[English] 日本語
Yorodumi
- EMDB-22622: CryoEM structure of DNA-PK catalytic subunit complexed with DNA (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22622
TitleCryoEM structure of DNA-PK catalytic subunit complexed with DNA (Complex I)
Map data
Sample
  • Complex: complex I
    • Protein or peptide: DNA-dependent protein kinase catalytic subunit
    • DNA: DNA (5'-D(*GP*CP*AP*TP*GP*CP*TP*CP*TP*AP*CP*TP*GP*CP*TP*TP*CP*GP*AP*TP*AP*TP*CP*G)-3')
    • DNA: DNA (5'-D(*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*GP*CP*AP*TP*GP*C)-3')
KeywordsNHEJ / V(D)J recombination / DNA repair / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of platelet formation / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / immature B cell differentiation ...positive regulation of platelet formation / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / immature B cell differentiation / nonhomologous end joining complex / immunoglobulin V(D)J recombination / regulation of smooth muscle cell proliferation / Cytosolic sensors of pathogen-associated DNA / double-strand break repair via alternative nonhomologous end joining / IRF3-mediated induction of type I IFN / telomere capping / regulation of epithelial cell proliferation / regulation of hematopoietic stem cell differentiation / U3 snoRNA binding / T cell lineage commitment / maturation of 5.8S rRNA / negative regulation of cGAS/STING signaling pathway / B cell lineage commitment / positive regulation of double-strand break repair via nonhomologous end joining / ectopic germ cell programmed cell death / somitogenesis / mitotic G1 DNA damage checkpoint signaling / activation of innate immune response / telomere maintenance / positive regulation of erythrocyte differentiation / negative regulation of protein phosphorylation / protein-DNA complex / small-subunit processome / positive regulation of translation / response to gamma radiation / Nonhomologous End-Joining (NHEJ) / peptidyl-threonine phosphorylation / protein destabilization / brain development / protein modification process / regulation of circadian rhythm / double-strand break repair via nonhomologous end joining / cellular response to insulin stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / rhythmic process / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / heart development / T cell differentiation in thymus / double-stranded DNA binding / peptidyl-serine phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / chromosome, telomeric region / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of apoptotic process / protein phosphorylation / protein domain specific binding / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / chromatin / negative regulation of apoptotic process / nucleolus / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
DNA-dependent protein kinase catalytic subunit, CC3 / DNA-dependent protein kinase catalytic subunit, catalytic domain / DNA-dependent protein kinase catalytic subunit, CC5 / DNA-dependent protein kinase catalytic subunit, CC1/2 / DNA-PKcs, N-terminal / DNA-dependent protein kinase catalytic subunit, CC3 / DNA-PKcs, CC5 / DNA-PKcs, N-terminal / DNA-dependent protein kinase catalytic subunit, CC1/2 / NUC194 ...DNA-dependent protein kinase catalytic subunit, CC3 / DNA-dependent protein kinase catalytic subunit, catalytic domain / DNA-dependent protein kinase catalytic subunit, CC5 / DNA-dependent protein kinase catalytic subunit, CC1/2 / DNA-PKcs, N-terminal / DNA-dependent protein kinase catalytic subunit, CC3 / DNA-PKcs, CC5 / DNA-PKcs, N-terminal / DNA-dependent protein kinase catalytic subunit, CC1/2 / NUC194 / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Armadillo-like helical / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
DNA-dependent protein kinase catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsChen X / Gellert M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Mol Cell / Year: 2021
Title: Structure of an activated DNA-PK and its implications for NHEJ.
Authors: Xuemin Chen / Xiang Xu / Yun Chen / Joyce C Cheung / Huaibin Wang / Jiansen Jiang / Natalia de Val / Tara Fox / Martin Gellert / Wei Yang /
Abstract: DNA-dependent protein kinase (DNA-PK), like all phosphatidylinositol 3-kinase-related kinases (PIKKs), is composed of conserved FAT and kinase domains (FATKINs) along with solenoid structures made of ...DNA-dependent protein kinase (DNA-PK), like all phosphatidylinositol 3-kinase-related kinases (PIKKs), is composed of conserved FAT and kinase domains (FATKINs) along with solenoid structures made of HEAT repeats. These kinases are activated in response to cellular stress signals, but the mechanisms governing activation and regulation remain unresolved. For DNA-PK, all existing structures represent inactive states with resolution limited to 4.3 Å at best. Here, we report the cryoelectron microscopy (cryo-EM) structures of DNA-PKcs (DNA-PK catalytic subunit) bound to a DNA end or complexed with Ku70/80 and DNA in both inactive and activated forms at resolutions of 3.7 Å overall and 3.2 Å for FATKINs. These structures reveal the sequential transition of DNA-PK from inactive to activated forms. Most notably, activation of the kinase involves previously unknown stretching and twisting within individual solenoid segments and loosens DNA-end binding. This unprecedented structural plasticity of helical repeats may be a general regulatory mechanism of HEAT-repeat proteins.
History
DepositionSep 7, 2020-
Header (metadata) releaseJan 6, 2021-
Map releaseJan 6, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7k19
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22622.png

Downloads & links

-
Map

FileDownload / File: emd_22622.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 352 pix.
= 408.32 Å		1.16 Å/pix.
x 352 pix.
= 408.32 Å		1.16 Å/pix.
x 352 pix.
= 408.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.03366881 - 0.05943378
Average (Standard dev.)0.000003834804 (±0.0021864017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 408.31998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z408.320408.320408.320
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.0340.0590.000

-
Supplemental data

-
Sample components

-
Entire : complex I

EntireName: complex I
Components
  • Complex: complex I
    • Protein or peptide: DNA-dependent protein kinase catalytic subunit
    • DNA: DNA (5'-D(*GP*CP*AP*TP*GP*CP*TP*CP*TP*AP*CP*TP*GP*CP*TP*TP*CP*GP*AP*TP*AP*TP*CP*G)-3')
    • DNA: DNA (5'-D(*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*GP*CP*AP*TP*GP*C)-3')

-
Supramolecule #1: complex I

SupramoleculeName: complex I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: DNA-dependent protein kinase catalytic subunit

MacromoleculeName: DNA-dependent protein kinase catalytic subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 469.673219 KDa
SequenceString: MAGSGAGVRC SLLRLQETLS AADRCGAALA GHQLIRGLGQ ECVLSSSPAV LALQTSLVFS RDFGLLVFVR KSLNSIEFRE CREEILKFL CIFLEKMGQK IAPYSVEIKN TCTSVYTKDR AAKCKIPALD LLIKLLQTFR SSRLMDEFKI GELFSKFYGE L ALKKKIPD ...String:
MAGSGAGVRC SLLRLQETLS AADRCGAALA GHQLIRGLGQ ECVLSSSPAV LALQTSLVFS RDFGLLVFVR KSLNSIEFRE CREEILKFL CIFLEKMGQK IAPYSVEIKN TCTSVYTKDR AAKCKIPALD LLIKLLQTFR SSRLMDEFKI GELFSKFYGE L ALKKKIPD TVLEKVYELL GLLGEVHPSE MINNAENLFR AFLGELKTQM TSAVREPKLP VLAGCLKGLS SLLCNFTKSM EE DPQTSRE IFNFVLKAIR PQIDLKRYAV PSAGLRLFAL HASQFSTCLL DNYVSLFEVL LKWCAHTNVE LKKAALSALE SFL KQVSNM VAKNAEMHKN KLQYFMEQFY GIIRNVDSNN KELSIAIRGY GLFAGPCKVI NAKDVDFMYV ELIQRCKQMF LTQT DTGDD RVYQMPSFLQ SVASVLLYLD TVPEVYTPVL EHLVVMQIDS FPQYSPKMQL VCCRAIVKVF LALAAKGPVL RNCIS TVVH QGLIRICSKP VVLPKGPESE SEDHRASGEV RTGKWKVPTY KDYVDLFRHL LSSDQMMDSI LADEAFFSVN SSSESL NHL LYDEFVKSVL KIVEKLDLTL EIQTVGEQEN GDEAPGVWMI PTSDPAANLH PAKPKDFSAF INLVEFCREI LPEKQAE FF EPWVYSFSYE LILQSTRLPL ISGFYKLLSI TVRNAKKIKY FEGVSPKSLK HSPEDPEKYS CFALFVKFGK EVAVKMKQ Y KDELLASCLT FLLSLPHNII ELDVRAYVPA LQMAFKLGLS YTPLAEVGLN ALEEWSIYID RHVMQPYYKD ILPCLDGYL KTSALSDETK NNWEVSALSR AAQKGFNKVV LKHLKKTKNL SSNEAISLEE IRIRVVQMLG SLGGQINKNL LTVTSSDEMM KSYVAWDRE KRLSFAVPFR EMKPVIFLDV FLPRVTELAL TASDRQTKVA ACELLHSMVM FMLGKATQMP EGGQGAPPMY Q LYKRTFPV LLRLACDVDQ VTRQLYEPLV MQLIHWFTNN KKFESQDTVA LLEAILDGIV DPVDSTLRDF CGRCIREFLK WS IKQITPQ QQEKSPVNTK SLFKRLYSLA LHPNAFKRLG ASLAFNNIYR EFREEESLVE QFVFEALVIY MESLALAHAD EKS LGTIQQ CCDAIDHLCR IIEKKHVSLN KAKKRRLPRG FPPSASLCLL DLVKWLLAHC GRPQTECRHK SIELFYKFVP LLPG NRSPN LWLKDVLKEE GVSFLINTFE GGGCGQPSGI LAQPTLLYLR GPFSLQATLC WLDLLLAALE CYNTFIGERT VGALQ VLGT EAQSSLLKAV AFFLESIAMH DIIAAEKCFG TGAAGNRTSP QEGERYNYSK CTVVVRIMEF TTTLLNTSPE GWKLLK KDL CNTHLMRVLV QTLCEPASIG FNIGDVQVMA HLPDVCVNLM KALKMSPYKD ILETHLREKI TAQSIEELCA VNLYGPD AQ VDRSRLAAVV SACKQLHRAG LLHNILPSQS TDLHHSVGTE LLSLVYKGIA PGDERQCLPS LDLSCKQLAS GLLELAFA F GGLCERLVSL LLNPAVLSTA SLGSSQGSVI HFSHGEYFYS LFSETINTEL LKNLDLAVLE LMQSSVDNTK MVSAVLNGM LDQSFRERAN QKHQGLKLAT TILQHWKKCD SWWAKDSPLE TKMAVLALLA KILQIDSSVS FNTSHGSFPE VFTTYISLLA DTKLDLHLK GQAVTLLPFF TSLTGGSLEE LRRVLEQLIV AHFPMQSREF PPGTPRFNNY VDCMKKFLDA LELSQSPMLL E LMTEVLCR EQQHVMEELF QSSFRRIARR GSCVTQVGLL ESVYEMFRKD DPRLSFTRQS FVDRSLLTLL WHCSLDALRE FF STIVVDA IDVLKSRFTK LNESTFDTQI TKKMGYYKIL DVMYSRLPKD DVHAKESKIN QVFHGSCITE GNELTKTLIK LCY DAFTEN MAGENQLLER RRLYHCAAYN CAISVICCVF NELKFYQGFL FSEKPEKNLL IFENLIDLKR RYNFPVEVEV PMER KKKYI EIRKEAREAA NGDSDGPSYM SSLSYLADST LSEEMSQFDF STGVQSYSYS SQDPRPATGR FRRREQRDPT VHDDV LELE MDELNRHECM APLTALVKHM HRSLGPPQGE EDSVPRDLPS WMKFLHGKLG NPIVPLNIRL FLAKLVINTE EVFRPY AKH WLSPLLQLAA SENNGGEGIH YMVVEIVATI LSWTGLATPT GVPKDEVLAN RLLNFLMKHV FHPKRAVFRH NLEIIKT LV ECWKDCLSIP YRLIFEKFSG KDPNSKDNSV GIQLLGIVMA NDLPPYDPQC GIQSSEYFQA LVNNMSFVRY KEVYAAAA E VLGLILRYVM ERKNILEESL CELVAKQLKQ HQNTMEDKFI VCLNKVTKSF PPLADRFMNA VFFLLPKFHG VLKTLCLEV VLCRVEGMTE LYFQLKSKDF VQVMRHRDDE RQKVCLDIIY KMMPKLKPVE LRELLNPVVE FVSHPSTTCR EQMYNILMWI HDNYRDPES ETDNDSQEIF KLAKDVLIQG LIDENPGLQL IIRNFWSHET RLPSNTLDRL LALNSLYSPK IEVHFLSLAT N FLLEMTSM SPDYPNPMFE HPLSECEFQE YTIDSDWRFR STVLTPMFVE TQASQGTLQT RTQEGSLSAR WPVAGQIRAT QQ QHDFTLT QTADGRSSFD WLTGSSTDPL VDHTSPSSDS LLFAHKRSER LQRAPLKSVG PDFGKKRLGL PGDEVDNKVK GAA GRTDLL RLRRRFMRDQ EKLSLMYARK GVAEQKREKE IKSELKMKQD AQVVLYRSYR HGDLPDIQIK HSSLITPLQA VAQR DPIIA KQLFSSLFSG ILKEMDKFKT LSEKNNITQK LLQDFNRFLN TTFSFFPPFV SCIQDISCQH AALLSLDPAA VSAGC LASL QQPVGIRLLE EALLRLLPAE LPAKRVRGKA RLPPDVLRWV ELAKLYRSIG EYDVLRGIFT SEIGTKQITQ SALLAE ARS DYSEAAKQYD EALNKQDWVD GEPTEAEKDF WELASLDCYN HLAEWKSLEY CSTASIDSEN PPDLNKIWSE PFYQETY LP YMIRSKLKLL LQGEADQSLL TFIDKAMHGE LQKAILELHY SQELSLLYLL QDDVDRAKYY IQNGIQSFMQ NYSSIDVL L HQSRLTKLQS VQALTEIQEF ISFISKQGNL SSQVPLKRLL NTWTNRYPDA KMDPMNIWDD IITNRCFFLS KIEEKLTPL PEDNSMNVDQ DGDPSDRMEV QEQEEDISSL IRSCKFSMKM KMIDSARKQN NFSLAMKLLK ELHKESKTRD DWLVSWVQSY CRLSHCRSR SQGCSEQVLT VLKTVSLLDE NNVSSYLSKN ILAFRDQNIL LGTTYRIIAN ALSSEPACLA EIEEDKARRI L ELSGSSSE DSEKVIAGLY QRAFQHLSEA VQAAEEEAQP PSWSCGPAAG VIDAYMTLAD FCDQQLRKEE ENASVIDSAE LQ AYPALVV EKMLKALKLN SNEARLKFPR LLQIIERYPE ETLSLMTKEI SSVPCWQFIS WISHMVALLD KDQAVAVQHS VEE ITDNYP QAIVYPFIIS SESYSFKDTS TGHKNKEFVA RIKSKLDQGG VIQDFINALD QLSNPELLFK DWSNDVRAEL AKTP VNKKN IEKMYERMYA ALGDPKAPGL GAFRRKFIQT FGKEFDKHFG KGGSKLLRMK LSDFNDITNM LLLKMNKDSK PPGNL KECS PWMSDFKVEF LRNELEIPGQ YDGRGKPLPE YHVRIAGFDE RVTVMASLRR PKRIIIRGHD EREHPFLVKG GEDLRQ DQR VEQLFQVMNG ILAQDSACSQ RALQLRTYSV VPMTSRLGLI EWLENTVTLK DLLLNTMSQE EKAAYLSDPR APPCEYK DW LTKMSGKHDV GAYMLMYKGA NRTETVTSFR KRESKVPADL LKRAFVRMST SPEAFLALRS HFASSHALIC ISHWILGI G DRHLNNFMVA METGGVIGID FGHAFGSATQ FLPVPELMPF RLTRQFINLM LPMKETGLMY SIMVHALRAF RSDPGLLTN TMDVFVKEPS FDWKNFEQKM LKKGGSWIQE INVAEKNWYP RQKICYAKRK LAGANPAVIT CDELLLGHEK APAFRDYVAV ARGSKDHNI RAQEPESGLS EETQVKCLMD QATDPNILGR TWEGWEPWM

UniProtKB: DNA-dependent protein kinase catalytic subunit

-
Macromolecule #2: DNA (5'-D(*GP*CP*AP*TP*GP*CP*TP*CP*TP*AP*CP*TP*GP*CP*TP*TP*CP*GP*...

MacromoleculeName: DNA (5'-D(*GP*CP*AP*TP*GP*CP*TP*CP*TP*AP*CP*TP*GP*CP*TP*TP*CP*GP*AP*TP*AP*TP*CP*G)-3')
type: dna / ID: 2 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 7.311714 KDa
SequenceString:
(DG)(DC)(DA)(DT)(DG)(DC)(DT)(DC)(DT)(DA) (DC)(DT)(DG)(DC)(DT)(DT)(DC)(DG)(DA)(DT) (DA)(DT)(DC)(DG)

-
Macromolecule #3: DNA (5'-D(*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*GP*CP*AP*TP*GP*C)-3')

MacromoleculeName: DNA (5'-D(*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*GP*CP*AP*TP*GP*C)-3')
type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 4.956243 KDa
SequenceString:
(DA)(DA)(DG)(DC)(DA)(DG)(DT)(DA)(DG)(DA) (DG)(DC)(DA)(DT)(DG)(DC)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.9
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62117
Initial angle assignmentType: OTHER / Details: RELION/3.0.8
Final angle assignmentType: OTHER / Details: RELION/3.0.8

+
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