[English] 日本語
Yorodumi
- EMDB-23118: Orexin Receptor 2 (OX2R) in Complex with G Protein and Natural Pe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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
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 / Orexin and neuropeptides FF and QRFP bind to their respective receptors / positive regulation of transmission of nerve impulse / neuropeptide receptor activity / regulation of neurotransmitter secretion ...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 / Orexin and neuropeptides FF and QRFP bind to their respective receptors / positive regulation of transmission of nerve impulse / neuropeptide receptor activity / regulation of neurotransmitter secretion / neuropeptide hormone activity / sleep / positive regulation of calcium ion transport / : / feeding behavior / locomotion / temperature homeostasis / eating behavior / negative regulation of DNA replication / response to starvation / negative regulation of potassium ion transport / peptide hormone binding / neuropeptide signaling pathway / rough endoplasmic reticulum / cellular response to hormone stimulus / regulation of cytosolic calcium ion concentration / excitatory postsynaptic potential / secretory granule / peptide 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 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 / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / 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 / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / synaptic vesicle / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / phospholipase C-activating G protein-coupled receptor signaling pathway / Ca2+ pathway / positive regulation of cold-induced thermogenesis / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / postsynapse / G alpha (q) signalling events / chemical synaptic transmission / cell population proliferation / Ras protein signal transduction / Extra-nuclear estrogen signaling / 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 / 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. / GGL 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. / 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. / 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
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 / Zamlynny B / Tummala S / Xiao L / Shipman JM / Partridge AT / Minnick C / Breslin MJ / Rudd MT ...Hong C / Byrne NJ / Zamlynny B / Tummala S / Xiao L / Shipman JM / Partridge AT / Minnick C / Breslin MJ / Rudd MT / Stachel SJ / Rada VL / Kern JC / Armacost KA / Hollingsworth SA / O'Brien JA / Hall DL / McDonald TP / Strickland C / Brooun A / Soisson SM / Hollenstein K
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-
UpdateFeb 17, 2021-
Current statusFeb 17, 2021Processing site: RCSB / Status: Released

-
Structure visualization

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

emd_23118.png

Downloads & links

-
Map

FileDownload / File: emd_23118.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.84 Å
Density
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

-
Supplemental data

-
Sample components

-
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

-
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)

-
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

-
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

-
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

-
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

-
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

-
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)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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: 20.0 nm / Pretreatment - Type: GLOW DISCHARGE / 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

-
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 / Digitization - Sampling interval: 5.0 µm / 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

+
Image processing

Particle selectionNumber selected: 14000000
CTF correctionSoftware - Name: cryoSPARC (ver. 2.15)
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

-
Atomic model buiding 1

Initial model
PDB IDChainDetails

7l1v

chain_id: Achain A

7l1v

chain_id: Bchain B

7l1v

chain_id: Cchain C

7l1v

chain_id: Hchain H

7l1v

chain_id: Rchain 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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more