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- EMDB-20308: Single Particle Reconstruction of Phosphatidylinositol (3,4,5) tr... -

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Entry
Database: EMDB / ID: EMD-20308
TitleSingle Particle Reconstruction of Phosphatidylinositol (3,4,5) trisphosphate-dependent Rac exchanger 1 bound to G protein beta gamma subunits
Map data
Sample
  • Complex: P-Rex1 bound to G protein beta gamma subunits
    • Complex: Phosphatidylinositol (3,4,5) trisphosphate-dependent Rac exchanger 1
      • Protein or peptide: Phosphatidylinositol (3,4,5) trisphosphate-dependent Rac exchanger 1
    • Complex: G protein beta-1 subunit
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Complex: G protein gamma-2 subunit
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
KeywordsRhoGEF / G protein / Complex / Phosphatase fold / SIGNALING PROTEIN
Function / homology
Function and homology information


regulation of signaling / regulation of dendrite development / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / neutrophil activation / regulation of actin filament polymerization / Activation of the phototransduction cascade / Activation of G protein gated Potassium channels / G-protein activation ...regulation of signaling / regulation of dendrite development / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / neutrophil activation / regulation of actin filament polymerization / Activation of the phototransduction cascade / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / Adrenaline,noradrenaline inhibits insulin secretion / 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 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / regulation of small GTPase mediated signal transduction / Extra-nuclear estrogen signaling / G alpha (z) signalling events / G alpha (s) signalling events / G alpha (q) signalling events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / RHOB GTPase cycle / NRAGE signals death through JNK / superoxide metabolic process / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOG GTPase cycle / T cell differentiation / RHOA GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / RAC1 GTPase cycle / actin filament polymerization / GTPase activator activity / guanyl-nucleotide exchange factor activity / neutrophil chemotaxis / dendritic shaft / phospholipid binding / photoreceptor disc membrane / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / sensory perception of taste / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / signaling receptor complex adaptor activity / retina development in camera-type eye / GTPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / growth cone / cell population proliferation / intracellular signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / GTPase activity / protein-containing complex binding / perinuclear region of cytoplasm / enzyme binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain ...Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / 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 / PH-like domain superfamily / G-protein beta WD-40 repeat / Winged helix DNA-binding domain superfamily / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
PREX1 / 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 / Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human) / Bos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsCash JN / Cianfrocco MA
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA221289 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL122416 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL071818 United States
CitationJournal: Sci Adv / Year: 2019
Title: Cryo-electron microscopy structure and analysis of the P-Rex1-Gβγ signaling scaffold.
Authors: Jennifer N Cash / Sarah Urata / Sheng Li / Sandeep K Ravala / Larisa V Avramova / Michael D Shost / J Silvio Gutkind / John J G Tesmer / Michael A Cianfrocco /
Abstract: PIP-dependent Rac exchanger 1 (P-Rex1) is activated downstream of G protein-coupled receptors to promote neutrophil migration and metastasis. The structure of more than half of the enzyme and its ...PIP-dependent Rac exchanger 1 (P-Rex1) is activated downstream of G protein-coupled receptors to promote neutrophil migration and metastasis. The structure of more than half of the enzyme and its regulatory G protein binding site are unknown. Our 3.2 Å cryo-EM structure of the P-Rex1-Gβγ complex reveals that the carboxyl-terminal half of P-Rex1 adopts a complex fold most similar to those of phosphoinositide phosphatases. Although catalytically inert, the domain coalesces with a DEP domain and two PDZ domains to form an extensive docking site for Gβγ. Hydrogen-deuterium exchange mass spectrometry suggests that Gβγ binding induces allosteric changes in P-Rex1, but functional assays indicate that membrane localization is also required for full activation. Thus, a multidomain assembly is key to the regulation of P-Rex1 by Gβγ and the formation of a membrane-localized scaffold optimized for recruitment of other signaling proteins such as PKA and PTEN.
History
DepositionJun 18, 2019-
Header (metadata) releaseJul 3, 2019-
Map releaseOct 23, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0361
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0361
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pcv
  • Surface level: 0.0361
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20308.png

Downloads & links

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Map

FileDownload / File: emd_20308.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.0361 / Movie #1: 0.0361
Minimum - Maximum-0.23757373 - 0.9838253
Average (Standard dev.)0.0003407711 (±0.008663468)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 300.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z300.000300.000300.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.2380.9840.000

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Supplemental data

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Mask #1

Fileemd_20308_msk_1.map
Projections & Slices
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Additional map: Sharpened map

Fileemd_20308_additional_1.map
AnnotationSharpened map
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Additional map: Unsharpened map

Fileemd_20308_additional_2.map
AnnotationUnsharpened map
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Half map: #2

Fileemd_20308_half_map_1.map
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Half map: #1

Fileemd_20308_half_map_2.map
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Sample components

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Entire : P-Rex1 bound to G protein beta gamma subunits

EntireName: P-Rex1 bound to G protein beta gamma subunits
Components
  • Complex: P-Rex1 bound to G protein beta gamma subunits
    • Complex: Phosphatidylinositol (3,4,5) trisphosphate-dependent Rac exchanger 1
      • Protein or peptide: Phosphatidylinositol (3,4,5) trisphosphate-dependent Rac exchanger 1
    • Complex: G protein beta-1 subunit
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Complex: G protein gamma-2 subunit
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Supramolecule #1: P-Rex1 bound to G protein beta gamma subunits

SupramoleculeName: P-Rex1 bound to G protein beta gamma subunits / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9 KDa

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Supramolecule #2: Phosphatidylinositol (3,4,5) trisphosphate-dependent Rac exchanger 1

SupramoleculeName: Phosphatidylinositol (3,4,5) trisphosphate-dependent Rac exchanger 1
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

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Supramolecule #3: G protein beta-1 subunit

SupramoleculeName: G protein beta-1 subunit / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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Supramolecule #4: G protein gamma-2 subunit

SupramoleculeName: G protein gamma-2 subunit / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3

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Macromolecule #1: Phosphatidylinositol (3,4,5) trisphosphate-dependent Rac exchanger 1

MacromoleculeName: Phosphatidylinositol (3,4,5) trisphosphate-dependent Rac exchanger 1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 184.840891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GEFAAARESE RQLRLRLCVL NEILGTERDY VGTLRFLQSA FLHRIRQNVA DSVEKGLTEE NVKVLFSNIE DILEVHKDFL AALEYCLHP EPQSQHELGN VFLKFKDKFC VYEEYCSNHE KALRLLVELN KIPTVRAFLL SCMLLGGRKT TDIPLEGYLL S PIQRICKY ...String:
GEFAAARESE RQLRLRLCVL NEILGTERDY VGTLRFLQSA FLHRIRQNVA DSVEKGLTEE NVKVLFSNIE DILEVHKDFL AALEYCLHP EPQSQHELGN VFLKFKDKFC VYEEYCSNHE KALRLLVELN KIPTVRAFLL SCMLLGGRKT TDIPLEGYLL S PIQRICKY PLLLKELAKR TPGKHPDHPA VQSALQAMKT VCSNINETKR QMEKLEALEQ LQSHIEGWEG SNLTDICTQL LL QGTLLKI SAGNIQERAF FLFDNLLVYC KRKSRVTGSK KSTKRTKSIN GSLYIFRGRI NTEVMEVENV EDGTADYHSN GYT VTNGWK IHNTAKNKWF VCMAKTAEEK QKWLDAIIRE REQRESLKLG MERDAYVMIA EKGEKLYHMM MNKKVNLIKD RRRK LSTVP KCFLGNEFVA WLLEIGEISK TEEGVNLGQA LLENGIIHHV SDKHQFKNEQ VMYRFRYDDG TYKARSELED IMSKG VRLY CRLHSLYTPV IKDRDYHLKT YKSVLPGSKL VDWLLAQGDC QTREEAVALG VGLCNNGFMH HVLEKSEFRD ESQYFR FHA DEEMEGTSSK NKQLRNDFKL VENILAKRLL ILPQEEDYGF DIEEKNKAVV VKSVQRGSLA EVAGLQVGRK IYSINED LV FLRPFSEVES ILNQSFCSRR PLRLLVATKA KEIIKIPDQP DTLCFQIRGA APPYVYAVGR GSEAMAAGLC AGQCILKV N GSNVMNDGAP EVLEHFQAFR SRREEALGLY QWIYHTHEDA QEARASQEAS TEDPSGEQAQ EEDQADSAFP LLSLGPRLS LCEDSPMVTL TVDNVHLEHG VVYEYVSTAG VRCHVLEKIV EPRGCFGLTA KILEAFAAND SVFVENCRRL MALSSAIVTM PHFEFRNIC DTKLESIGQR IACYQEFAAQ LKSRVSPPFK QAPLEPHPLC GLDFCPTNCH INLMEVSYPK TTPSVGRSFS I RFGRKPSL IGLDPEQGHL NPMSYTQHCI TTMAAPSWKC LPAAEGDPQG QGLHDGSFGP ASGTLGQEDR GLSFLLKQED RE IQDAYLQ LFTKLDVALK EMKQYVTQIN RLLSTITEPT SGGSCDASLA EEASSLPLVS EESEMDRSDH GGIKKVCFKV AEE DQEDSG HDTMSYRDSY SECNSNRDSV LSYTSVRSNS SYLGSDEMGS GDELPCDMRI PSDKQDKLHG CLEHLFNQVD SINA LLKGP VMSRAFEETK HFPMNHSLQE FKQKEECTIR GRSLIQISIQ EDPWNLPNSI KTLVDNIQRY VEDGKNQLLL ALLKC TDTE LQLRRDAIFC QALVAAVCTF SEQLLAALGY RYNNNGEYEE SSRDASRKWL EQVAATGVLL HCQSLLSPAT VKEERT MLE DIWVTLSELD NVTFSFKQLD ENYVANTNVF YHIEGSRQAL KVIFYLDSYH FSKLPSRLEG GASLRLHTAL FTKVLEN VE GLPSPGSQAA EDLQQDINAQ SLEKVQQYYR KLRAFYLERS NLPTDASTTA VKIDQLIRPI NALDELCRLM KSFVHPKP G AAGSVGAGLI PISSELCYRL GACQMVMCGT GMQRSTLSVS LEQAAILARS HGLLPKCIMQ ATDIMRKQGP RVEILAKNL RVKDQMPQGA PRLYRLCQPP VDGDLHHHHH HHHHH

UniProtKB: PREX1

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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: Bos taurus (cattle)
Molecular weightTheoretical: 37.41693 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String:
MSELDQLRQE 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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 9.226547 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
HHHHHHHHHH 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.7 mg/mL
BufferpH: 8
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 75 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 2 / Number real images: 6746 / Average electron dose: 47.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 905464
Details: 600,588 particles (untilted) and 304,876 particles (30 degree tilted)
Startup modelType of model: OTHER
Details: cryoSPARC ab initio model calculation was used to create initial model
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v0.65)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v0.65)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v0.65) / Number images used: 205599
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3v5w

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

3v5w

chain_id: G, source_name: PDB, initial_model_type: experimental model

3qik

chain_id: A, residue_range: 622-706, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 83
Output model

PDB-6pcv:
Single Particle Reconstruction of Phosphatidylinositol (3,4,5) trisphosphate-dependent Rac exchanger 1 bound to G protein beta gamma subunits

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