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- EMDB-16824: Cryo-EM structure of a pre-dimerized human IL-23 complete extrace... -

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Entry
Database: EMDB / ID: EMD-16824
TitleCryo-EM structure of a pre-dimerized human IL-23 complete extracellular signaling complex.
Map dataMain map: Unfiltered, non-sharpened map of the human IL23:IL12Rbeta1-DAPK1:IL23R-Calmodulin complex used for model refinement in Phenix. Additional map: deepEMhancer sharpened map.
Sample
  • Complex: Human IL-23 in complex with hIL-12Rbeta1-DAPK1 and hIL-23R-Calmodulin.
    • Protein or peptide: Interleukin-12 subunit beta
    • Protein or peptide: Interleukin-23 subunit alpha
    • Protein or peptide: Interleukin-23 receptor,Calmodulin-1
    • Protein or peptide: Interleukin-12 receptor subunit beta-1,Death-associated protein kinase 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsComplex / Cytokine / Receptor / SIGNALING PROTEIN
Function / homology
Function and homology information


late endosome lumen / interleukin-23-mediated signaling pathway / regulation of tyrosine phosphorylation of STAT protein / interleukin-23 receptor binding / interleukin-27 receptor activity / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of natural killer cell activation ...late endosome lumen / interleukin-23-mediated signaling pathway / regulation of tyrosine phosphorylation of STAT protein / interleukin-23 receptor binding / interleukin-27 receptor activity / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of natural killer cell activation / positive regulation of lymphocyte proliferation / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of tissue remodeling / cellular response to hydroperoxide / positive regulation of activation of Janus kinase activity / tissue remodeling / sexual reproduction / positive regulation of T-helper 1 type immune response / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / positive regulation of NK T cell activation / positive regulation of smooth muscle cell apoptotic process / positive regulation of mononuclear cell proliferation / interleukin-12 receptor binding / positive regulation of memory T cell differentiation / interleukin-12 receptor complex / natural killer cell activation / T-helper cell differentiation / interleukin-23 receptor complex / defense response to tumor cell / positive regulation of osteoclast differentiation / Interleukin-23 signaling / Caspase activation via Dependence Receptors in the absence of ligand / negative regulation of interleukin-17 production / positive regulation of T-helper 17 type immune response / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / positive regulation of neutrophil chemotaxis / Interleukin-12 signaling / response to UV-B / regulation of NMDA receptor activity / CaM pathway / Cam-PDE 1 activation / positive regulation of natural killer cell proliferation / positive regulation of granulocyte macrophage colony-stimulating factor production / Sodium/Calcium exchangers / syntaxin-1 binding / Calmodulin induced events / Reduction of cytosolic Ca++ levels / calcium/calmodulin-dependent protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / cytokine receptor activity / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / T-helper 1 type immune response / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / Activation of RAC1 downstream of NMDARs / negative regulation of interleukin-10 production / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / positive regulation of activated T cell proliferation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / defense response to protozoan / response to type II interferon / Phase 0 - rapid depolarisation / positive regulation of interleukin-17 production / cytokine binding / protein phosphatase activator activity / RHO GTPases activate PAKs / Interleukin-10 signaling / positive regulation of phosphoprotein phosphatase activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / Ion transport by P-type ATPases / Long-term potentiation / positive regulation of interleukin-10 production / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / positive regulation of cell adhesion / DARPP-32 events / detection of calcium ion / extrinsic apoptotic signaling pathway via death domain receptors
Similarity search - Function
Interleukin-23 alpha / Interleukin 23 subunit alpha / Interleukin-12 beta / Interleukin-12 beta, central domain / Cytokine interleukin-12p40 C-terminus / Death-associated protein kinase 1 / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. ...Interleukin-23 alpha / Interleukin 23 subunit alpha / Interleukin-12 beta / Interleukin-12 beta, central domain / Cytokine interleukin-12p40 C-terminus / Death-associated protein kinase 1 / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / Roc domain profile. / Roc domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Four-helical cytokine-like, core / Death-like domain superfamily / Ankyrin repeat / Fibronectin type III domain / Fibronectin type 3 domain / EF-hand domain pair / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Ankyrin repeats (3 copies) / Fibronectin type-III domain profile. / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Fibronectin type III / Ankyrin repeat / Fibronectin type III superfamily / Ankyrin repeat-containing domain superfamily / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Ig-like domain profile. / Immunoglobulin-like domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Immunoglobulin-like domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Calmodulin-1 / Interleukin-12 subunit beta / Interleukin-12 receptor subunit beta-1 / Death-associated protein kinase 1 / Interleukin-23 receptor / Interleukin-23 subunit alpha
Similarity search - Component
Biological speciesMus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBloch Y / Felix J / Savvides SN
Funding support Belgium, 2 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)12S0519N Belgium
Research Foundation - Flanders (FWO)G0B4918N Belgium
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structures of complete extracellular receptor assemblies mediated by IL-12 and IL-23.
Authors: Yehudi Bloch / Jan Felix / Romain Merceron / Mathias Provost / Royan Alipour Symakani / Robin De Backer / Elisabeth Lambert / Ahmad R Mehdipour / Savvas N Savvides /
Abstract: Cell-surface receptor complexes mediated by pro-inflammatory interleukin (IL)-12 and IL-23, both validated therapeutic targets, are incompletely understood due to the lack of structural insights into ...Cell-surface receptor complexes mediated by pro-inflammatory interleukin (IL)-12 and IL-23, both validated therapeutic targets, are incompletely understood due to the lack of structural insights into their complete extracellular assemblies. Furthermore, there is a paucity of structural details describing the IL-12-receptor interaction interfaces, in contrast to IL-23-receptor complexes. Here we report structures of fully assembled mouse IL-12/human IL-23-receptor complexes comprising the complete extracellular segments of the cognate receptors determined by electron cryo-microscopy. The structures reveal key commonalities but also surprisingly diverse features. Most notably, whereas IL-12 and IL-23 both utilize a conspicuously presented aromatic residue on their α-subunit as a hotspot to interact with the N-terminal Ig domain of their high-affinity receptors, only IL-12 juxtaposes receptor domains proximal to the cell membrane. Collectively, our findings will help to complete our understanding of cytokine-mediated assemblies of tall cytokine receptors and will enable a cytokine-specific interrogation of IL-12/IL-23 signaling in physiology and disease.
History
DepositionMar 10, 2023-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16824.png

Downloads & links

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Map

FileDownload / File: emd_16824.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map: Unfiltered, non-sharpened map of the human IL23:IL12Rbeta1-DAPK1:IL23R-Calmodulin complex used for model refinement in Phenix. Additional map: deepEMhancer sharpened map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 320 pix.
= 314.08 Å		0.98 Å/pix.
x 320 pix.
= 314.08 Å		0.98 Å/pix.
x 320 pix.
= 314.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9815 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.21190277 - 0.52166134
Average (Standard dev.)0.00028738737 (±0.010982596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 314.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16824_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: DeepEMhancer sharpened map of the human IL23:IL12Rbeta1-DAPK1:IL23R-Calmodulin complex,...

Fileemd_16824_additional_1.map
AnnotationDeepEMhancer sharpened map of the human IL23:IL12Rbeta1-DAPK1:IL23R-Calmodulin complex, used for model building in Coot and visualization.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of the human IL23:IL12Rbeta1-DAPK1:IL23R-Calmodulin complex....

Fileemd_16824_half_map_1.map
AnnotationHalf map 2 of the human IL23:IL12Rbeta1-DAPK1:IL23R-Calmodulin complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of the human IL23:IL12Rbeta1-DAPK1:IL23R-Calmodulin complex....

Fileemd_16824_half_map_2.map
AnnotationHalf map 1 of the human IL23:IL12Rbeta1-DAPK1:IL23R-Calmodulin complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human IL-23 in complex with hIL-12Rbeta1-DAPK1 and hIL-23R-Calmodulin.

EntireName: Human IL-23 in complex with hIL-12Rbeta1-DAPK1 and hIL-23R-Calmodulin.
Components
  • Complex: Human IL-23 in complex with hIL-12Rbeta1-DAPK1 and hIL-23R-Calmodulin.
    • Protein or peptide: Interleukin-12 subunit beta
    • Protein or peptide: Interleukin-23 subunit alpha
    • Protein or peptide: Interleukin-23 receptor,Calmodulin-1
    • Protein or peptide: Interleukin-12 receptor subunit beta-1,Death-associated protein kinase 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Human IL-23 in complex with hIL-12Rbeta1-DAPK1 and hIL-23R-Calmodulin.

SupramoleculeName: Human IL-23 in complex with hIL-12Rbeta1-DAPK1 and hIL-23R-Calmodulin.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 168 KDa

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Macromolecule #1: Interleukin-12 subunit beta

MacromoleculeName: Interleukin-12 subunit beta / type: protein_or_peptide / ID: 1
Details: N-glycosylation mutant: Asparagine 303 (N303) is mutated to Aspartic acid (D303).
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.74093 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IWELKKDVYV VELDWYPDAP GEMVVLTCDT PEEDGITWTL DQSSEVLGSG KTLTIQVKEF GDAGQYTCHK GGEVLSHSLL LLHKKEDGI WSTDILKDQK EPKNKTFLRC EAKNYSGRFT CWWLTTISTD LTFSVKSSRG SSDPQGVTCG AATLSAERVR G DNKEYEYS ...String:
IWELKKDVYV VELDWYPDAP GEMVVLTCDT PEEDGITWTL DQSSEVLGSG KTLTIQVKEF GDAGQYTCHK GGEVLSHSLL LLHKKEDGI WSTDILKDQK EPKNKTFLRC EAKNYSGRFT CWWLTTISTD LTFSVKSSRG SSDPQGVTCG AATLSAERVR G DNKEYEYS VECQEDSACP AAEESLPIEV MVDAVHKLKY ENYTSSFFIR DIIKPDPPKN LQLKPLKNSR QVEVSWEYPD TW STPHSYF SLTFCVQVQG KSKREKKDRV FTDKTSATVI CRKDASISVR AQDRYYSSSW SEWASVPCS

UniProtKB: Interleukin-12 subunit beta

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Macromolecule #2: Interleukin-23 subunit alpha

MacromoleculeName: Interleukin-23 subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.650117 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
RAVPGGSSPA WTQCQQLSQK LCTLAWSAHP LVGHMDLREE GDEETTNDVP HIQCGDGCDP QGLRDNSQFC LQRIHQGLIF YEKLLGSDI FTGEPSLLPD SPVGQLHASL LGLSQLLQPE GHHWETQQIP SLSPSQPWQR LLLRFKILRS LQAFVAVAAR V FAHGAATL SPGDEVDGHH HHHHHHHH

UniProtKB: Interleukin-23 subunit alpha

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Macromolecule #3: Interleukin-23 receptor,Calmodulin-1

MacromoleculeName: Interleukin-23 receptor,Calmodulin-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.991391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GITNINCSGH IWVEPATIFK MGMNISIYCQ AAIKNCQPRK LHFYKNGIKE RFQITRINKT TARLWYKNFL EPHASMYCTA ECPKHFQET LICGKDISSG YPPDIPDEVT CVIYEYSGNM TCTWNAGKLT YIDTKYVVHV KSLETEEEQQ YLTSSYINIS T DSLQGGKK ...String:
GITNINCSGH IWVEPATIFK MGMNISIYCQ AAIKNCQPRK LHFYKNGIKE RFQITRINKT TARLWYKNFL EPHASMYCTA ECPKHFQET LICGKDISSG YPPDIPDEVT CVIYEYSGNM TCTWNAGKLT YIDTKYVVHV KSLETEEEQQ YLTSSYINIS T DSLQGGKK YLVWVQAANA LGMEESKQLQ IHLDDIVIPS AAVISRAETI NATVPKTIIY WDSQTTIEKV SCEMRYKATT NQ TWNVKEF DTNFTYVQQS EFYLEPNIKY VFQVRCQETG KRYWQPWSSL FFHKTPETVP QVTSKAFQHD TWNSGLTVAS IST GHLTSD NRGDGTGGSG GSGGLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTI DFPEF LTMMARKMKD TDSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQ MMTA K

UniProtKB: Interleukin-23 receptor, Calmodulin-1

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Macromolecule #4: Interleukin-12 receptor subunit beta-1,Death-associated protein k...

MacromoleculeName: Interleukin-12 receptor subunit beta-1,Death-associated protein kinase 1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.187316 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: CRTSECCFQD PPYPDADSGS ASGPRDLRCY RISSDRYECS WQYEGPTAGV SHFLRCCLSS GRCCYFAAGS ATRLQFSDQA GVSVLYTVT LWVESWARNQ TEKSPEVTLQ LYNSVKYEPP LGDIKVSKLA GQLRMEWETP DNQVGAEVQF RHRTPSSPWK L GDCGPQDD ...String:
CRTSECCFQD PPYPDADSGS ASGPRDLRCY RISSDRYECS WQYEGPTAGV SHFLRCCLSS GRCCYFAAGS ATRLQFSDQA GVSVLYTVT LWVESWARNQ TEKSPEVTLQ LYNSVKYEPP LGDIKVSKLA GQLRMEWETP DNQVGAEVQF RHRTPSSPWK L GDCGPQDD DTESCLCPLE MNVAQEFQLR RRQLGSQGSS WSKWSSPVCV PPENPPQPQV RFSVEQLGQD GRRRLTLKEQ PT QLELPEG CQGLAPGTEV TYRLQLHMLS CPCKAKATRT LHLGKMPYLS GAAYNVAVIS SNQFGPGLNQ TWHIPADTHT EPV ALNISV GTNGTTMYWP ARAQSMTYCI EWQPVGQDGG LATCSLTAPQ DPDPAGMATY SWSRESGAMG QEKCYYITIF ASAH PEKLT LWSTVLSTYH FGGNASAAGT PHHVSVKNHS LDSVSVDWAP SLLSTCPGVL KEYVVRCRDE DSKQVSEHPV QPTET QVTL SGLRAGVAYT VQVRADTAWL RGVWSQPQRF SIEGTGGSGG SGGAARKKWK QSVRLISLCQ RLS

UniProtKB: Interleukin-12 receptor subunit beta-1, Death-associated protein kinase 1

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
25.0 mMC8H18N2O4SHEPES
5.0 mMCaClcalcium chloride

Details: HEPES-buffered saline (HBS) with added calcium chloride: 25 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM CaCl
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA PLUNGER / Details: Leica EM GP2, 4.5 s. blotting time..

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 6660 / Average exposure time: 3.37 sec. / Average electron dose: 61.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 60000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 2053974
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 315005
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8oe4:
Cryo-EM structure of a pre-dimerized human IL-23 complete extracellular signaling complex.

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