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- EMDB-48164: Buspirone-bound serotonin 1A (5-HT1A) receptor-Gz protein complex -

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Basic information

Entry
Database: EMDB / ID: EMD-48164
TitleBuspirone-bound serotonin 1A (5-HT1A) receptor-Gz protein complex
Map data
Sample
  • Complex: Serotonin 1A (5-HT1A) receptor-Gz protein complex
    • Complex: Serotonin 1A (5-HT1A) receptor
      • Protein or peptide: Soluble cytochrome b562,5-hydroxytryptamine receptor 1A
    • Complex: Gz protein
      • Protein or peptide: Guanine nucleotide-binding protein G(z) 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: Buspirone
  • Ligand: CHOLESTEROL
  • Ligand: [(2R)-1-[oxidanyl-[(2R,3R,5S,6R)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-3-tetradecanoyloxy-propan-2-yl] (5E,8E)-hexadeca-5,8,11,14-tetraenoate
KeywordsGPCR Signaling Complex / Serotonin Receptor / SIGNALING PROTEIN
Function / homology
Function and homology information


regulation of serotonin secretion / Gi/o-coupled serotonin receptor activity / regulation of hormone secretion / G protein-coupled serotonin receptor signaling pathway / regulation of behavior / receptor-receptor interaction / Serotonin receptors / serotonin receptor activity / G protein-coupled serotonin receptor activity / regulation of dopamine metabolic process ...regulation of serotonin secretion / Gi/o-coupled serotonin receptor activity / regulation of hormone secretion / G protein-coupled serotonin receptor signaling pathway / regulation of behavior / receptor-receptor interaction / Serotonin receptors / serotonin receptor activity / G protein-coupled serotonin receptor activity / regulation of dopamine metabolic process / serotonin receptor signaling pathway / neurotransmitter receptor activity / serotonin metabolic process / serotonin binding / gamma-aminobutyric acid signaling pathway / exploration behavior / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / regulation of vasoconstriction / behavioral fear response / adenylate cyclase inhibitor activity / G protein-coupled serotonin receptor binding / adenylate cyclase-inhibiting serotonin receptor signaling pathway / negative regulation of insulin secretion / electron transport chain / G protein-coupled receptor binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / 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-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 / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / 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 / ADP signalling through P2Y purinoceptor 1 / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / adenylate cyclase-activating dopamine receptor signaling pathway / nuclear envelope / GPER1 signaling / Inactivation, recovery and regulation of the phototransduction cascade / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / sensory perception of taste / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / cell body / GTPase binding / Ca2+ pathway / fibroblast proliferation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / chemical synaptic transmission / G alpha (q) signalling events / Ras protein signal transduction / periplasmic space / electron transfer activity / Extra-nuclear estrogen signaling / cell population proliferation / G protein-coupled receptor signaling pathway / iron ion binding / lysosomal membrane / GTPase activity / positive regulation of cell population proliferation / heme binding / dendrite / synapse / GTP binding / protein-containing complex binding / endoplasmic reticulum / signal transduction / extracellular exosome / metal ion binding / membrane / plasma membrane / cytosol
Similarity search - Function
5-Hydroxytryptamine 1A receptor / 5-hydroxytryptamine receptor family / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit ...5-Hydroxytryptamine 1A receptor / 5-hydroxytryptamine receptor family / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G-protein alpha subunit, group I / 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 / G protein beta WD-40 repeat protein / 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. / 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
5-hydroxytryptamine receptor 1A / Soluble cytochrome b562 / Guanine nucleotide-binding protein G(z) 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsWarren AL / Zilberg G / Wacker D
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 133504 United States
Other privateMcKnight Foundation
Other privateIrma T. Hirschl/Monique Weill-Caulier Trust
CitationJournal: Sci Adv / Year: 2025
Title: Structural determinants of G protein subtype selectivity at the serotonin receptor 5-HT1A.
Authors: Audrey L Warren / Gregory Zilberg / Anwar Abbassi / Alejandro Abraham / Shifan Yang / Daniel Wacker /
Abstract: Activation of the serotonin receptor 5-HT1A has been shown to regulate mood and cognition, making 5-HT1A an important target in the treatment of anxiety, depression, and psychosis. Although the ...Activation of the serotonin receptor 5-HT1A has been shown to regulate mood and cognition, making 5-HT1A an important target in the treatment of anxiety, depression, and psychosis. Although the receptor signals through inhibitory G proteins, more work is necessary to understand differences in transducer coupling and its relation to functional activity. To develop a molecular understanding of the differences underlying transducer coupling and activation, we performed structure-activity relationship studies of 5-HT1A with distinct G proteins. Through a combination of in vitro assays, we identified a potent partial agonist that selectively engages a G protein subtype. We further investigated the differences in G protein engagement at 5-HT1A with cryo-electron microscopy, determining structures of 5-HT1A bound to distinct ligands and G protein subtypes. Combined with subsequent structure-guided mutagenesis and signaling assays, our studies uncover both orthosteric and allosteric determinants of agonist-specific stimulation of distinct transducers.
History
DepositionDec 5, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48164.png

Downloads & links

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Map

FileDownload / File: emd_48164.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 277.248 Å		1.08 Å/pix.
x 256 pix.
= 277.248 Å		1.08 Å/pix.
x 256 pix.
= 277.248 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

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Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-1.1413312 - 1.6329541
Average (Standard dev.)-0.000000000289716 (±0.032455564)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 277.248 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map made with the DeepEM Enhancer program

Fileemd_48164_additional_1.map
AnnotationSharpened map made with the DeepEM Enhancer program
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_48164_half_map_1.map
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Half map: #1

Fileemd_48164_half_map_2.map
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Sample components

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Entire : Serotonin 1A (5-HT1A) receptor-Gz protein complex

EntireName: Serotonin 1A (5-HT1A) receptor-Gz protein complex
Components
  • Complex: Serotonin 1A (5-HT1A) receptor-Gz protein complex
    • Complex: Serotonin 1A (5-HT1A) receptor
      • Protein or peptide: Soluble cytochrome b562,5-hydroxytryptamine receptor 1A
    • Complex: Gz protein
      • Protein or peptide: Guanine nucleotide-binding protein G(z) 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: Buspirone
  • Ligand: CHOLESTEROL
  • Ligand: [(2R)-1-[oxidanyl-[(2R,3R,5S,6R)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-3-tetradecanoyloxy-propan-2-yl] (5E,8E)-hexadeca-5,8,11,14-tetraenoate

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Supramolecule #1: Serotonin 1A (5-HT1A) receptor-Gz protein complex

SupramoleculeName: Serotonin 1A (5-HT1A) receptor-Gz protein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Serotonin 1A (5-HT1A) receptor-Gz protein complex with components purified separately and assembled in vitro.

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Supramolecule #2: Serotonin 1A (5-HT1A) receptor

SupramoleculeName: Serotonin 1A (5-HT1A) receptor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: Gz protein

SupramoleculeName: Gz protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2, #4
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: Guanine nucleotide-binding protein G(z) subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.978699 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCRQSSEEK EAARRSRRID RHLRSESQRQ RREIKLLLLG TSNSGKSTIV KQMKIIHSGG FNLEACKEYK PLIIYNAIDS LTRIIRALA ALRIDFHNPD RAYDAVQLFA LTGPAESKGE ITPELLGVMR RLWADPGAQA CFSRSSEYHL EDNAAYYLND L ERIAAADY ...String:
MGCRQSSEEK EAARRSRRID RHLRSESQRQ RREIKLLLLG TSNSGKSTIV KQMKIIHSGG FNLEACKEYK PLIIYNAIDS LTRIIRALA ALRIDFHNPD RAYDAVQLFA LTGPAESKGE ITPELLGVMR RLWADPGAQA CFSRSSEYHL EDNAAYYLND L ERIAAADY IPTVEDILRS RDMTTGIVEN KFTFKELTFK MVDVGGQRSE RKKWIHCFEG VTAIIFCVEL SGYDLKLYED NQ TSRMAES LRLFDSICNN NWFINTSLIL FLNKKDLLAE KIRRIPLTIC FPEYKGQNTY EEAAVYIQRQ FEDLNRNKET KEI YSHFTC ATDTSNIQFV FDAVTDVIIQ NNLKYIGLC

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

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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: 39.418086 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHLEV LFQGPGSSGS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLV SASQDGKLII WDSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG H TGYLSCCR ...String:
MHHHHHHLEV LFQGPGSSGS 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

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

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Macromolecule #3: Soluble cytochrome b562,5-hydroxytryptamine receptor 1A

MacromoleculeName: Soluble cytochrome b562,5-hydroxytryptamine receptor 1A
type: protein_or_peptide / ID: 3
Details: N-terminally truncated 5-HT1A receptor with a flag and his tag followed by a TEV cleavage site and BRIL at the N-terminus.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.37593 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDAKLQTMH HHHHHHHHHE NLYFQGGTTA DLEDNWETLN DNLKVIEKAD NAAQVKDALT KMRAAALDA QKATPPKLED KSPDSPEMKD FRHGFDILVG QIDDALKLAN EGKVKEAQAA AEQLKTTRNA YIQKYLTGIS D VTVSYQVI ...String:
MKTIIALSYI FCLVFADYKD DDDAKLQTMH HHHHHHHHHE NLYFQGGTTA DLEDNWETLN DNLKVIEKAD NAAQVKDALT KMRAAALDA QKATPPKLED KSPDSPEMKD FRHGFDILVG QIDDALKLAN EGKVKEAQAA AEQLKTTRNA YIQKYLTGIS D VTVSYQVI TSLLLGTLIF CAVLGNACVV AAIALERSLQ NVANYLIGSL AVTDLMVSVL VLPMAALYQV LNKWTLGQVT CD LFIALDV LCCTSSIWHL CAIALDRYWA ITDPIDYVNK RTPRRAAALI SLTWLIGFLI SIPPMLGWRT PEDRSDPDAC TIS KDHGYT IYSTFGAFYI PLLLMLVLYG RIFRAARFRI RKTVKKVEKT GADTRHGASP APQPKKSVNG ESGSRNWRLG VESK AGGAL CANGAVRQGD DGAALEVIEV HRVGNSKEHL PLPSEAGPTP CAPASFERKN ERNAEAKRKM ALARERKTVK TLGII MGTF ILCWLPFFIV ALVLPFCESS CHMPTLLGAI INWLGYSNSL LNPVIYAYFN KDFQNAFKKI IKCKFCRQ

UniProtKB: Soluble cytochrome b562, 5-hydroxytryptamine receptor 1A

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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
Details: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 with a GSAGSAGSA linker connecting it to the N-terminus of Guanine nucleotide-binding protein G(z) subunit alpha
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.506765 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI LGSAGSAGSA

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

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Macromolecule #5: Buspirone

MacromoleculeName: Buspirone / type: ligand / ID: 5 / Number of copies: 2 / Formula: YLX
Molecular weightTheoretical: 385.503 Da

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Macromolecule #6: CHOLESTEROL

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

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #7: [(2R)-1-[oxidanyl-[(2R,3R,5S,6R)-2,3,5,6-tetrakis(oxidanyl)-4-pho...

MacromoleculeName: [(2R)-1-[oxidanyl-[(2R,3R,5S,6R)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-3-tetradecanoyloxy-propan-2-yl] (5E,8E)-hexadeca-5,8,11,14-tetraenoate
type: ligand / ID: 7 / Number of copies: 2 / Formula: J40
Molecular weightTheoretical: 854.895 Da
Chemical component information

ChemComp-J40:
[(2R)-1-[oxidanyl-[(2R,3R,5S,6R)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-3-tetradecanoyloxy-propan-2-yl] (5E,8E)-hexadeca-5,8,11,14-tetraenoate

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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

Concentration18 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
20.0 mMHEPES
100.0 mMsodium chloride
0.001 % (w/v)LMNG
0.0001 % (w/v)CHS
0.0001 % (w/v)GDN
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP
Details: Blot force 3 for 3-5 seconds was used and subsequent grids were screened for ice thickness prior to data collection..
DetailsSample was mono disperse following gel filtration. The sample was immediately concentrated for CryoEM grid preparation.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 5849 / Average electron dose: 51.33 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4465303
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 447065
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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