[English] 日本語
Yorodumi
- EMDB-30602: Cryo-EM structure of the beclomethasone-bound adhesion receptor G... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30602
TitleCryo-EM structure of the beclomethasone-bound adhesion receptor GPR97-Go complex
Map data
Sample
  • Complex: Beclomethasone-bound adhesion receptor GPR97-Go complex
    • Complex: Adhesion G protein-coupled receptor G3; GPR97
      • Protein or peptide: Adhesion G protein-coupled receptor G3; GPR97
    • Complex: Go
      • Protein or peptide: Guanine nucleotide-binding protein G(o) subunit alpha
      • 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
  • Ligand: PALMITIC ACID
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: (8~{S},9~{R},10~{S},11~{S},13~{S},14~{S},16~{S},17~{R})-9-chloranyl-10,13,16-trimethyl-11,17-bis(oxidanyl)-17-(2-oxidanylethanoyl)-6,7,8,11,12,14,15,16-octahydrocyclopenta[a]phenanthren-3-one
  • Ligand: CHOLESTEROL
KeywordsGPCR / GPR97 / complex / adhesion G protein-coupled receptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of CREB transcription factor activity / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / vesicle docking involved in exocytosis / negative regulation of non-canonical NF-kappaB signal transduction / G protein-coupled dopamine receptor signaling pathway / regulation of heart contraction / negative regulation of insulin secretion / specific granule membrane / G protein-coupled serotonin receptor binding ...negative regulation of CREB transcription factor activity / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / vesicle docking involved in exocytosis / negative regulation of non-canonical NF-kappaB signal transduction / G protein-coupled dopamine receptor signaling pathway / regulation of heart contraction / negative regulation of insulin secretion / specific granule membrane / G protein-coupled serotonin receptor binding / muscle contraction / regulation of cell migration / B cell differentiation / locomotory behavior / G protein-coupled receptor activity / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / 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 / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / cell body / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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 / lysosomal membrane / GTPase activity / dendrite / Neutrophil degranulation / synapse / protein-containing complex binding / GTP binding / signal transduction / extracellular exosome / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GPCR, family 2, orphan receptor, GPR1/GPR3/GPR5 / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. ...GPCR, family 2, orphan receptor, GPR1/GPR3/GPR5 / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / 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 / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / 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. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / 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(o) subunit alpha / 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 G3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsPing Y / Mao C
CitationJournal: Nature / Year: 2021
Title: Structures of the glucocorticoid-bound adhesion receptor GPR97-G complex.
Authors: Yu-Qi Ping / Chunyou Mao / Peng Xiao / Ru-Jia Zhao / Yi Jiang / Zhao Yang / Wen-Tao An / Dan-Dan Shen / Fan Yang / Huibing Zhang / Changxiu Qu / Qingya Shen / Caiping Tian / Zi-Jian Li / ...Authors: Yu-Qi Ping / Chunyou Mao / Peng Xiao / Ru-Jia Zhao / Yi Jiang / Zhao Yang / Wen-Tao An / Dan-Dan Shen / Fan Yang / Huibing Zhang / Changxiu Qu / Qingya Shen / Caiping Tian / Zi-Jian Li / Shaolong Li / Guang-Yu Wang / Xiaona Tao / Xin Wen / Ya-Ni Zhong / Jing Yang / Fan Yi / Xiao Yu / H Eric Xu / Yan Zhang / Jin-Peng Sun /
Abstract: Adhesion G-protein-coupled receptors (GPCRs) are a major family of GPCRs, but limited knowledge of their ligand regulation or structure is available. Here we report that glucocorticoid stress ...Adhesion G-protein-coupled receptors (GPCRs) are a major family of GPCRs, but limited knowledge of their ligand regulation or structure is available. Here we report that glucocorticoid stress hormones activate adhesion G-protein-coupled receptor G3 (ADGRG3; also known as GPR97), a prototypical adhesion GPCR. The cryo-electron microscopy structures of GPR97-G complexes bound to the anti-inflammatory drug beclomethasone or the steroid hormone cortisol revealed that glucocorticoids bind to a pocket within the transmembrane domain. The steroidal core of glucocorticoids is packed against the 'toggle switch' residue W, which senses the binding of a ligand and induces activation of the receptor. Active GPR97 uses a quaternary core and HLY motif to fasten the seven-transmembrane bundle and to mediate G protein coupling. The cytoplasmic side of GPR97 has an open cavity, where all three intracellular loops interact with the G protein, contributing to the high basal activity of GRP97. Palmitoylation at the cytosolic tail of the G protein was found to be essential for efficient engagement with GPR97 but is not observed in other solved GPCR complex structures. Our work provides a structural basis for ligand binding to the seven-transmembrane domain of an adhesion GPCR and subsequent G protein coupling.
History
DepositionOct 3, 2020-
Header (metadata) releaseFeb 3, 2021-
Map releaseFeb 3, 2021-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7d76
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30602.png

Downloads & links

-
Map

FileDownload / File: emd_30602.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 192 pix.
= 194.688 Å		1.01 Å/pix.
x 192 pix.
= 194.688 Å		1.01 Å/pix.
x 192 pix.
= 194.688 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.23593968 - 0.352162
Average (Standard dev.)-0.00020747592 (±0.009342182)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 194.68802 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z194.688194.688194.688
α/β/γ90.00090.00090.000
start NX/NY/NZ-210-210-210
NX/NY/NZ420420420
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.2360.352-0.000

-
Supplemental data

-
Sample components

+
Entire : Beclomethasone-bound adhesion receptor GPR97-Go complex

EntireName: Beclomethasone-bound adhesion receptor GPR97-Go complex
Components
  • Complex: Beclomethasone-bound adhesion receptor GPR97-Go complex
    • Complex: Adhesion G protein-coupled receptor G3; GPR97
      • Protein or peptide: Adhesion G protein-coupled receptor G3; GPR97
    • Complex: Go
      • Protein or peptide: Guanine nucleotide-binding protein G(o) subunit alpha
      • 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
  • Ligand: PALMITIC ACID
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: (8~{S},9~{R},10~{S},11~{S},13~{S},14~{S},16~{S},17~{R})-9-chloranyl-10,13,16-trimethyl-11,17-bis(oxidanyl)-17-(2-oxidanylethanoyl)-6,7,8,11,12,14,15,16-octahydrocyclopenta[a]phenanthren-3-one
  • Ligand: CHOLESTEROL

+
Supramolecule #1: Beclomethasone-bound adhesion receptor GPR97-Go complex

SupramoleculeName: Beclomethasone-bound adhesion receptor GPR97-Go complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

+
Supramolecule #2: Adhesion G protein-coupled receptor G3; GPR97

SupramoleculeName: Adhesion G protein-coupled receptor G3; GPR97 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #3: Go

SupramoleculeName: Go / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: Guanine nucleotide-binding protein G(o) subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.286922 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTLSAEERAA LERSKAIEKN LKEDGISAAK DVKLLLLGAD NSGKSTIVKQ MKIIHGGSGG SGGTTGIVET HFTFKNLHFR LFDVGGQRS ERKKWIHCFE DVTAIIFCVD LSDYNRMHES LMLFDSICNN KFFIDTSIIL FLNKKDLFGE KIKKSPLTIC F PEYTGPNT ...String:
MTLSAEERAA LERSKAIEKN LKEDGISAAK DVKLLLLGAD NSGKSTIVKQ MKIIHGGSGG SGGTTGIVET HFTFKNLHFR LFDVGGQRS ERKKWIHCFE DVTAIIFCVD LSDYNRMHES LMLFDSICNN KFFIDTSIIL FLNKKDLFGE KIKKSPLTIC F PEYTGPNT YEDAAAYIQA QFESKNRSPN KEIYCHMTCA TDTNNAQVIF DAVTDIIIAN NLRGCGLY

+
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: 38.245801 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String:
MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD INAICFFPNG NA FATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAGHDNRVSC LGV TDDGMA VATGSWDSFL KIWNHHHHHH

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

+
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: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

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

+
Macromolecule #4: Adhesion G protein-coupled receptor G3; GPR97

MacromoleculeName: Adhesion G protein-coupled receptor G3; GPR97 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.767098 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDAKL QTMHHHHHHH HHHENLYFQG GTQEKPTEGP RNTCLGSNNM YDIFNLNDKA LCFTKCRQSG SDSCNVENLQ RYWLNYEAH LMKEGLTQKV NTPFLKALVQ NLSTNTAEDF YFSLEPSQVP RQVMKDEDKP PDRVRLPKSL FRSLPGNRSV V RLAVTILD ...String:
DYKDDDDAKL QTMHHHHHHH HHHENLYFQG GTQEKPTEGP RNTCLGSNNM YDIFNLNDKA LCFTKCRQSG SDSCNVENLQ RYWLNYEAH LMKEGLTQKV NTPFLKALVQ NLSTNTAEDF YFSLEPSQVP RQVMKDEDKP PDRVRLPKSL FRSLPGNRSV V RLAVTILD IGPGTLFKGP RLGLGDGSGV LNNRLVGLSV GQMHVTKLAE PLEIVFSHQR PPPNMTLTCV FWDVTKGTTG DW SSEGCST EVRPEGTVCC CDALAFFALL LRPTLDQSTV HILTRISQAG CGVSMIFLAF TIILYAFLRL SRERFKSEDA PKI HVALGG SLFLLNLAFL VNVGSGSKGS DAACWARGAV FHYFLLCAFT WMGLEAFHLY LLAVRVFNTY FGHYFLKLSL VGWG LPALM VIGTGSANSY GLYTIRDREN RTSLELCWFR EGTTMYALYI TVHGYFLITF LFGMVVLALV VWKIFTLSRA TAVKE RGKN RKKVLTLLGL SSLVGVTWGL AIFTPLGLST VYIFALFNSL QGVFICCWFT ILYLPSQSTT VSSSTARLDQ AHSASQ E

+
Macromolecule #5: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 5 / Number of copies: 3 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

+
Macromolecule #6: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

+
Macromolecule #7: (8~{S},9~{R},10~{S},11~{S},13~{S},14~{S},16~{S},17~{R})-9-chloran...

MacromoleculeName: (8~{S},9~{R},10~{S},11~{S},13~{S},14~{S},16~{S},17~{R})-9-chloranyl-10,13,16-trimethyl-11,17-bis(oxidanyl)-17-(2-oxidanylethanoyl)-6,7,8,11,12,14,15,16-octahydrocyclopenta[a]phenanthren-3-one
type: ligand / ID: 7 / Number of copies: 1 / Formula: GXR
Molecular weightTheoretical: 408.916 Da
Chemical component information

ChemComp-GXR:
(8~{S},9~{R},10~{S},11~{S},13~{S},14~{S},16~{S},17~{R})-9-chloranyl-10,13,16-trimethyl-11,17-bis(oxidanyl)-17-(2-oxidanylethanoyl)-6,7,8,11,12,14,15,16-octahydrocyclopenta[a]phenanthren-3-one

+
Macromolecule #8: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 8 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration20 mg/mL
BufferpH: 7.5
GridModel: Quantifoil / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 2707 / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49310 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 29000
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: 2026926
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0-beta2) / Number images used: 166116
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6g79


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-7d76:
Cryo-EM structure of the beclomethasone-bound adhesion receptor GPR97-Go 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