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- EMDB-39356: Cryo-EM structure of human GPR156-Gi3 complex -

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Entry
Database: EMDB / ID: EMD-39356
TitleCryo-EM structure of human GPR156-Gi3 complex
Map data
Sample
  • Organelle or cellular component: GPR156-Gi3 complex
    • Protein or peptide: Probable G-protein coupled receptor 156
    • 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: Guanine nucleotide-binding protein G(i) subunit alpha-3
  • Protein or peptide: Probable G-protein coupled receptor 156
  • Ligand: (21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate
  • Ligand: CHOLESTEROL
KeywordsGPCR / class C / GPR156 / cryo-EM / homodimer / active state / MEMBRANE PROTEIN
Function / homology
Function and homology information


stereocilium bundle organization / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / negative regulation of adenylate cyclase activity / 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 ...stereocilium bundle organization / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / negative regulation of adenylate cyclase activity / 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 / 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 / GTP metabolic process / G alpha (i) signalling events / gamma-aminobutyric acid signaling pathway / 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 / 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 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / G alpha (q) signalling events / photoreceptor outer segment membrane / spectrin binding / G alpha (i) signalling events / G protein-coupled dopamine receptor signaling pathway / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / alkylglycerophosphoethanolamine phosphodiesterase activity / positive regulation of macroautophagy / photoreceptor outer segment / Adenylate cyclase inhibitory pathway / cardiac muscle cell apoptotic process / photoreceptor inner segment / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / ADP signalling through P2Y purinoceptor 12 / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / GDP binding / GPER1 signaling / sensory perception of taste / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / GTPase binding / retina development in camera-type eye / positive regulation of cytosolic calcium ion concentration / cell body / midbody / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / G alpha (s) signalling events / cellular response to hypoxia / cell population proliferation / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / GTPase activity / centrosome / dendrite / synapse / protein-containing complex binding / GTP binding / nucleolus / Golgi apparatus / extracellular exosome / nucleoplasm / membrane
Similarity search - Function
GPR156, 7TM domain / GPCR family 3, GABA-B receptor / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / 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. ...GPR156, 7TM domain / GPCR family 3, GABA-B receptor / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / 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(i) subunit alpha-3 / 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 / Probable G-protein coupled receptor 156
Similarity search - Component
Biological speciesHomo sapiens (human) / Rattus norvegicus (Norway rat) / Bos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsMa XY / Chen LN / Liao MH / Zhang LY / Xi K / Guo JM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Molecular insights into the activation mechanism of GPR156 in maintaining auditory function.
Authors: Xiangyu Ma / Li-Nan Chen / Menghui Liao / Liyan Zhang / Kun Xi / Jiamin Guo / Cangsong Shen / Dan-Dan Shen / Pengjun Cai / Qingya Shen / Jieyu Qi / Huibing Zhang / Shao-Kun Zang / Ying-Jun ...Authors: Xiangyu Ma / Li-Nan Chen / Menghui Liao / Liyan Zhang / Kun Xi / Jiamin Guo / Cangsong Shen / Dan-Dan Shen / Pengjun Cai / Qingya Shen / Jieyu Qi / Huibing Zhang / Shao-Kun Zang / Ying-Jun Dong / Luwei Miao / Jiao Qin / Su-Yu Ji / Yue Li / Jianfeng Liu / Chunyou Mao / Yan Zhang / Renjie Chai /
Abstract: The class C orphan G-protein-coupled receptor (GPCR) GPR156, which lacks the large extracellular region, plays a pivotal role in auditory function through G. Here, we firstly demonstrate that GPR156 ...The class C orphan G-protein-coupled receptor (GPCR) GPR156, which lacks the large extracellular region, plays a pivotal role in auditory function through G. Here, we firstly demonstrate that GPR156 with high constitutive activity is essential for maintaining auditory function, and further reveal the structural basis of the sustained role of GPR156. We present the cryo-EM structures of human apo GPR156 and the GPR156-G complex, unveiling a small extracellular region formed by extracellular loop 2 (ECL2) and the N-terminus. The GPR156 dimer in both apo state and G protein-coupled state adopt a transmembrane (TM)5/6-TM5/6 interface, indicating the high constitutive activity of GPR156 in the apo state. Furthermore, C-terminus in G-bound subunit of GPR156 plays a dual role in promoting G protein binding within G-bound subunit while preventing the G-free subunit from binding to additional G protein. Together, these results explain how GPR156 constitutive activity is maintained through dimerization and provide a mechanistic insight into the sustained role of GPR156 in maintaining auditory function.
History
DepositionMar 3, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39356.png

Downloads & links

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Map

FileDownload / File: emd_39356.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.)
0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.49383894 - 1.3232607
Average (Standard dev.)-0.0038144505 (±0.038770434)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39356_half_map_1.map
Projections & Slices
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Density Histograms

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Half map: #2

Fileemd_39356_half_map_2.map
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Sample components

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Entire : GPR156-Gi3 complex

EntireName: GPR156-Gi3 complex
Components
  • Organelle or cellular component: GPR156-Gi3 complex
    • Protein or peptide: Probable G-protein coupled receptor 156
    • 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: Guanine nucleotide-binding protein G(i) subunit alpha-3
  • Protein or peptide: Probable G-protein coupled receptor 156
  • Ligand: (21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate
  • Ligand: CHOLESTEROL

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Supramolecule #1: GPR156-Gi3 complex

SupramoleculeName: GPR156-Gi3 complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Probable G-protein coupled receptor 156

MacromoleculeName: Probable G-protein coupled receptor 156 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.797066 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: RPLHDLCKTT ITSSHHSSKT ISSLSPVLLG IVWTFLSCGL LLILFFLAFT IHCRKNRIVK MSSPNLNIVT LLGSCLTYSS AYLFGIQDV LVGSSMETLI QTRLSMLCIG TSLVFGPILG KSWRLYKVFT QRVPDKRVII KDLQLLGLVA ALLMADVILL M TWVLTDPI ...String:
RPLHDLCKTT ITSSHHSSKT ISSLSPVLLG IVWTFLSCGL LLILFFLAFT IHCRKNRIVK MSSPNLNIVT LLGSCLTYSS AYLFGIQDV LVGSSMETLI QTRLSMLCIG TSLVFGPILG KSWRLYKVFT QRVPDKRVII KDLQLLGLVA ALLMADVILL M TWVLTDPI QCLQILSVSM TVTGKDVSCT STSTHFCASR YSDVWIALIW GCKGLLLLYG AYLAGLTGHV SSPPVNQSLT IM VGVNLLV LAAGLLFVVT RYLHSWPNLV FGLTSGGIFV CTTTINCFIF IPQLKQWKAF E

UniProtKB: Probable G-protein coupled receptor 156

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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: 37.198656 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLVS ASQDGKLIIW DSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG HTGYLSCCRF LDDNQIVTSS G DTTCALWD ...String:
ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLVS ASQDGKLIIW DSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG HTGYLSCCRF LDDNQIVTSS G DTTCALWD IETGQQTTTF TGHTGDVMSL SLAPDTRLFV SGACDASAKL WDVREGMCRQ TFTGHESDIN AICFFPNGNA FA TGSDDAT CRLFDLRADQ ELMTYSHDNI ICGITSVSFS KSGRLLLAGY DDFNCNVWDA LKADRAGVLA GHDNRVSCLG VTD DGMAVA TGSWDSFLKI WN

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

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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: 6.28924 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
ASIAQARKLV EQLKMEANID RIKVSKAAAD LMAYCEAHAK EDPLLTPVPA SENPFRE

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

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Macromolecule #4: Guanine nucleotide-binding protein G(i) subunit alpha-3

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-3
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.078512 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SAEDKAAVER SKMIDRNLRE DGEKAAKEVK LLLLGAGESG KNTIVKQMKI IHEDGYSEDE CKQYKVVVYS NTIQSIIAII RAMGRLKID FGEAARADDA RQLFVLAGSA EEGVMTPELA GVIKRLWRDG GVQACFSRSR EYQLNDSASY YLNDLDRISQ S NYIPTQQD ...String:
SAEDKAAVER SKMIDRNLRE DGEKAAKEVK LLLLGAGESG KNTIVKQMKI IHEDGYSEDE CKQYKVVVYS NTIQSIIAII RAMGRLKID FGEAARADDA RQLFVLAGSA EEGVMTPELA GVIKRLWRDG GVQACFSRSR EYQLNDSASY YLNDLDRISQ S NYIPTQQD VLRTRVKTTG IVETHFTFKD LYFKMFDVGA QRSERKKWIH CFEGVTAIIF CVALSDYDLV LAEDEEMNRM HA SMKLFDS ICNNKWFTET SIILFLNKKD LFEEKIKRSP LTICYPEYTG SNTYEEAAAY IQCQFEDLNR RKDTKEIYTH FTC STDTKN VQFVFDAVTD VIIKNNLKEC GLY

UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-3

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Macromolecule #5: Probable G-protein coupled receptor 156

MacromoleculeName: Probable G-protein coupled receptor 156 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.083629 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: RPLHDLCKTT ITSSHHSSKT ISSLSPVLLG IVWTFLSCGL LLILFFLAFT IHCRKNRIVK MSSPNLNIVT LLGSCLTYSS AYLFGIQDV LVGSSMETLI QTRLSMLCIG TSLVFGPILG KSWRLYKVFT QRVPDKRVII KDLQLLGLVA ALLMADVILL M TWVLTDPI ...String:
RPLHDLCKTT ITSSHHSSKT ISSLSPVLLG IVWTFLSCGL LLILFFLAFT IHCRKNRIVK MSSPNLNIVT LLGSCLTYSS AYLFGIQDV LVGSSMETLI QTRLSMLCIG TSLVFGPILG KSWRLYKVFT QRVPDKRVII KDLQLLGLVA ALLMADVILL M TWVLTDPI QCLQILSVSM TVTGKDVSCT STSTHFCASR YSDVWIALIW GCKGLLLLYG AYLAGLTGHV SSPPVNQSLT IM VGVNLLV LAAGLLFVVT RYLHSWPNLV FGLTSGGIFV CTTTINCFIF IPQLKQWKAF EEENQTIRRM AKYFSTPNKS

UniProtKB: Probable G-protein coupled receptor 156

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Macromolecule #6: (21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24l...

MacromoleculeName: (21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate
type: ligand / ID: 6 / Number of copies: 4 / Formula: MW9
Molecular weightTheoretical: 777.06 Da
Chemical component information

ChemComp-MW9:
(21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate

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Macromolecule #7: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 7 / Number of copies: 11 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1153971
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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