[English] 日本語
Yorodumi
- EMDB-58252: Cryo-EM structure of Dopamine 3 receptor:Go complex bound to bito... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-58252
TitleCryo-EM structure of Dopamine 3 receptor:Go complex bound to bitopic AB13-46A
Map dataCryo-EM map of Dopamine 3 Receptor:Go complex bound to bitopic AB13-46A
Sample
  • Complex: Dopamine 3 Receptor:Go complex bound to bitopic AB13-46A
    • 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
    • Protein or peptide: Green fluorescent protein,D(3) dopamine receptor
  • Ligand: ~{N}-[2-[(1~{R},2~{S})-2-[[(2~{S},5~{S})-2-(6-azanylpyridin-3-yl)-5-methyl-morpholin-4-yl]methyl]cyclopropyl]ethyl]-6-methoxy-1~{H}-indole-2-carboxamide
KeywordsBitopic molecules / dopamine receptor / drug selectivity / structure-based drug design / GPCRs / G protein-coupled receptors / ligand-triggered receptor conformation / MEMBRANE PROTEIN
Function / homology
Function and homology information


musculoskeletal movement, spinal reflex action / acid secretion / dopamine neurotransmitter receptor activity, coupled via Gi/Go / response to histamine / regulation of potassium ion transport / adenylate cyclase-inhibiting dopamine receptor signaling pathway / Dopamine receptors / regulation of dopamine uptake involved in synaptic transmission / phospholipase C-activating dopamine receptor signaling pathway / positive regulation of dopamine receptor signaling pathway ...musculoskeletal movement, spinal reflex action / acid secretion / dopamine neurotransmitter receptor activity, coupled via Gi/Go / response to histamine / regulation of potassium ion transport / adenylate cyclase-inhibiting dopamine receptor signaling pathway / Dopamine receptors / regulation of dopamine uptake involved in synaptic transmission / phospholipase C-activating dopamine receptor signaling pathway / positive regulation of dopamine receptor signaling pathway / negative regulation of oligodendrocyte differentiation / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / G alpha (z) signalling events / G protein-coupled dopamine receptor signaling pathway / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G protein-coupled receptor internalization / Vasopressin regulates renal water homeostasis via Aquaporins / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / negative regulation of synaptic transmission, glutamatergic / G alpha (q) signalling events / G alpha (i) signalling events / Thrombin signalling through proteinase activated receptors (PARs) / arachidonate secretion / photoreceptor outer segment membrane / response to morphine / spectrin binding / dopamine metabolic process / positive regulation of cytokinesis / negative regulation of cytosolic calcium ion concentration / sensory perception of taste / alkylglycerophosphoethanolamine phosphodiesterase activity / retina development in camera-type eye / parallel fiber to Purkinje cell synapse / regulation of dopamine secretion / social behavior / negative regulation of insulin secretion / negative regulation of protein secretion / cardiac muscle cell apoptotic process / photoreceptor outer segment / prepulse inhibition / postsynaptic modulation of chemical synaptic transmission / negative regulation of blood pressure / behavioral response to cocaine / positive regulation of mitotic nuclear division / photoreceptor inner segment / muscle contraction / visual learning / learning / adenylate cyclase-inhibiting serotonin receptor signaling pathway / G protein-coupled serotonin receptor binding / locomotory behavior / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / bioluminescence / circadian regulation of gene expression / response to cocaine / generation of precursor metabolites and energy / intracellular calcium ion homeostasis / cell population proliferation / GABA-ergic synapse / G protein-coupled receptor activity / G-protein beta/gamma-subunit complex binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / 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 / ADP signalling through P2Y purinoceptor 1 / cellular response to catecholamine stimulus / G beta:gamma signalling through PI3Kgamma / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus
Similarity search - Function
Dopamine D3 receptor / Dopamine receptor family / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / G protein alpha subunit, helical insertion / G protein alpha subunit ...Dopamine D3 receptor / Dopamine receptor family / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / 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 / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 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. / 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 / D(3) dopamine receptor / Green fluorescent protein / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsArroyo-Urea S / Garcia-Nafria J
Funding support Spain, 2 items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2020-113359GA-I00 Spain
Ministerio de Ciencia e Innovacion (MCIN)PID2023-148739NB-I00 Spain
CitationJournal: JACS Au / Year: 2026
Title: A Ligand-Triggered Receptor Conformation Enables the Design of Selective Agonists for the Dopamine 3 Receptor (DR) Using a Bitopic Strategy.
Authors: Sandra Arroyo-Urea / Antonina L Nazarova / Alexander Knieb / Hawau Abdulsalam / Khorshada Jahan / Ting Du / Song Gao / Amy Hauck Newman / Vsevolod Katritch / Javier García-Nafría / Alessandro Bonifazi /
Abstract: While G protein-coupled receptors (GPCRs) represent the largest drug target family, designing subtype-selective molecules is still a challenge, especially to distinguish among closely related ...While G protein-coupled receptors (GPCRs) represent the largest drug target family, designing subtype-selective molecules is still a challenge, especially to distinguish among closely related subtypes. One of the most challenging cases is the distinction between dopamine DR and DR, pivotal receptors in motor functions and cognition, and targets of Parkinson's disease treatments, schizophrenia, or substance use disorders. Attempts to design DR-selective molecules with ligands binding toward the first transmembrane helix (the most sequence-diverse and conformationally flexible segment in GPCRs but rarely participating in ligand binding) allowed us to discover a ligand-induced ordering of TM1 unique to DR, yielding an unexploited selectivity site for drug development. Using rational bitopic drug design and the ligand-triggered conformation of the DR we designed, synthesized, and characterized the most selective DR agonists to date, >100,000-fold more selective than available ligands. More specifically, we report DR partial agonists AB12-82 () and AB13-73A (), with >575,000- and >750,000-fold subtype selectivity, picomolar potency, and 85% and 49% efficacy, respectively. We also present the most selective full agonists reported to date, AB13-08 () and AB13-46A (), presenting low and subnanomolar potencies with >2,800- and 6,300-fold selectivity for DR. Overall, we introduce a first-in-class pharmacological toolbox to dissect the (patho)-physiology of DR, open new avenues for the design of improved neurotherapeutics, and show that using ligand-induced TM1 reorganizations might represent a promising strategy for the design of subtype-selective molecules in other GPCRs.
History
DepositionMay 22, 2026-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_58252.png

Downloads & links

-
Map

FileDownload / File: emd_58252.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of Dopamine 3 Receptor:Go complex bound to bitopic AB13-46A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 263.616 Å		0.82 Å/pix.
x 320 pix.
= 263.616 Å		0.82 Å/pix.
x 320 pix.
= 263.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8238 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.431
Minimum - Maximum-1.7149497 - 2.3135293
Average (Standard dev.)-0.00054259715 (±0.048284303)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 263.616 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half-map A

Fileemd_58252_half_map_1.map
AnnotationHalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map B

Fileemd_58252_half_map_2.map
AnnotationHalf-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Dopamine 3 Receptor:Go complex bound to bitopic AB13-46A

EntireName: Dopamine 3 Receptor:Go complex bound to bitopic AB13-46A
Components
  • Complex: Dopamine 3 Receptor:Go complex bound to bitopic AB13-46A
    • 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
    • Protein or peptide: Green fluorescent protein,D(3) dopamine receptor
  • Ligand: ~{N}-[2-[(1~{R},2~{S})-2-[[(2~{S},5~{S})-2-(6-azanylpyridin-3-yl)-5-methyl-morpholin-4-yl]methyl]cyclopropyl]ethyl]-6-methoxy-1~{H}-indole-2-carboxamide

-
Supramolecule #1: Dopamine 3 Receptor:Go complex bound to bitopic AB13-46A

SupramoleculeName: Dopamine 3 Receptor:Go complex bound to bitopic AB13-46A
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
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
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.097438 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGCTLSAEER AALERSKAIE KNLKEDGISA AKDVKLLLLG AGESGKNTIV KQMEIIHEDG FSGEDVKQYK PVVYSNTIQS LAAIVRAMD TLGIEYGDKE RKADAKMVCD VVSRMEDTEP FSAELLSAMM RLWGDSGIQE CFNRSREYQL NDSAKYYLDS L DRIGAADY ...String:
MGCTLSAEER AALERSKAIE KNLKEDGISA AKDVKLLLLG AGESGKNTIV KQMEIIHEDG FSGEDVKQYK PVVYSNTIQS LAAIVRAMD TLGIEYGDKE RKADAKMVCD VVSRMEDTEP FSAELLSAMM RLWGDSGIQE CFNRSREYQL NDSAKYYLDS L DRIGAADY QPTEQDILRT RVKTTGIVET HFTFKNLHFR LFDVGAQRSE RKKWIHCFED VTAIIFCVAL SGYDQVLHED ET TNRMHAS LKLFDSICNN KFFIDTSIIL FLNKKDLFGE KIKKSPLTIC FPEYTGPNTY EDAAAYIQAQ FESKNRSPNK EIY CHMTCS TDTNNIQVVF DAVTDIIIAN NLRGCGLY

UniProtKB: Guanine nucleotide-binding protein G(o) subunit alpha

-
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 / Details: His-Gbeta-1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 39.373992 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHHHE NLYFQGSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSAS QDGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG Y LSCCRFLD ...String:
MHHHHHHHHE NLYFQGSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSAS QDGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG Y LSCCRFLD DNQIVTSSGD TTCALWDIET GQQTTTFTGH TGDVMSLSLA PDTRLFVSGA CDASAKLWDV REGMCRQTFT GH ESDINAI CFFPNGNAFA TGSDDATCRL FDLRADQELM TYSHDNIICG ITSVSFSKSG RLLLAGYDDF NCNVWDALKA DRA GVLAGH DNRVSCLGVT DDGMAVATGS WDSFLKIWN

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: Trichoplusia ni (cabbage looper)
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: Green fluorescent protein,D(3) dopamine receptor

MacromoleculeName: Green fluorescent protein,D(3) dopamine receptor / type: protein_or_peptide / ID: 4 / Details: HASS-FLAG-eGFP-D3R,HASS-FLAG-eGFP-D3R / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.660891 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKTIIALSYI FCLVFADYKD DDDKVSKGEE LFTGVVPILV ELDGDVNGHK FSVSGEGEGD ATYGKLTLKF ICTTGKLPVP WPTLVTTLT YGVQCFSRYP DHMKQHDFFK SAMPEGYVQE RTIFFKDDGN YKTRAEVKFE GDTLVNRIEL KGIDFKEDGN I LGHKLEYN ...String:
MKTIIALSYI FCLVFADYKD DDDKVSKGEE LFTGVVPILV ELDGDVNGHK FSVSGEGEGD ATYGKLTLKF ICTTGKLPVP WPTLVTTLT YGVQCFSRYP DHMKQHDFFK SAMPEGYVQE RTIFFKDDGN YKTRAEVKFE GDTLVNRIEL KGIDFKEDGN I LGHKLEYN YNSHNVYIMA DKQKNGIKVN FKIRHNIEDG SVQLADHYQQ NTPIGDGPVL LPDNHYLSTQ SALSKDPNEK RD HMVLLEF VTAAGITLGM DELYKLEVLF QGPASLSQLS SHLNYTCGAE NSTGASQARP HAYYALSYCA LILAIVFGNG LVC MAVLKE RALQTTTNYL VVSLAVADLL VATLVMPWVV YLEVTGGVWN FSRICCDVFV TLDVMMCTAS ILNLCAISID RYTA VVMPV HYQHGTGQSS CRRVALMITA VWVLAFAVSC PLLFGFNTTG DPTVCSISNP DFVIYSSVVS FYLPFGVTVL VYARI YVVL KQRRRKRILT RQNSQCNSVR PGFPQQTLSP DPAHLELKRY YSICQDTALG GPGFQERGGE LKREEKTRNS LSPTIA PKL SLEVRKLSNG RLSTSLKLGP LQPRGVPLRE KKATQMVAIV LGAFIVCWLP FFLTHVLNTH CQTCHVSPEL YSATTWL GY VNSALNPVIY TTFNIEFRKA FLKILSC

UniProtKB: Green fluorescent protein, D(3) dopamine receptor

-
Macromolecule #5: ~{N}-[2-[(1~{R},2~{S})-2-[[(2~{S},5~{S})-2-(6-azanylpyridin-3-yl)...

MacromoleculeName: ~{N}-[2-[(1~{R},2~{S})-2-[[(2~{S},5~{S})-2-(6-azanylpyridin-3-yl)-5-methyl-morpholin-4-yl]methyl]cyclopropyl]ethyl]-6-methoxy-1~{H}-indole-2-carboxamide
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1J83
Molecular weightTheoretical: 463.572 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.8 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1/1 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number real images: 13180 / Average electron dose: 52.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: RELION (ver. 5.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Initial model was obtained from the 2D particles.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 120394
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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