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- EMDB-32836: Tethered peptide activation mechanism of adhesion GPCRs ADGRG2 an... -

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Entry
Database: EMDB / ID: EMD-32836
TitleTethered peptide activation mechanism of adhesion GPCRs ADGRG2 and ADGRG4
Map dataCryo-EM structure of the ADGRG2-FL-IP15-Gs complex
Sample
  • Complex: Cryo-EM structure of the ADGRG2-FL-IP15-Gs complex
    • Complex: Gs
      • Protein or peptide: mini-Gs
      • 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
    • Complex: Nanobody-35Single-domain antibody
      • Protein or peptide: Nanobody-35Single-domain antibody
    • Complex: Adhesion G-protein coupled receptor G2
      • Protein or peptide: Adhesion G-protein coupled receptor G2,mCherry
    • Complex: scFv16
      • Protein or peptide: scFv16
    • Complex: IP15
      • Protein or peptide: IP15
Function / homology
Function and homology information


G protein-coupled receptor activity / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / 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 ...G protein-coupled receptor activity / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / 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 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / adenylate cyclase-activating G protein-coupled receptor signaling pathway / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / 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 / heterotrimeric G-protein complex / Inactivation, recovery and regulation of the phototransduction cascade / extracellular vesicle / G alpha (12/13) signalling events / 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 / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / apical plasma membrane / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding / signal transduction / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GPS domain profile. / G-protein-coupled receptor proteolytic site domain / 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 ...GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GPS domain profile. / G-protein-coupled receptor proteolytic site domain / 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, 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
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 / Adhesion G-protein coupled receptor G2
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama) / Mus musculus (house mouse) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsGuo SC / He QT / Xiao P / Sun JP / Yu X
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971195 China
National Natural Science Foundation of China (NSFC)11922410 China
CitationJournal: Nature / Year: 2022
Title: Tethered peptide activation mechanism of the adhesion GPCRs ADGRG2 and ADGRG4.
Authors: Peng Xiao / Shengchao Guo / Xin Wen / Qing-Tao He / Hui Lin / Shen-Ming Huang / Lu Gou / Chao Zhang / Zhao Yang / Ya-Ni Zhong / Chuan-Cheng Yang / Yu Li / Zheng Gong / Xiao-Na Tao / Zhi- ...Authors: Peng Xiao / Shengchao Guo / Xin Wen / Qing-Tao He / Hui Lin / Shen-Ming Huang / Lu Gou / Chao Zhang / Zhao Yang / Ya-Ni Zhong / Chuan-Cheng Yang / Yu Li / Zheng Gong / Xiao-Na Tao / Zhi-Shuai Yang / Yan Lu / Shao-Long Li / Jun-Yan He / Chuanxin Wang / Lei Zhang / Liangliang Kong / Jin-Peng Sun / Xiao Yu /
Abstract: Adhesion G protein-coupled receptors (aGPCRs) constitute an evolutionarily ancient family of receptors that often undergo autoproteolysis to produce α and β subunits. A tethered agonism mediated by ...Adhesion G protein-coupled receptors (aGPCRs) constitute an evolutionarily ancient family of receptors that often undergo autoproteolysis to produce α and β subunits. A tethered agonism mediated by the 'Stachel sequence' of the β subunit has been proposed to have central roles in aGPCR activation. Here we present three cryo-electron microscopy structures of aGPCRs coupled to the G heterotrimer. Two of these aGPCRs are activated by tethered Stachel sequences-the ADGRG2-β-G complex and the ADGRG4-β-G complex (in which β indicates the β subunit of the aGPCR)-and the other is the full-length ADGRG2 in complex with the exogenous ADGRG2 Stachel-sequence-derived peptide agonist IP15 (ADGRG2(FL)-IP15-G). The Stachel sequences of both ADGRG2-β and ADGRG4-β assume a U shape and insert deeply into the seven-transmembrane bundles. Constituting the FXφφφXφ motif (in which φ represents a hydrophobic residue), five residues of ADGRG2-β or ADGRG4-β extend like fingers to mediate binding to the seven-transmembrane domain and activation of the receptor. The structure of the ADGRG2(FL)-IP15-G complex reveals the structural basis for the improved binding affinity of IP15 compared with VPM-p15 and indicates that rational design of peptidic agonists could be achieved by exploiting aGPCR-β structures. By converting the 'finger residues' to acidic residues, we develop a method to generate peptidic antagonists towards several aGPCRs. Collectively, our study provides structural and biochemical insights into the tethered activation mechanism of aGPCRs.
History
DepositionFeb 8, 2022-
Header (metadata) releaseApr 27, 2022-
Map releaseApr 27, 2022-
UpdateMay 11, 2022-
Current statusMay 11, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32836.png

Downloads & links

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Map

FileDownload / File: emd_32836.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the ADGRG2-FL-IP15-Gs complex
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.12475119 - 0.18038431
Average (Standard dev.)2.9154397e-05 (±0.0050779907)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of the ADGRG2-FL-IP15-Gs complex

EntireName: Cryo-EM structure of the ADGRG2-FL-IP15-Gs complex
Components
  • Complex: Cryo-EM structure of the ADGRG2-FL-IP15-Gs complex
    • Complex: Gs
      • Protein or peptide: mini-Gs
      • 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
    • Complex: Nanobody-35Single-domain antibody
      • Protein or peptide: Nanobody-35Single-domain antibody
    • Complex: Adhesion G-protein coupled receptor G2
      • Protein or peptide: Adhesion G-protein coupled receptor G2,mCherry
    • Complex: scFv16
      • Protein or peptide: scFv16
    • Complex: IP15
      • Protein or peptide: IP15

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Supramolecule #1: Cryo-EM structure of the ADGRG2-FL-IP15-Gs complex

SupramoleculeName: Cryo-EM structure of the ADGRG2-FL-IP15-Gs complex / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightExperimental: 253 kDa/nm

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Supramolecule #2: Gs

SupramoleculeName: Gs / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: aculovirus expression vector pFastBac1-HM

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Supramolecule #3: Nanobody-35

SupramoleculeName: Nanobody-35 / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Lama glama (llama)
Recombinant expressionOrganism: Escherichia phage EcSzw-2 (virus)

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Supramolecule #4: Adhesion G-protein coupled receptor G2

SupramoleculeName: Adhesion G-protein coupled receptor G2 / type: complex / Chimera: Yes / ID: 4 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM

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Supramolecule #5: scFv16

SupramoleculeName: scFv16 / type: complex / Chimera: Yes / ID: 5 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM

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Supramolecule #6: IP15

SupramoleculeName: IP15 / type: complex / Chimera: Yes / ID: 6 / Parent: 1 / Macromolecule list: #7

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Macromolecule #1: mini-Gs

MacromoleculeName: mini-Gs / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.879465 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MGCTLSAEDK AAVERSKMIE KQLQKDKQVY RATHRLLLLG ADNSGKSTIV KQMRIYHVNG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMIE KQLQKDKQVY RATHRLLLLG ADNSGKSTIV KQMRIYHVNG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTSGIFETK FQVDKVNFHM FDVGAQRDER RKWIQCFNDV TAIIFVVDSS DYNRLQEALN DF KSIWNNR WLRTISVILF LNKQDLLAEK VLAGKSKIED YFPEFARYTT PEDATPEPGE DPRVTRAKYF IRDEFLRIST ASG DGRHYC YPHFTCSVDT ENARRIFNDC RDIIQRMHLR QYELL

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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: 39.48916 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MHHHHHHLEV LFQGPGSSQS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLV SASQDGKLII WDSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG H TGYLSCCR ...String:
MHHHHHHLEV LFQGPGSSQS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLV SASQDGKLII WDSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG H TGYLSCCR FLDDNQIVTS SGDTTCALWD IETGQQTTTF TGHTGDVMSL SLAPDTRLFV SGACDASAKL WDVREGMCRQ TF TGHESDI NAICFFPNGN AFATGSDDAT CRLFDLRADQ ELMTYSHDNI ICGITSVSFS KSGRLLLAGY DDFNCNVWDA LKA DRAGVL AGHDNRVSCL GVTDDGMAVA TGSWDSFLKI WN

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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: 6.375332 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString:
NTASIAQARK LVEQLKMEAN IDRIKVSKAA ADLMAYCEAH AKEDPLLTPV PASENPFR

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Macromolecule #4: Nanobody-35

MacromoleculeName: Nanobody-35 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.885439 KDa
Recombinant expressionOrganism: Escherichia phage EcSzw-2 (virus)
SequenceString:
QVQLQESGGG LVQPGGSLRL SCAASGFTFS NYKMNWVRQA PGKGLEWVSD ISQSGASISY TGSVKGRFTI SRDNAKNTLY LQMNSLKPE DTAVYYCARC PAPFTRDCFD VTSTTYAYRG QGTQVTVSS

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Macromolecule #5: Adhesion G-protein coupled receptor G2,mCherry

MacromoleculeName: Adhesion G-protein coupled receptor G2,mCherry / type: protein_or_peptide / ID: 5
Details: residues 892-916 = The replacement of GPR120 tail, residues 917-924 = His tag, residues 925-927 = linker, residues 928-934 = TEV site
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 126.852211 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MKTIIALSYI FCLVFALKEN GNSSLLSPSA ESSLVSLIPY SNGTPDAASE VLSTLNKTEK SKITIVKTFN ASGVKSQRNI CNLSSLCND SVFFRGEIVF QHDEDHNVTQ NQDTANGTFA GVLSLSELKR SELNKTLQTL SETYFIVCAT AEAQSTVNCT F TVKLNETM ...String:
MKTIIALSYI FCLVFALKEN GNSSLLSPSA ESSLVSLIPY SNGTPDAASE VLSTLNKTEK SKITIVKTFN ASGVKSQRNI CNLSSLCND SVFFRGEIVF QHDEDHNVTQ NQDTANGTFA GVLSLSELKR SELNKTLQTL SETYFIVCAT AEAQSTVNCT F TVKLNETM NVCAMMVTFQ TVQIRPMEQC CCSPRTPCPS SPEELEKLQC ELQDPIVCLA DQPHGPPLSS SSKPVVPQAT II SHVASDF SLAEPLDHAL MTPSTPSLTQ ESNLPSPQPT IPLASSPATD LPVQSVVVSS LPQTDLSHTL SPVQSSIPSP TTP APSVPT ELVTISTPPG ETVVNTSTVS DLEAQVSQME KALSLGSLEP NLAGEMVNRV SKLLHSPPAL LAPLAQRLLK VVDA IGLQL NFSSTTISLT SPSLALAVIR VNASNFNTTT FAAQDPTNLQ VSLETPPPEN SIGAITLPSS LMNNLPANDV ELASR IQFN FFETPALFQD PSLENLTLIS YVISSSVTNM TIKNLTRNVT VALKHINPSP DDLTVKCVFW DLGRNGGKGG WSSDGC SVK DKRMNETICT CSALASFGIL LDLSRTSLPP SQMMALTFIT YIGCGLSSIF LSVTLVTYIA FEKIRRDYPS KILIQLC AA LLLLNLIFLL DSWIALYNTR GFCIAVAVFL HYFLLVSFTW MGLEAFHMYL ALVKVFNTYI RKYILKFCIV GWGIPAVV V SIVLTISPDN YGIGSYGKFP NGTPDDFCWI NSNVVFYITV VGYFCVIFLL NVSMFIVVLV QLCRIKKKKQ LGAQRKTSI QDLRSIAGLT FLLGITWGFA FFAWGPVNVT FMYLFAIFNT LQGFFIFIFY CAAKENVRKQ WRRYLCCGKL FWFPEKGAIL TDTSVKRND LSIISGHHHH HHHHGSAENL YFQGMVSKGE EDNMAIIKEF MRFKVHMEGS VNGHEFEIEG EGEGRPYEGT Q TAKLKVTK GGPLPFAWDI LSPQFMYGSK AYVKHPADIP DYLKLSFPEG FKWERVMNFE DGGVVTVTQD SSLQDGEFIY KV KLRGTNF PSDGPVMQKK TMGWEASSER MYPEDGALKG EIKQRLKLKD GGHYDAEVKT TYKAKKPVQL PGAYNVNIKL DIT SHNEDY TIVEQYERAE GRHSTGGMDE LYK

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Macromolecule #6: scFv16

MacromoleculeName: scFv16 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 26.610615 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL KGS

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Macromolecule #7: IP15

MacromoleculeName: IP15 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.646948 KDa
SequenceString:
IS(4PH)GILLDLS RTSLP

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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

7d77

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1095986

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