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- EMDB-33227: Isoproterenol-activated dog beta3 adrenergic receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-33227
TitleIsoproterenol-activated dog beta3 adrenergic receptor
Map data
Sample
  • Complex: Dog beta3 adrenergic receptor bound to mirabegron in complex with a miniGs heterotrimer
    • Complex: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
      • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • Complex: 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(T) subunit beta-1
    • Complex: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: nanobody Nb35
      • Protein or peptide: Nanobody-35Single-domain antibody
    • Complex: Beta-3 adrenergic receptor
      • Protein or peptide: Beta-3 adrenergic receptor
  • Ligand: ISOPRENALINE
Function / homology
Function and homology information


beta3-adrenergic receptor activity / beta-adrenergic receptor activity / beta-3 adrenergic receptor binding / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / negative regulation of multicellular organism growth / G-protein activation / Activation of the phototransduction cascade / Olfactory Signaling Pathway / Glucagon-type ligand receptors ...beta3-adrenergic receptor activity / beta-adrenergic receptor activity / beta-3 adrenergic receptor binding / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / negative regulation of multicellular organism growth / G-protein activation / Activation of the phototransduction cascade / Olfactory Signaling Pathway / 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 / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / G alpha (z) signalling events / diet induced thermogenesis / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / Thrombin signalling through proteinase activated receptors (PARs) / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / Adrenaline,noradrenaline inhibits insulin secretion / 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 / Glucagon-type ligand receptors / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / alkylglycerophosphoethanolamine phosphodiesterase activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (s) signalling events / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (q) signalling events / photoreceptor outer segment membrane / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / PKA activation in glucagon signalling / brown fat cell differentiation / Vasopressin regulates renal water homeostasis via Aquaporins / spectrin binding / positive regulation of cAMP-mediated signaling / hair follicle placode formation / intracellular transport / adenylate cyclase-activating adrenergic receptor signaling pathway / developmental growth / Hedgehog 'off' state / cardiac muscle cell apoptotic process / photoreceptor outer segment / activation of adenylate cyclase activity / adenylate cyclase activator activity / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / response to cold / trans-Golgi network membrane / Glucagon-type ligand receptors / G-protein beta/gamma-subunit complex binding / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / photoreceptor inner segment / sensory perception of taste / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / GPER1 signaling / heterotrimeric G-protein complex / adenylate cyclase-activating G protein-coupled receptor signaling pathway / bone development / signaling receptor complex adaptor activity / cognition / ADORA2B mediated anti-inflammatory cytokines production / phospholipase C-activating G protein-coupled receptor signaling pathway / GTPase binding / platelet aggregation / retina development in camera-type eye / G alpha (i) signalling events / positive regulation of cold-induced thermogenesis / positive regulation of GTPase activity / sensory perception of smell / G alpha (s) signalling events / cell body
Similarity search - Function
Beta 3 adrenoceptor / Adrenoceptor family / G-protein alpha subunit, group S / Serpentine type 7TM GPCR chemoreceptor Srsx / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein, gamma subunit ...Beta 3 adrenoceptor / Adrenoceptor family / G-protein alpha subunit, group S / Serpentine type 7TM GPCR chemoreceptor Srsx / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / 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 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 circular profile. / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats 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
Beta-3 adrenergic 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 (cattle) / unidentified (others) / Canis lupus familiaris (dog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsShihoya W / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H05037 Japan
CitationJournal: Mol Cell / Year: 2021
Title: Cryo-EM structure of the β3-adrenergic receptor reveals the molecular basis of subtype selectivity.
Authors: Chisae Nagiri / Kazuhiro Kobayashi / Atsuhiro Tomita / Masahiko Kato / Kan Kobayashi / Keitaro Yamashita / Tomohiro Nishizawa / Asuka Inoue / Wataru Shihoya / Osamu Nureki /
Abstract: The β-adrenergic receptor (βAR) is predominantly expressed in adipose tissue and urinary bladder and has emerged as an attractive drug target for the treatment of type 2 diabetes, obesity, and ...The β-adrenergic receptor (βAR) is predominantly expressed in adipose tissue and urinary bladder and has emerged as an attractive drug target for the treatment of type 2 diabetes, obesity, and overactive bladder (OAB). Here, we report the cryogenic electron microscopy structure of the βAR-G signaling complex with the selective agonist mirabegron, a first-in-class drug for OAB. Comparison of this structure with the previously reported βAR and βAR structures reveals a receptor activation mechanism upon mirabegron binding to the orthosteric site. Notably, the narrower exosite in βAR creates a perpendicular pocket for mirabegron. Mutational analyses suggest that a combination of both the exosite shape and the amino-acid-residue substitutions defines the drug selectivity of the βAR agonists. Our findings provide a molecular basis for βAR subtype selectivity, allowing the design of more-selective agents with fewer adverse effects.
History
DepositionApr 18, 2022-
Header (metadata) releaseMay 4, 2022-
Map releaseMay 4, 2022-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_33227.map.gz / Format: CCP4 / Size: 12.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 148 pix.
= 162.098 Å
1.1 Å/pix.
x 148 pix.
= 162.098 Å
1.1 Å/pix.
x 148 pix.
= 162.098 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09526 Å
Density
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.17119035 - 0.26464275
Average (Standard dev.)0.0008742204 (±0.010736841)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions148148148
Spacing148148148
CellA=B=C: 162.09848 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33227_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_33227_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_33227_half_map_2.map
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Sample components

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Entire : Dog beta3 adrenergic receptor bound to mirabegron in complex with...

EntireName: Dog beta3 adrenergic receptor bound to mirabegron in complex with a miniGs heterotrimer
Components
  • Complex: Dog beta3 adrenergic receptor bound to mirabegron in complex with a miniGs heterotrimer
    • Complex: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
      • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • Complex: 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(T) subunit beta-1
    • Complex: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: nanobody Nb35
      • Protein or peptide: Nanobody-35Single-domain antibody
    • Complex: Beta-3 adrenergic receptor
      • Protein or peptide: Beta-3 adrenergic receptor
  • Ligand: ISOPRENALINE

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Supramolecule #1: Dog beta3 adrenergic receptor bound to mirabegron in complex with...

SupramoleculeName: Dog beta3 adrenergic receptor bound to mirabegron in complex with a miniGs heterotrimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

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Supramolecule #2: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

SupramoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

SupramoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

SupramoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: complex / Chimera: Yes / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Bos taurus (cattle)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #5: nanobody Nb35

SupramoleculeName: nanobody Nb35 / type: complex / Chimera: Yes / ID: 5 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: unidentified (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #6: Beta-3 adrenergic receptor

SupramoleculeName: Beta-3 adrenergic receptor / type: complex / Chimera: Yes / ID: 6 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Canis lupus familiaris (dog)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

MacromoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.255664 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: GNSKTEDQRN EEKAQREANK KIEKQLQKDK QVYRATHRLL LLGADNSGKS TIVKQMRIYH VNGFNGEGGE EDPQAARSNS DGEKATKVQ DIKNNLKEAI ETIVAAMSNL VPPVELANPE NQFRVDYILS VMNVPDFDFP PEFYEHAKAL WEDEGVRACY E RSNEYQLI ...String:
GNSKTEDQRN EEKAQREANK KIEKQLQKDK QVYRATHRLL LLGADNSGKS TIVKQMRIYH VNGFNGEGGE EDPQAARSNS DGEKATKVQ DIKNNLKEAI ETIVAAMSNL VPPVELANPE NQFRVDYILS VMNVPDFDFP PEFYEHAKAL WEDEGVRACY E RSNEYQLI DCAQYFLDKI DVIKQADYVP SDQDLLRCRV LTSGIFETKF QVDKVNFHMF DVGGQRDERR KWIQCFNDVT AI IFVVDSS DYNRLQEALN LFKSIWNNRW LRTISVILFL NKQDLLAEKV LAGKSKIEDY FPEFARYTTP EDATPEPGED PRV TRAKYF IRDEFLRIST ASGDGRHYCY PHFTCAVDTE NARRIFNDCR DIIQRMHLRQ YELL

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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: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 37.784301 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: GSLLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQD GKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY LSCCRFLDDN Q IVTSSGDT ...String:
GSLLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQD GKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY LSCCRFLDDN Q IVTSSGDT TCALWDIETG QQTTTFTGHT GDVMSLSLAP DTRLFVSGAC DASAKLWDVR EGMCRQTFTG HESDINAICF FP NGNAFAT GSDDATCRLF DLRADQELMT YSHDNIICGI TSVSFSKSGR LLLAGYDDFN CNVWDALKAD RAGVLAGHDN RVS CLGVTD DGMAVATGSW DSFLKIWN

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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: Bos taurus (cattle)
Molecular weightTheoretical: 7.547685 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFS

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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: unidentified (others)
Molecular weightTheoretical: 15.015728 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGQVQLQESG GGLVQPGGSL RLSCAASGFT FSNYKMNWVR QAPGKGLEWV SDISQSGASI SYTGSVKGRF TISRDNAKNT LYLQMNSLK PEDTAVYYCA RCPAPFTRDC FDVTSTTYAY RGQGTQVTVS SLHHHHHH

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Macromolecule #5: Beta-3 adrenergic receptor

MacromoleculeName: Beta-3 adrenergic receptor / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 42.441293 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: DYKDDDDAMG APWPHGNGSV ASWPAAPTPT PDAANTSGLP GAPWAVALAG ALLALEVLAT VGGNLLVIVA IARTPRLQTM TNVFVTSLA TADLVVGLLV VPPGATLALT GRWPLGATGC ELWTSVDVLC VTASIETLCA LAVDRYLAVT NPLRYGALVT K RRARAAVV ...String:
DYKDDDDAMG APWPHGNGSV ASWPAAPTPT PDAANTSGLP GAPWAVALAG ALLALEVLAT VGGNLLVIVA IARTPRLQTM TNVFVTSLA TADLVVGLLV VPPGATLALT GRWPLGATGC ELWTSVDVLC VTASIETLCA LAVDRYLAVT NPLRYGALVT K RRARAAVV LVWVVSAAVS FAPIMSKWWR VGADAEAQRC HSNPHCCAFA SNIPYALLSS SVSFYLPLLV MLFVYARVFL VA TRQLRLL RRELGRFPPA ESPPAASRSR SPGPARRCAS PAAVPSDRLR PARLLPLREH RALRTLGLIV GTFTLCWLPF FVA NVMRAL GGPSLVPSPA LLALNWLGYA NSAFNPLIYC RSPDFRSAFR RLLCRCRREE HRAAASPPGD PSENLYFQG

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Macromolecule #6: ISOPRENALINE

MacromoleculeName: ISOPRENALINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: 5FW
Molecular weightTheoretical: 211.258 Da
Chemical component information

ChemComp-5FW:
ISOPRENALINE / medication, agonist*YM / Isoprenaline

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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

Concentration7 mg/mL
BufferpH: 8
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: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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:
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104835
FSC plot (resolution estimation)

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