GKSVEDAQEA SMALTQRGVK VFAVGVRNID SEEVGKIASN SATAFRVGN VQELSELSEQ VLETLHDAMH ETLCPGVTDV SKACNLDVIL GFDGSGDQNV FVAQKGLEPK VDTILRRIS QMQKISCSGS QLPTVRVSVV ALTPSGPVEA FDFAEYQPEL FEKFQNMRAQ H PYVLTADT LKLYQNKFRQ ASMDNVKVVI HFTDGVDGDL ADLQRASEEL RQEGVRALIL VG LERVANL EQLMQLEFGR GFTYNRPLRL NLLDLDYELA EQLDNIAEKA CCGIPCKCSG QRG DRGPIG SIGPKGIPGE DGYRGYPGDE GGPGERGPPG VNGTQGFQGC PGQRGVKGSR GFPG EKGEL GEIGLDGLDG EDGDKGLPGT SGEKGSPGRR GDKGPKGDKG ERGDVGIRGD PGNSG QDSQ QRGAKGETGD IGPVVQCSPF LPVQSNLPLC GSCGGRGGSP PRSTYVGILL LQGPPG PTG PPGLIGEQGI PGPRVSLAWT LSKSGEPGDP GPKGSIGNRG PRGETGDDGR DGVGSEG RI GKKVFICRGG NPGEPGTDGP PGPKGIRGRR GNSGPPGIAG QKGDPGYPGP SGYKGSRG D SMDQCALVQS IKDKCRPLEC PVFPTELAFA LDTSEGVTQD RFSQMREVVL KILDDLTIA ESNCPRGARV AVVTYNNEVT TEIRFADSKK KSVLLDKIKN LQVSLTSKQQ SLETAMSFVA RNTFKRVRS GFLMRKVAVF FSNKPTRATP QLREAVLKLS DAGITPLFLT SQEDRQLINA L QINNTAVG HALVLPAGGD LTDFLKNVLT CHVCLDICNI DPSCGFGSWR PSFRDRRAAG SD VDIDMAF ILDSSESTTP FQFNEMRKYI EYLVRQLDVS PDPKASQHFA RVAVVQHAPY EAV DNASVP PVKVEFSLTD YGSKEKLLAF LGSRMTQLQG TRALGRAIDY TIENIFESAP NPRD LKIVV LMLTGEVQKQ QLEEAQRAIL QAKCKGYFFV ILGIGRKVNV KELYSSASEP NDVFF KLVD KSTELNEEPL MRFGRLLPSF VSSKDAFYLS PDIRKQCDWF QADQPAKNLV QFGYKQ INV PNNVTSSPTS KLVTTTKPVI TTTKPITVVN LPASKPAATR PVDERPAAGR SVATKMD SA RPVATKTEAT KPAAAAKPAA AKPAPARPPT AARSMATRSE APRPQAVKLA ASRPGAAK P VVKAPREIHV SEVTENSAKL HWERPEPPSP YLYNLTVTSA HDQAVVLKQN LTVTDRVIG GLLPGQTYHV TVTCSLRSQV RAIYQGSFST KKIQPPPPQT ERSASSATIN LVVSADRLAG SKADICKLP KDGGTCREFV LKWYYDSVTE NCARFWYGGC GGNENRFNSQ DECEKVCPPV P IKQPGVIA AMGT

UniProtKB: Collagen alpha-3(VI) chain

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
400.0 mMNaClsodium chloride
20.0 mMTris-HClTrizma base
2.5 mMCaCl2Calcium chloride
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 29595 / Average exposure time: 2.3 sec. / Average electron dose: 22.165 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 145555
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 12.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 47488
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 50 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

+
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