[English] 日本語
Yorodumi
- EMDB-23390: Allosteric modulator LY3154207 binding to SKF-81297-bound dopamin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23390
TitleAllosteric modulator LY3154207 binding to SKF-81297-bound dopamine receptor 1 in complex with miniGs protein
Map data
Sample
  • Complex: LY3154207 and SKF-81297-bound dopamine receptor 1 in complex with Gi protein
    • Protein or peptide: D(1A) dopamine receptor
    • Protein or peptide: Engineered human Gs alpha subunit
    • 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: Nanoboy 35
  • Ligand: (1R)-6-chloro-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine-7,8-diol
  • Ligand: 2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-3-oxidanyl-butyl)-3,4-dihydro-1H-isoquinolin-2-yl]ethanone
  • Ligand: CHOLESTEROL
  • Ligand: PALMITIC ACID
KeywordsDopamine receptor 2 / Gs protein / SKF-81297 / PAM / LY3154207 / SIGNALING PROTEIN
Function / homology
Function and homology information


dopamine neurotransmitter receptor activity, coupled via Gs / dopamine neurotransmitter receptor activity / cerebral cortex GABAergic interneuron migration / operant conditioning / Dopamine receptors / regulation of dopamine uptake involved in synaptic transmission / dopamine binding / phospholipase C-activating dopamine receptor signaling pathway / heterotrimeric G-protein binding / modification of postsynaptic structure ...dopamine neurotransmitter receptor activity, coupled via Gs / dopamine neurotransmitter receptor activity / cerebral cortex GABAergic interneuron migration / operant conditioning / Dopamine receptors / regulation of dopamine uptake involved in synaptic transmission / dopamine binding / phospholipase C-activating dopamine receptor signaling pathway / heterotrimeric G-protein binding / modification of postsynaptic structure / peristalsis / regulation of dopamine metabolic process / G protein-coupled receptor complex / grooming behavior / positive regulation of neuron migration / habituation / sensitization / dopamine transport / astrocyte development / dentate gyrus development / conditioned taste aversion / striatum development / positive regulation of potassium ion transport / maternal behavior / 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 / arrestin family protein binding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / G alpha (z) signalling events / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / non-motile cilium / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / long-term synaptic depression / G alpha (i) signalling events / mating behavior / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (12/13) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through BTK / adult walking behavior / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G protein-coupled dopamine receptor signaling pathway / G alpha (s) signalling events / ciliary membrane / photoreceptor outer segment membrane / G alpha (q) signalling events / G alpha (i) signalling events / spectrin binding / temperature homeostasis / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / D-glucose import / transmission of nerve impulse / alkylglycerophosphoethanolamine phosphodiesterase activity / dopamine metabolic process / behavioral response to cocaine / PKA activation in glucagon signalling / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / hair follicle placode formation / photoreceptor outer segment / G-protein alpha-subunit binding / developmental growth / behavioral fear response / D1 dopamine receptor binding / intracellular transport / prepulse inhibition / vascular endothelial cell response to laminar fluid shear stress / neuronal action potential / renal water homeostasis / Hedgehog 'off' state / synapse assembly
Similarity search - Function
Dopamine D1 receptor / Dopamine receptor family / G-protein alpha subunit, group S / Serpentine type 7TM GPCR chemoreceptor Srsx / 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 ...Dopamine D1 receptor / Dopamine receptor family / G-protein alpha subunit, group S / Serpentine type 7TM GPCR chemoreceptor Srsx / 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 coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / 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
D(1A) dopamine receptor / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human) / Rattus norvegicus (Norway rat) / Bos taurus (domestic cattle) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhuang Y / Krumm B
Funding support China, United States, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81922071 China
National Natural Science Foundation of China (NSFC)31770796 China
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)RO1MH112205 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128641 United States
Citation
Journal: Cell Res / Year: 2021
Title: Mechanism of dopamine binding and allosteric modulation of the human D1 dopamine receptor.
Authors: Youwen Zhuang / Brian Krumm / Huibing Zhang / X Edward Zhou / Yue Wang / Xi-Ping Huang / Yongfeng Liu / Xi Cheng / Yi Jiang / Hualiang Jiang / Cheng Zhang / Wei Yi / Bryan L Roth / Yan Zhang / H Eric Xu /
#1: Journal: Biorxiv / Year: 2021
Title: Mechanism of dopamine binding and allosteric modulation of the human D1 dopamine receptor
Authors: Zhuang Y / Krumm B / Zhang H / Zhou XE / Wang Y / Guo J / Huang X-P / Liu Y / Wang L / Cheng X / Jiang Y / Jiang H / Melcher K / Zhang C / Yi W / Roth BL / Zhang Y / Xu HE
History
DepositionJan 28, 2021-
Header (metadata) releaseMar 3, 2021-
Map releaseMar 3, 2021-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7ljc
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23390.png

Downloads & links

-
Map

FileDownload / File: emd_23390.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 180 pix.
= 188.1 Å		1.05 Å/pix.
x 180 pix.
= 188.1 Å		1.05 Å/pix.
x 180 pix.
= 188.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.023 / Movie #1: 0.05
Minimum - Maximum-0.020833662 - 1.734762
Average (Standard dev.)0.0027162668 (±0.037162688)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 188.09999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0451.0451.045
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z188.100188.100188.100
α/β/γ90.00090.00090.000
start NX/NY/NZ645365
NX/NY/NZ139143124
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0211.7350.003

-
Supplemental data

-
Sample components

+
Entire : LY3154207 and SKF-81297-bound dopamine receptor 1 in complex with...

EntireName: LY3154207 and SKF-81297-bound dopamine receptor 1 in complex with Gi protein
Components
  • Complex: LY3154207 and SKF-81297-bound dopamine receptor 1 in complex with Gi protein
    • Protein or peptide: D(1A) dopamine receptor
    • Protein or peptide: Engineered human Gs alpha subunit
    • 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: Nanoboy 35
  • Ligand: (1R)-6-chloro-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine-7,8-diol
  • Ligand: 2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-3-oxidanyl-butyl)-3,4-dihydro-1H-isoquinolin-2-yl]ethanone
  • Ligand: CHOLESTEROL
  • Ligand: PALMITIC ACID

+
Supramolecule #1: LY3154207 and SKF-81297-bound dopamine receptor 1 in complex with...

SupramoleculeName: LY3154207 and SKF-81297-bound dopamine receptor 1 in complex with Gi protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: D(1A) dopamine receptor

MacromoleculeName: D(1A) dopamine receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.668707 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDVDM GQPGNGSAFL LAPNGSHAPD HDVTQQRDEE NLYFQGASMR TLNTSAMDGT GLVVERDFSV RILTACFLSL LILSTLLGN TLVCAAVIRF RHLRSKVTNF FVISLAVSDL LVAVLVMPWK AVAEIAGFWP FGSFCNIWVA FDIMCSTASI L NLCVISVD ...String:
DYKDDDDVDM GQPGNGSAFL LAPNGSHAPD HDVTQQRDEE NLYFQGASMR TLNTSAMDGT GLVVERDFSV RILTACFLSL LILSTLLGN TLVCAAVIRF RHLRSKVTNF FVISLAVSDL LVAVLVMPWK AVAEIAGFWP FGSFCNIWVA FDIMCSTASI L NLCVISVD RYWAISSPFR YERKMTPKAA FILISVAWTL SVLISFIPVQ LSWHKAKPTS PSDGNATSLA ETIDNCDSSL SR TYAISSS VISFYIPVAI MIVTYTRIYR IAQKQIRRIA ALERAAVHAK NCQTTTGNGK PVECSQPESS FKMSFKRETK VLK TLSVIM GVFVCCWLPF FILNCILPFC GSGETQPFCI DSNTFDVFVW FGWANSSLNP IIYAFNADFR KAFSTLLGCY RLCP ATNNA IETVSINNNG AAMFSSHHEP RGSISKECNL VYLIPHAVGS SEDLKKEEAA GIARPLEKLS PALSVILDYD TDVSL EKIQ PITQNGQHPT HHHHHHHH

UniProtKB: D(1A) dopamine receptor

+
Macromolecule #2: Engineered human Gs alpha subunit

MacromoleculeName: Engineered human Gs alpha subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.048932 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCLGNSKTE DQRNEEKAQR EANKMIEKQL QKDKQVYRAT HRLLLLGADN SGKSTIVKQM RIYHVNSGIF ETKFQVDKVN FHMFDVGAQ RDERRKWIQC FNDVTAIIFV VDSSDYNRLQ EALNDFKSIW NNRWLRTISV ILFLNKQDLL AEKVLAGKSK I EDYFPEFA ...String:
MGCLGNSKTE DQRNEEKAQR EANKMIEKQL QKDKQVYRAT HRLLLLGADN SGKSTIVKQM RIYHVNSGIF ETKFQVDKVN FHMFDVGAQ RDERRKWIQC FNDVTAIIFV VDSSDYNRLQ EALNDFKSIW NNRWLRTISV ILFLNKQDLL AEKVLAGKSK I EDYFPEFA RYTTPEDATP EPGEDPRVTR AKYFIRDEFL RISTASGDGR HYCYPHFTCS VDTENARRIF NDCRDIIQRM HL RQYELL

+
Macromolecule #3: 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: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 39.020664 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HHHHHHHHMG SLLQSELDQL RQEAEQLKNQ IRDARKACAD ATLSQITNNI DPVGRIQMRT RRTLRGHLAK IYAMHWGTDS RLLVSASQD GKLIIWDSYT TNKVHAIPLR SSWVMTCAYA PSGNYVACGG LDNICSIYNL KTREGNVRVS RELAGHTGYL S CCRFLDDN ...String:
HHHHHHHHMG SLLQSELDQL RQEAEQLKNQ IRDARKACAD ATLSQITNNI DPVGRIQMRT RRTLRGHLAK IYAMHWGTDS RLLVSASQD GKLIIWDSYT TNKVHAIPLR SSWVMTCAYA PSGNYVACGG LDNICSIYNL KTREGNVRVS RELAGHTGYL S CCRFLDDN QIVTSSGDTT CALWDIETGQ QTTTFTGHTG DVMSLSLAPD TRLFVSGACD ASAKLWDVRE GMCRQTFTGH ES DINAICF FPNGNAFATG SDDATCRLFD LRADQELMTY SHDNIICGIT SVSFSKSGRL LLAGYDDFNC NVWDALKADR AGV LAGHDN RVSCLGVTDD GMAVATGSWD SFLKIWN

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

+
Macromolecule #4: 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: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 7.432554 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
ASNNTASIAQ ARKLVEQLKM EANIDRIKVS KAAADLMAYC EAHAKEDPLL TPVPASENPF REKKFFC

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

+
Macromolecule #5: Nanoboy 35

MacromoleculeName: Nanoboy 35 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 14.845516 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQVQLQESGG GLVQPGGSLR LSCAASGFTF SNYKMNWVRQ APGKGLEWVS DISQSGASIS YTGSVKGRFT ISRDNAKNTL YLQMNSLKP EDTAVYYCAR CPAPFTRDCF DVTSTTYAYR GQGTQVTVSS HHHHHH

+
Macromolecule #6: (1R)-6-chloro-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine-7,8-diol

MacromoleculeName: (1R)-6-chloro-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine-7,8-diol
type: ligand / ID: 6 / Number of copies: 1 / Formula: SK0
Molecular weightTheoretical: 289.757 Da
Chemical component information

ChemComp-SK0:
(1R)-6-chloro-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine-7,8-diol

+
Macromolecule #7: 2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methy...

MacromoleculeName: 2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-3-oxidanyl-butyl)-3,4-dihydro-1H-isoquinolin-2-yl]ethanone
type: ligand / ID: 7 / Number of copies: 1 / Formula: G4C
Molecular weightTheoretical: 450.398 Da
Chemical component information

ChemComp-G4C:
2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-3-oxidanyl-butyl)-3,4-dihydro-1H-isoquinolin-2-yl]ethanone

+
Macromolecule #8: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 8 / Number of copies: 6 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

+
Macromolecule #9: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 9 / Number of copies: 6 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 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

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3sn6

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 212256
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
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