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- EMDB-23118: Orexin Receptor 2 (OX2R) in Complex with G Protein and Natural Pe... -

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Entry
Database: EMDB / ID: EMD-23118
TitleOrexin Receptor 2 (OX2R) in Complex with G Protein and Natural Peptide-Agonist Orexin B (OxB)
Map data
Sample
  • Complex: Orexin Receptor 2 (OX2R) in Complex with G Protein and Natural Peptide-Agonist Orexin B (OxB)
    • Protein or peptide: Engineered Guanine nucleotide-binding protein 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
    • Protein or peptide: single-chain antibody Fv fragment (svFv16)
    • Protein or peptide: Hypocretin receptor type 2
  • Protein or peptide: Orexin
KeywordsClass A GPCR / Orexin receptor 2 / OX2R / membrane protein / Peptide agonist
Function / homology
Function and homology information


type 1 orexin receptor binding / type 2 orexin receptor binding / regulation of circadian sleep/wake cycle, wakefulness / circadian sleep/wake cycle process / orexin receptor activity / negative regulation of transmission of nerve impulse / positive regulation of transmission of nerve impulse / Orexin and neuropeptides FF and QRFP bind to their respective receptors / neuronal dense core vesicle lumen / neuropeptide receptor activity ...type 1 orexin receptor binding / type 2 orexin receptor binding / regulation of circadian sleep/wake cycle, wakefulness / circadian sleep/wake cycle process / orexin receptor activity / negative regulation of transmission of nerve impulse / positive regulation of transmission of nerve impulse / Orexin and neuropeptides FF and QRFP bind to their respective receptors / neuronal dense core vesicle lumen / neuropeptide receptor activity / regulation of neurotransmitter secretion / neuropeptide hormone activity / positive regulation of calcium ion transport / sleep / locomotion / feeding behavior / response to alcohol / eating behavior / temperature homeostasis / response to starvation / negative regulation of DNA replication / negative regulation of potassium ion transport / peptide hormone binding / neuropeptide signaling pathway / regulation of cytosolic calcium ion concentration / cellular response to hormone stimulus / rough endoplasmic reticulum / excitatory postsynaptic potential / 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 / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / 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 / photoreceptor disc membrane / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / synaptic vesicle / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / 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) / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / positive regulation of cytosolic calcium ion concentration / 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 / G alpha (q) signalling events / chemical synaptic transmission / Ras protein signal transduction / Extra-nuclear estrogen signaling / cell population proliferation / postsynapse / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding / perinuclear region of cytoplasm / signal transduction / extracellular exosome / extracellular region / nucleoplasm / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Prepro-orexin / Prepro-orexin / Orexin receptor 2 / Orexin receptor type 2 / Orexin receptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily ...Prepro-orexin / Prepro-orexin / Orexin receptor 2 / Orexin receptor type 2 / Orexin receptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / 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
Similarity search - Domain/homology
Hypocretin neuropeptide precursor / Orexin receptor type 2 / 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 / Orexin receptor type 2
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHong C / Byrne NJ
CitationJournal: Nat Commun / Year: 2021
Title: Structures of active-state orexin receptor 2 rationalize peptide and small-molecule agonist recognition and receptor activation.
Authors: Chuan Hong / Noel J Byrne / Beata Zamlynny / Srivanya Tummala / Li Xiao / Jennifer M Shipman / Andrea T Partridge / Christina Minnick / Michael J Breslin / Michael T Rudd / Shawn J Stachel / ...Authors: Chuan Hong / Noel J Byrne / Beata Zamlynny / Srivanya Tummala / Li Xiao / Jennifer M Shipman / Andrea T Partridge / Christina Minnick / Michael J Breslin / Michael T Rudd / Shawn J Stachel / Vanessa L Rada / Jeffrey C Kern / Kira A Armacost / Scott A Hollingsworth / Julie A O'Brien / Dawn L Hall / Terrence P McDonald / Corey Strickland / Alexei Brooun / Stephen M Soisson / Kaspar Hollenstein /
Abstract: Narcolepsy type 1 (NT1) is a chronic neurological disorder that impairs the brain's ability to control sleep-wake cycles. Current therapies are limited to the management of symptoms with modest ...Narcolepsy type 1 (NT1) is a chronic neurological disorder that impairs the brain's ability to control sleep-wake cycles. Current therapies are limited to the management of symptoms with modest effectiveness and substantial adverse effects. Agonists of the orexin receptor 2 (OXR) have shown promise as novel therapeutics that directly target the pathophysiology of the disease. However, identification of drug-like OXR agonists has proven difficult. Here we report cryo-electron microscopy structures of active-state OXR bound to an endogenous peptide agonist and a small-molecule agonist. The extended carboxy-terminal segment of the peptide reaches into the core of OXR to stabilize an active conformation, while the small-molecule agonist binds deep inside the orthosteric pocket, making similar key interactions. Comparison with antagonist-bound OXR suggests a molecular mechanism that rationalizes both receptor activation and inhibition. Our results enable structure-based discovery of therapeutic orexin agonists for the treatment of NT1 and other hypersomnia disorders.
History
DepositionDec 15, 2020-
Header (metadata) releaseFeb 10, 2021-
Map releaseFeb 10, 2021-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7l1u
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23118.png

Downloads & links

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Map

FileDownload / File: emd_23118.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 300 pix.
= 252. Å		0.84 Å/pix.
x 300 pix.
= 252. Å		0.84 Å/pix.
x 300 pix.
= 252. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1226 / Movie #1: 0.16
Minimum - Maximum-0.7858491 - 1.2577966
Average (Standard dev.)0.0014255107 (±0.025900263)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 251.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.840.840.84
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z252.000252.000252.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.7861.2580.001

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Supplemental data

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Sample components

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Entire : Orexin Receptor 2 (OX2R) in Complex with G Protein and Natural Pe...

EntireName: Orexin Receptor 2 (OX2R) in Complex with G Protein and Natural Peptide-Agonist Orexin B (OxB)
Components
  • Complex: Orexin Receptor 2 (OX2R) in Complex with G Protein and Natural Peptide-Agonist Orexin B (OxB)
    • Protein or peptide: Engineered Guanine nucleotide-binding protein 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
    • Protein or peptide: single-chain antibody Fv fragment (svFv16)
    • Protein or peptide: Hypocretin receptor type 2
  • Protein or peptide: Orexin

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Supramolecule #1: Orexin Receptor 2 (OX2R) in Complex with G Protein and Natural Pe...

SupramoleculeName: Orexin Receptor 2 (OX2R) in Complex with G Protein and Natural Peptide-Agonist Orexin B (OxB)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Engineered Guanine nucleotide-binding protein subunit alpha

MacromoleculeName: Engineered Guanine nucleotide-binding protein subunit alpha
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.040881 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GTLSAEDKAA VERSKMIEKQ LQKDKQVYRR TLRLLLLGAD NSGKSTIVKQ MRILHGGSGG SGGTSGIFET KFQVDKVNFH MFDVGGQRD ERRKWIQCFN DVTAIIFVVD SSDYNRLQEA LNDFKSIWNN RWLRTISVIL FLNKQDLLAE KVLAGKSKIE D YFPEFARY ...String:
GTLSAEDKAA VERSKMIEKQ LQKDKQVYRR TLRLLLLGAD NSGKSTIVKQ MRILHGGSGG SGGTSGIFET KFQVDKVNFH MFDVGGQRD ERRKWIQCFN DVTAIIFVVD SSDYNRLQEA LNDFKSIWNN RWLRTISVIL FLNKQDLLAE KVLAGKSKIE D YFPEFARY TTPEDATPEP GEDPRVTRAK YFIRKEFVDI STASGDGRHI CYPHFTCAVD TENARRIFND CKDIILQMNL RE YNLV

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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: 38.579148 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGHHHHHHHH SELDQLRQEA EQLKNQIRDA RKACADATLS QITNNIDPVG RIQMRTRRTL RGHLAKIYAM HWGTDSRLLV SASQDGKLI IWDSYTTNKV HAIPLRSSWV MTCAYAPSGN YVACGGLDNI CSIYNLKTRE GNVRVSRELA GHTGYLSCCR F LDDNQIVT ...String:
MGHHHHHHHH SELDQLRQEA EQLKNQIRDA RKACADATLS QITNNIDPVG RIQMRTRRTL RGHLAKIYAM HWGTDSRLLV SASQDGKLI IWDSYTTNKV HAIPLRSSWV MTCAYAPSGN YVACGGLDNI CSIYNLKTRE GNVRVSRELA GHTGYLSCCR F LDDNQIVT SSGDTTCALW DIETGQQTTT FTGHTGDVMS LSLAPDTRLF VSGACDASAK LWDVREGMCR QTFTGHESDI NA ICFFPNG NAFATGSDDA TCRLFDLRAD QELMTYSHDN IICGITSVSF SKSGRLLLAG YDDFNCNVWD ALKADRAGVL AGH DNRVSC LGVTDDGMAV ATGSWDSFLK IWN

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: 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: single-chain antibody Fv fragment (svFv16)

MacromoleculeName: single-chain antibody Fv fragment (svFv16) / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.610615 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSDVQLVESG GGLVQPGGSR KLSCSASGFA FSSFGMHWVR QAPEKGLEWV AYISSGSGTI YYADTVKGRF TISRDDPKNT LFLQMTSLR SEDTAMYYCV RSIYYYGSSP FDFWGQGTTL TVSSGGGGSG GGGSGGGGSD IVMTQATSSV PVTPGESVSI S CRSSKSLL ...String:
GSDVQLVESG GGLVQPGGSR KLSCSASGFA FSSFGMHWVR QAPEKGLEWV AYISSGSGTI YYADTVKGRF TISRDDPKNT LFLQMTSLR SEDTAMYYCV RSIYYYGSSP FDFWGQGTTL TVSSGGGGSG GGGSGGGGSD IVMTQATSSV PVTPGESVSI S CRSSKSLL HSNGNTYLYW FLQRPGQSPQ LLIYRMSNLA SGVPDRFSGS GSGTAFTLTI SRLEAEDVGV YYCMQHLEYP LT FGAGTKL ELK

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Macromolecule #5: Hypocretin receptor type 2

MacromoleculeName: Hypocretin receptor type 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.470875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDAMGT KLEDSPPCRN WSSASELNET QEPFLNPTDY DDEEFLRYLW REYLHPKEYE WVLIAGYIIV FVVALIGNVL VCVAVWKNH HMRTVTNYFI VNLSLADVLV TITCLPATLV VDITETWFFG QSLCKVIPYL QTVSVSVSVL TLSCIALDRW Y AICHPLMF ...String:
DYKDDDAMGT KLEDSPPCRN WSSASELNET QEPFLNPTDY DDEEFLRYLW REYLHPKEYE WVLIAGYIIV FVVALIGNVL VCVAVWKNH HMRTVTNYFI VNLSLADVLV TITCLPATLV VDITETWFFG QSLCKVIPYL QTVSVSVSVL TLSCIALDRW Y AICHPLMF KSTAKRARNS IVIIWIVSCI IMIPQAIVME CSTVFPGLAN KTTLFTVCDE RWGGEIYPKM YHICFFLVTY MA PLCLMVL AYLQIFRKLW CRQIPGTSSE IKQIRARRKT ARMLMVVLLV FAICYLPISI LNVLKRVFGM FAHTEDRETV YAW FTFSHW LVYANSAANP IIYNFLSGKF REEFKAAFSC CCLGVHHRHH HHHHHHHH

UniProtKB: Orexin receptor type 2

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Macromolecule #6: Orexin

MacromoleculeName: Orexin / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.902364 KDa
SequenceString:
RSGPPGLQGR LQRLLQASGN HAAGILTM(NH2)

UniProtKB: Hypocretin neuropeptide precursor

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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

Concentration5 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
25.0 mMTrisTris
50.0 mMNH4OAcAmmonium acetate
0.02 percentDDMDDM
0.002 percentCHSCHS
0.5 mMEDTAEDTA
GridModel: C-flat / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa / Details: Carbon side facing up
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 83.0 K / Max: 93.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5700 pixel / Digitization - Dimensions - Height: 4100 pixel / Number grids imaged: 3 / Number real images: 38810 / Average exposure time: 0.05 sec. / Average electron dose: 1.0625 e/Å2 / Details: 40 frames with total 2second exposure
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.2 µm / Calibrated defocus min: 0.6 µm / Calibrated magnification: 59524 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
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

Particle selectionNumber selected: 14000000
Startup modelType of model: OTHER / Details: Ab initio in cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Details: Gold standard and masking effect correction / Number images used: 800000
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.15) / Details: Ab initio in cryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.15) / Details: cryoSPARC
Final 3D classificationNumber classes: 1 / Avg.num./class: 800000 / Software - Name: cryoSPARC (ver. 2.15) / Details: One good class from 3D classification

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Atomic model buiding 1

Initial model
PDB IDChainDetails

7l1v

chain_id: A, source_name: PDB, initial_model_type: experimental modelchain A

7l1v

chain_id: B, source_name: PDB, initial_model_type: experimental modelchain B

7l1v

chain_id: C, source_name: PDB, initial_model_type: experimental modelchain C

7l1v

chain_id: H, source_name: PDB, initial_model_type: experimental modelchain H

7l1v

chain_id: R, source_name: PDB, initial_model_type: experimental modelchain R
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 131 / Target criteria: Correlation
Output model

PDB-7l1u:
Orexin Receptor 2 (OX2R) in Complex with G Protein and Natural Peptide-Agonist Orexin B (OxB)

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