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- EMDB-17756: Structure of the murine trace amine-associated receptor TAAR7f bo... -

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Entry
Database: EMDB / ID: EMD-17756
TitleStructure of the murine trace amine-associated receptor TAAR7f bound to N,N-dimethylcyclohexylamine (DMCH) in complex with mini-Gs trimeric G protein
Map dataConsensus map of the mTAAR7f receptor bound to NDMCH in complex with miniGs trimer
Sample
  • Complex: A complex of mouse trace-amine associated receptor 7f solubilized in LMNG/CHS bound to N,N-dimethylcyclohexylamine and coupled to: Engineered guanine nucleotide-binding protein G(s) subunit alpha isoform short + 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 + Nanobody 35
    • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • 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: Nanobody 35Single-domain antibody
    • Protein or peptide: Trace amine-associated receptor 7f
  • Ligand: ~{N},~{N}-dimethylcyclohexanamine
  • Ligand: CHOLESTEROL HEMISUCCINATE
Keywordstrace-amine associated receptor / TAAR / mTAAR7f / GPCR / receptor / G protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


trace-amine receptor activity / sensory perception of chemical stimulus / 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 activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels ...trace-amine receptor activity / sensory perception of chemical stimulus / 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 activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / sensory perception of taste / GPER1 signaling / G-protein beta-subunit binding / heterotrimeric G-protein complex / Inactivation, recovery and regulation of the phototransduction cascade / extracellular vesicle / G alpha (12/13) signalling events / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / GTPase binding / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding / signal transduction / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Trace amine associated receptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / 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 ...Trace amine associated receptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / 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. / 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 / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
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 / Trace amine-associated receptor 7f
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsGusach A / Lee Y / Edwards PC / Huang F / Weyand SN / Tate CG
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105197215 United Kingdom
CitationJournal: bioRxiv / Year: 2023
Title: Molecular recognition of an aversive odorant by the murine trace amine-associated receptor TAAR7f.
Authors: Anastasiia Gusach / Yang Lee / Armin Nikpour Khoshgrudi / Elizaveta Mukhaleva / Ning Ma / Eline J Koers / Qingchao Chen / Patricia C Edwards / Fanglu Huang / Jonathan Kim / Filippo Mancia / ...Authors: Anastasiia Gusach / Yang Lee / Armin Nikpour Khoshgrudi / Elizaveta Mukhaleva / Ning Ma / Eline J Koers / Qingchao Chen / Patricia C Edwards / Fanglu Huang / Jonathan Kim / Filippo Mancia / Dmitry B Verprintsev / Nagarajan Vaidehi / Simone N Weyand / Christopher G Tate /
Abstract: There are two main families of G protein-coupled receptors that detect odours in humans, the odorant receptors (ORs) and the trace amine-associated receptors (TAARs). Their amino acid sequences are ...There are two main families of G protein-coupled receptors that detect odours in humans, the odorant receptors (ORs) and the trace amine-associated receptors (TAARs). Their amino acid sequences are distinct, with the TAARs being most similar to the aminergic receptors such as those activated by adrenaline, serotonin and histamine. To elucidate the structural determinants of ligand recognition by TAARs, we have determined the cryo-EM structure of a murine receptor, mTAAR7f, coupled to the heterotrimeric G protein G and bound to the odorant N,N-dimethylcyclohexylamine (DMCH) to an overall resolution of 2.9 Å. DMCH is bound in a hydrophobic orthosteric binding site primarily through van der Waals interactions and a strong charge-charge interaction between the tertiary amine of the ligand and an aspartic acid residue. This site is distinct and non-overlapping with the binding site for the odorant propionate in the odorant receptor OR51E2. The structure, in combination with mutagenesis data and molecular dynamics simulations suggests that the activation of the receptor follows a similar pathway to that of the β-adrenoceptors, with the significant difference that DMCH interacts directly with one of the main activation microswitch residues.
History
DepositionJun 28, 2023-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateAug 9, 2023-
Current statusAug 9, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17756.png

Downloads & links

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Map

FileDownload / File: emd_17756.map.gz / Format: CCP4 / Size: 196.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map of the mTAAR7f receptor bound to NDMCH in complex with miniGs trimer
Voxel sizeX=Y=Z: 0.824 Å
Density
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.020913893 - 0.8474175
Average (Standard dev.)0.0003119182 (±0.0126297595)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions372372372
Spacing372372372
CellA=B=C: 306.528 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17756_msk_1.map
Projections & Slices
AxesZYX

Projections

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Mask #2

Fileemd_17756_msk_2.map
Projections & Slices
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Additional map: Receptor-focused map

Fileemd_17756_additional_1.map
AnnotationReceptor-focused map
Projections & Slices
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Half map: #2

Fileemd_17756_half_map_1.map
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Half map: #1

Fileemd_17756_half_map_2.map
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Sample components

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Entire : A complex of mouse trace-amine associated receptor 7f solubilized...

EntireName: A complex of mouse trace-amine associated receptor 7f solubilized in LMNG/CHS bound to N,N-dimethylcyclohexylamine and coupled to: Engineered guanine nucleotide-binding protein G(s) subunit ...Name: A complex of mouse trace-amine associated receptor 7f solubilized in LMNG/CHS bound to N,N-dimethylcyclohexylamine and coupled to: Engineered guanine nucleotide-binding protein G(s) subunit alpha isoform short + 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 + Nanobody 35
Components
  • Complex: A complex of mouse trace-amine associated receptor 7f solubilized in LMNG/CHS bound to N,N-dimethylcyclohexylamine and coupled to: Engineered guanine nucleotide-binding protein G(s) subunit alpha isoform short + 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 + Nanobody 35
    • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • 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: Nanobody 35Single-domain antibody
    • Protein or peptide: Trace amine-associated receptor 7f
  • Ligand: ~{N},~{N}-dimethylcyclohexanamine
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: A complex of mouse trace-amine associated receptor 7f solubilized...

SupramoleculeName: A complex of mouse trace-amine associated receptor 7f solubilized in LMNG/CHS bound to N,N-dimethylcyclohexylamine and coupled to: Engineered guanine nucleotide-binding protein G(s) subunit ...Name: A complex of mouse trace-amine associated receptor 7f solubilized in LMNG/CHS bound to N,N-dimethylcyclohexylamine and coupled to: Engineered guanine nucleotide-binding protein G(s) subunit alpha isoform short + 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 + Nanobody 35
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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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: 28.964734 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: GNSKTEDQRN EEKAQREANK KIEKQLQKDK QVYRATHRLL LLGADNSGKS TIVKQMRILH GGSGGSGGTS GIFETKFQVD KVNFHMFDV GGQRDERRKW IQCFNDVTAI IFVVDSSDYN RLQEALNLFK SIWNNRWLRT ISVILFLNKQ DLLAEKVLAG K SKLEDYFP ...String:
GNSKTEDQRN EEKAQREANK KIEKQLQKDK QVYRATHRLL LLGADNSGKS TIVKQMRILH GGSGGSGGTS GIFETKFQVD KVNFHMFDV GGQRDERRKW IQCFNDVTAI IFVVDSSDYN RLQEALNLFK SIWNNRWLRT ISVILFLNKQ DLLAEKVLAG K SKLEDYFP EFARYTTPED ATPEPGEDPR VTRAKYFIRD EFLRISTASG DGRHYCYPHF TCAVDTENAR RIFNDCRDII QR MHLRQYE LL

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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: 37.342785 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String:
GSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD INAICFFPNG NA FATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAGHDNRVSC LGV TDDGMA VATGSWDSFL KIWN

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 / Details: There is an engineered mutation C68S introduced / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.845078 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFSAI L

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

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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: Lama glama (llama)
Molecular weightTheoretical: 16.926076 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MKYLLPTAAA GLLLLAAQPA MAQVQLQESG GGLVQPGGSL RLSCAASGFT FSNYKMNWVR QAPGKGLEWV SDISQSGASI SYTGSVKGR FTISRDNAKN TLYLQMNSLK PEDTAVYYCA RCPAPFTRDC FDVTSTTYAY RGQGTQVTVS SHHHHHH

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Macromolecule #5: Trace amine-associated receptor 7f

MacromoleculeName: Trace amine-associated receptor 7f / type: protein_or_peptide / ID: 5
Details: mTAAR7f sequence contains cleaved protease sites: TEV (S residue on the N terminus) and HRV-3C (C terminus)
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 41.012539 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SMSIADETVS WNQDSILSRD LFSATSAELC YENLNRSCVR SPYSPGPRLI LYAVFGFGAV LAVCGNLLVM TSILHFRQLH SPANFLVAS LACADFLVGV MVMPFSMVRS VEGCWYFGDS YCKLHTCFDV SFCYCSLFHL CFISVDRYIA VSDPLAYPTR F TASVSGKC ...String:
SMSIADETVS WNQDSILSRD LFSATSAELC YENLNRSCVR SPYSPGPRLI LYAVFGFGAV LAVCGNLLVM TSILHFRQLH SPANFLVAS LACADFLVGV MVMPFSMVRS VEGCWYFGDS YCKLHTCFDV SFCYCSLFHL CFISVDRYIA VSDPLAYPTR F TASVSGKC ITFSWLLSIS YGFSLIYTGA SEAGLEDLVS SLTCVGGCQI AVNQTWVFIN FSVFLIPTLV MITVYSKIFL IA KQQAQNI EKMSKQTARA SDSYKDRVAK RERKAAKTLG IAVAAFLLSW LPYFIDSFID AFLGFITPTY VYEILVWIVY YNS AMNPLI YAFFYPWFRK AIKLTVTGKI LRENSSTTNL FSELEVLFQ

UniProtKB: Trace amine-associated receptor 7f

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Macromolecule #6: ~{N},~{N}-dimethylcyclohexanamine

MacromoleculeName: ~{N},~{N}-dimethylcyclohexanamine / type: ligand / ID: 6 / Number of copies: 1 / Formula: 8IA
Molecular weightTheoretical: 127.227 Da
Chemical component information

ChemComp-8IA:
~{N},~{N}-dimethylcyclohexanamine

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Macromolecule #7: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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

Concentration0.8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H17KN2O4SHEPES/KOH
150.0 mMKCLPotassium chloride
10.0 mMNaClSodium chlorideSodium chloride
10.0 mMMgCl2Magnesium chloride
0.01 %Lauryl Maltose Neopentyl Glycol
0.002 %Cholesteryl Hemisuccinate
6.7 mMN,N-dimethylcyclohexylamine
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: OTHER
Details: Forward Power of 38 W, Reflected Power of 2W; Fischione
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.4 µm / Calibrated defocus min: 2.4 µm / Calibrated magnification: 96000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 0.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 11157 / Average exposure time: 7.84 sec. / Average electron dose: 55.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 9199357 / Details: Particles were heavily over-picked
Startup modelType of model: OTHER / Details: Ab-initio generated by cryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1+patch23011029)
Final 3D classificationNumber classes: 40 / Avg.num./class: 5000 / Software - Name: cryoSPARC (ver. 4.1.1+patch23011029) / Details: Followed by heterogenous refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1+patch23011029)
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1+patch23011029) / Number images used: 172639
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other
Details: Initial models of heterotrimeric mini-Gs and Nb35 were sourced from PDB 7T9I. A de novo model of TAAR7f was generated from the focused map and protein sequence using ModelAngelo
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8pm2:
Structure of the murine trace amine-associated receptor TAAR7f bound to N,N-dimethylcyclohexylamine (DMCH) in complex with mini-Gs trimeric G protein

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