[English] 日本語
Yorodumi
- EMDB-32890: ADGRL3/Gi complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32890
TitleADGRL3/Gi complex
Map data
Sample
  • Complex: GPCR/G-protein complex
    • Complex: GPCR/G-protein complex
      • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
      • Protein or peptide: scFv16
    • Complex: ADGRL3
      • Protein or peptide: Isoform 3 of Adhesion G protein-coupled receptor L3
Function / homology
Function and homology information


locomotion involved in locomotory behavior / maintenance of postsynaptic specialization structure / cell-cell adhesion via plasma-membrane adhesion molecules / positive regulation of synapse assembly / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization ...locomotion involved in locomotory behavior / maintenance of postsynaptic specialization structure / cell-cell adhesion via plasma-membrane adhesion molecules / positive regulation of synapse assembly / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / synapse assembly / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / response to cocaine / Regulation of insulin secretion / G protein-coupled receptor binding / G protein-coupled receptor activity / synapse organization / neuron migration / Olfactory Signaling Pathway / G-protein beta/gamma-subunit complex binding / Activation of the phototransduction cascade / Schaffer collateral - CA1 synapse / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / response to peptide hormone / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / sensory perception of taste / GPER1 signaling / G-protein beta-subunit binding / GDP binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / cell-cell junction / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / GTPase binding / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / cell cortex / midbody / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / postsynaptic membrane / carbohydrate binding / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / cell surface receptor signaling pathway / cell cycle / G protein-coupled receptor signaling pathway / lysosomal membrane / axon / cell division / GTPase activity / centrosome / synapse / glutamatergic synapse / calcium ion binding / protein-containing complex binding / GTP binding / nucleolus / magnesium ion binding / signal transduction / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
GPCR, family 2, latrophilin, C-terminal / GPCR, family 2, latrophilin / Latrophilin Cytoplasmic C-terminal region / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / D-galactoside/L-rhamnose binding SUEL lectin domain / Galactose binding lectin domain / SUEL-type lectin domain profile. / Olfactomedin-like domain ...GPCR, family 2, latrophilin, C-terminal / GPCR, family 2, latrophilin / Latrophilin Cytoplasmic C-terminal region / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / D-galactoside/L-rhamnose binding SUEL lectin domain / Galactose binding lectin domain / SUEL-type lectin domain profile. / Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GPS domain profile. / G-protein-coupled receptor proteolytic site domain / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / G-protein alpha subunit, group I / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(i) subunit alpha-1 / Adhesion G protein-coupled receptor L3
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsHe Y / Qian Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070048 China
CitationJournal: Mol Cell / Year: 2022
Title: Structural insights into adhesion GPCR ADGRL3 activation and G, G, G, and G coupling.
Authors: Yu Qian / Zhengxiong Ma / Chunhong Liu / Xinzhi Li / Xinyan Zhu / Na Wang / Zhenmei Xu / Ruixue Xia / Jiale Liang / Yaning Duan / Han Yin / Yangjie Xiong / Anqi Zhang / Changyou Guo / Zheng ...Authors: Yu Qian / Zhengxiong Ma / Chunhong Liu / Xinzhi Li / Xinyan Zhu / Na Wang / Zhenmei Xu / Ruixue Xia / Jiale Liang / Yaning Duan / Han Yin / Yangjie Xiong / Anqi Zhang / Changyou Guo / Zheng Chen / Zhiwei Huang / Yuanzheng He /
Abstract: Adhesion G-protein-coupled receptors (aGPCRs) play key roles in a diversity of physiologies. A hallmark of aGPCR activation is the removal of the inhibitory GAIN domain and the dipping of the cleaved ...Adhesion G-protein-coupled receptors (aGPCRs) play key roles in a diversity of physiologies. A hallmark of aGPCR activation is the removal of the inhibitory GAIN domain and the dipping of the cleaved stalk peptide into the ligand-binding pocket of receptors; however, the detailed mechanism remains obscure. Here, we present cryoelectron microscopy (cryo-EM) structures of ADGRL3 in complex with G, G, G, and G. The structures reveal unique ligand-engaging mode, distinctive activation conformation, and key mechanisms of aGPCR activation. The structures also reveal the uncharted structural information of GPCR/G coupling. A comparison of G, G, G, and G engagements with ADGRL3 reveals the key determinant of G-protein coupling on the far end of αH5 of Gα. A detailed analysis of the engagements allows us to design mutations that specifically enhance one pathway over others. Taken together, our study lays the groundwork for understanding aGPCR activation and G-protein-coupling selectivity.
History
DepositionFeb 15, 2022-
Header (metadata) releaseOct 26, 2022-
Map releaseOct 26, 2022-
UpdateNov 30, 2022-
Current statusNov 30, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32890.png

Downloads & links

-
Map

FileDownload / File: emd_32890.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.025463942 - 2.4219925
Average (Standard dev.)0.00089890376 (±0.019442396)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : GPCR/G-protein complex

EntireName: GPCR/G-protein complex
Components
  • Complex: GPCR/G-protein complex
    • Complex: GPCR/G-protein complex
      • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
      • Protein or peptide: scFv16
    • Complex: ADGRL3
      • Protein or peptide: Isoform 3 of Adhesion G protein-coupled receptor L3

-
Supramolecule #1: GPCR/G-protein complex

SupramoleculeName: GPCR/G-protein complex / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #2: GPCR/G-protein complex

SupramoleculeName: GPCR/G-protein complex / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: ADGRL3

SupramoleculeName: ADGRL3 / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Guanine nucleotide-binding protein G(i) subunit alpha-1

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.414047 KDa
Recombinant expressionOrganism: Insect BA phytoplasma (bacteria)
SequenceString: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKNTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKNTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTTGIVETH FTFKDLHFKM FDVGAQRSER KKWIHCFEGV TAIIFCVALS DYDLVLAEDE EM NRMHASM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY PEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCS TDTKNVQFVF DAVTDVIIKN NLKDCGLF

-
Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.915496 KDa
Recombinant expressionOrganism: Insect BA phytoplasma (bacteria)
SequenceString: MGSLLQSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD ...String:
MGSLLQSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD TTCALWDIET GQQTTTFTGH TGDVMSLSLA PDTRLFVSGA CDASAKLWDV REGMCRQTFT GHESDINAIC FF PNGNAFA TGSDDATCRL FDLRADQELM TYSHDNIICG ITSVSFSKSG RLLLAGYDDF NCNVWDALKA DRAGVLAGHD NRV SCLGVT DDGMAVATGS WDSFLKIWN

-
Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Insect BA phytoplasma (bacteria)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

-
Macromolecule #4: scFv16

MacromoleculeName: scFv16 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.277299 KDa
Recombinant expressionOrganism: Insect BA phytoplasma (bacteria)
SequenceString: VQLVESGGGL VQPGGSRKLS CSASGFAFSS FGMHWVRQAP EKGLEWVAYI SSGSGTIYYA DTVKGRFTIS RDDPKNTLFL QMTSLRSED TAMYYCVRSI YYYGSSPFDF WGQGTTLTVS AGGGGSGGGG SGGGGSADIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
VQLVESGGGL VQPGGSRKLS CSASGFAFSS FGMHWVRQAP EKGLEWVAYI SSGSGTIYYA DTVKGRFTIS RDDPKNTLFL QMTSLRSED TAMYYCVRSI YYYGSSPFDF WGQGTTLTVS AGGGGSGGGG SGGGGSADIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL

-
Macromolecule #5: Isoform 3 of Adhesion G protein-coupled receptor L3

MacromoleculeName: Isoform 3 of Adhesion G protein-coupled receptor L3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 172.044625 KDa
Recombinant expressionOrganism: Insect BA phytoplasma (bacteria)
SequenceString: MWPPQLLILT MLLAPVVHGG KHNERHPALA APLRHAERSP GGALPPRHLL QQPAAERSTA HRGQGPRGAA RGVRGPGAPG AQIAAQAFS RAPIPMAVVR RELSCESYPI ELRCPGTDVI MIESANYGRT DDKICDSDPA QMENIRCYLP DAYKIMSQRC N NRTQCAVV ...String:
MWPPQLLILT MLLAPVVHGG KHNERHPALA APLRHAERSP GGALPPRHLL QQPAAERSTA HRGQGPRGAA RGVRGPGAPG AQIAAQAFS RAPIPMAVVR RELSCESYPI ELRCPGTDVI MIESANYGRT DDKICDSDPA QMENIRCYLP DAYKIMSQRC N NRTQCAVV AGPDVFPDPC PGTYKYLEVQ YECVPYKVEQ KVFLCPGLLK GVYQSEHLFE SDHQSGAWCK DPLQASDKIY YM PWTPYRT DTLTEYSSKD DFIAGRPTTT YKLPHRVDGT GFVVYDGALF FNKERTRNIV KFDLRTRIKS GEAIIANANY HDT SPYRWG GKSDIDLAVD ENGLWVIYAT EQNNGKIVIS QLNPYTLRIE GTWDTAYDKR SASNAFMICG ILYVVKSVYE DDDN EATGN KIDYIYNTDQ SKDSLVDVPF PNSYQYIAAV DYNPRDNLLY VWNNYHVVKY SLDFGPLDSR SGPVHHGQVS YISPP IHLD SELERPPVRG ISTTGSLGMG STTTSTTLRT TTWNIGRSTT ASLPGRRNRS TSTPSPAVEV LDDVTTHLPS AASQIP AME ESCEAVEARE IMWFKTRQGQ VAKQPCPAGT IGVSTYLCLA PDGIWDPQGP DLSNCSSPWV NHITQKLKSG ETAANIA RE LAEQTRNHLN AGDITYSVRA MDQLVGLLDV QLRNLTPGGK DSAARSLNKL QKRERSCRAY VQAMVETVNN LLQPQALN A WRDLTTSDQL RAATMLLDTV EESAFVLADN LLKTDIVREN TDNIQLEVAR LSTEGNLEDL KFPENMGHGS TIQLSANTL KQNGRNGEIR VAFVLYNNLG PYLSTENASM KLGTEAMSTN HSVIVNSPVI TAAINKEFSN KVYLADPVVF TVKHIKQSEE NFNPNCSFW SYSKRTMTGY WSTQGCRLLT TNKTHTTCSC NHLTNFAVLM AHVEVKHSDA VHDLLLDVIT WVGILLSLVC L LICIFTFC FFRGLQSDRN TIHKNLCISL FVAELLFLIG INRTDQPIAC AVFAALLHFF FLAAFTWMFL EGVQLYIMLV EV FESEHSR RKYFYLVGYG MPALIVAVSA AVDYRSYGTD KVCWLRLDTY FIWSFIGPAT LIIMLNVIFL GIALYKMFHH TAI LKPESG CLDNINYEDN RPFIKSWVIG AIALLCLLGL TWAFGLMYIN ESTVIMAYLF TIFNSLQGMF IFIFHCVLQK KVRK EYGKC LRTHCCSGKS TESSIGSGKT SGSRTPGRYS TGSQSRIRRM WNDTVRKQSE SSFITGDINS SASLNREPYR ETKGL LNNA RDTSVMDTLP LNGNHGNSYS IAGGEYLSNC VQIIDRGYNH NETALEKKIL KELTSNYIPS YLNNHERSSE QNRNMM NKL VNNLGSGSED DAIVLDDAAS FNHEESLGLE LIHEESDAPL LPPRVYSTDN HQPHHYSRRR FPQDHSESFF PLLTDEH TE DLQSPHRDSL YTSMPALAGV PAADSVTTST QTEAAAAKGG DAEDVYYKSM PNLGSRNHVH PLHAYYQLGR GSSDGFIV P PNKDGASPEG TSKGPAHLVT SL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6vms

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 360000
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6vms


Chain - Chain ID: A
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7wyb:
ADGRL3/Gi complex

+
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