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- EMDB-44413: PI4KA complex bound to C-terminus of EFR3A -

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Basic information

Entry
Database: EMDB / ID: EMD-44413
TitlePI4KA complex bound to C-terminus of EFR3A
Map dataPI4KA-TTC7B-FAM126A-EFR3Acterm Map
Sample
  • Complex: Dimer of heterotetramers of PI4KA,TTC7B,FAM126A, and EFR3A c-terminus
    • Protein or peptide: Protein EFR3 homolog A
    • Protein or peptide: Phosphatidylinositol 4-kinase alpha
    • Protein or peptide: Tetratricopeptide repeat protein 7B
    • Protein or peptide: Hyccin
KeywordsPI4KA / TTC7B / FAM126A / EFR3A / EFR3 / Lipid Signaling / PI4KIIIa / Phosphoinositide Kinase / SIGNALING PROTEIN
Function / homology
Function and homology information


reorganization of cellular membranes to establish viral sites of replication / Synthesis of PIPs at the ER membrane / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / Synthesis of PIPs at the Golgi membrane / host-mediated perturbation of viral process / Golgi-associated vesicle membrane / phosphatidylinositol biosynthetic process / phosphatidylinositol-mediated signaling / synaptic vesicle priming ...reorganization of cellular membranes to establish viral sites of replication / Synthesis of PIPs at the ER membrane / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / Synthesis of PIPs at the Golgi membrane / host-mediated perturbation of viral process / Golgi-associated vesicle membrane / phosphatidylinositol biosynthetic process / phosphatidylinositol-mediated signaling / synaptic vesicle priming / phosphatidylinositol phosphate biosynthetic process / myelination / protein localization to plasma membrane / presynapse / neuron projection / cadherin binding / focal adhesion / glutamatergic synapse / signal transduction / extracellular exosome / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / : / EFR3, armadillo repeat / PI4-kinase, N-terminal / PI4-kinase N-terminal region / Hyccin / Tetratricopeptide repeat protein 7, N-terminal / Hyccin / Tetratricopeptide repeat protein 7 N-terminal / : ...: / : / EFR3, armadillo repeat / PI4-kinase, N-terminal / PI4-kinase N-terminal region / Hyccin / Tetratricopeptide repeat protein 7, N-terminal / Hyccin / Tetratricopeptide repeat protein 7 N-terminal / : / Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Tetratricopeptide repeat / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Phosphatidylinositol 4-kinase alpha / Protein EFR3 homolog A / Tetratricopeptide repeat protein 7B / Hyccin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsShaw AL / Suresh S / Yip CK / Burke JE
Funding support Canada, 4 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)NSERC-2020-04241 Canada
Canadian Institutes of Health Research (CIHR)PJT-168907 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-03951 Canada
Canadian Institutes of Health Research (CIHR)PJT-195808 Canada
CitationJournal: Sci Adv / Year: 2024
Title: Molecular basis for plasma membrane recruitment of PI4KA by EFR3.
Authors: Sushant Suresh / Alexandria L Shaw / Joshua G Pemberton / Mackenzie K Scott / Noah J Harris / Matthew A H Parson / Meredith L Jenkins / Pooja Rohilla / Alejandro Alvarez-Prats / Tamas Balla ...Authors: Sushant Suresh / Alexandria L Shaw / Joshua G Pemberton / Mackenzie K Scott / Noah J Harris / Matthew A H Parson / Meredith L Jenkins / Pooja Rohilla / Alejandro Alvarez-Prats / Tamas Balla / Calvin K Yip / John E Burke /
Abstract: The lipid kinase phosphatidylinositol 4 kinase III α (PI4KIIIα/PI4KA) is a master regulator of the lipid composition and asymmetry of the plasma membrane. PI4KA exists primarily in a heterotrimeric ...The lipid kinase phosphatidylinositol 4 kinase III α (PI4KIIIα/PI4KA) is a master regulator of the lipid composition and asymmetry of the plasma membrane. PI4KA exists primarily in a heterotrimeric complex with its regulatory proteins TTC7 and FAM126. Fundamental to PI4KA activity is its targeted recruitment to the plasma membrane by the lipidated proteins EFR3A and EFR3B. Here, we report a cryogenic electron microscopy structure of the C terminus of EFR3A bound to the PI4KA-TTC7B-FAM126A complex, with extensive validation using both hydrogen deuterium exchange mass spectrometry, and mutational analysis. The EFR3A C terminus undergoes a disorder-order transition upon binding to the PI4KA complex, with an unexpected direct interaction with both TTC7B and FAM126A. Complex disrupting mutations in TTC7B, FAM126A, and EFR3 decrease PI4KA recruitment to the plasma membrane. Multiple posttranslational modifications and disease linked mutations map to this site, providing insight into how PI4KA membrane recruitment can be regulated and disrupted in human disease.
History
DepositionApr 4, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44413.png

Downloads & links

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Map

FileDownload / File: emd_44413.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPI4KA-TTC7B-FAM126A-EFR3Acterm Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.77 Å/pix.
x 600 pix.
= 462. Å		0.77 Å/pix.
x 600 pix.
= 462. Å		0.77 Å/pix.
x 600 pix.
= 462. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.77 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0284
Minimum - Maximum-0.1000331 - 0.20783226
Average (Standard dev.)0.00032433352 (±0.0060740644)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 462.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: PI4KA-TTC7B-FAM126A-EFR3Acterm Half Map A

Fileemd_44413_half_map_1.map
AnnotationPI4KA-TTC7B-FAM126A-EFR3Acterm Half Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PI4KA-TTC7B-FAM126A-EFR3Acterm Half Map B

Fileemd_44413_half_map_2.map
AnnotationPI4KA-TTC7B-FAM126A-EFR3Acterm Half Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimer of heterotetramers of PI4KA,TTC7B,FAM126A, and EFR3A c-terminus

EntireName: Dimer of heterotetramers of PI4KA,TTC7B,FAM126A, and EFR3A c-terminus
Components
  • Complex: Dimer of heterotetramers of PI4KA,TTC7B,FAM126A, and EFR3A c-terminus
    • Protein or peptide: Protein EFR3 homolog A
    • Protein or peptide: Phosphatidylinositol 4-kinase alpha
    • Protein or peptide: Tetratricopeptide repeat protein 7B
    • Protein or peptide: Hyccin

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Supramolecule #1: Dimer of heterotetramers of PI4KA,TTC7B,FAM126A, and EFR3A c-terminus

SupramoleculeName: Dimer of heterotetramers of PI4KA,TTC7B,FAM126A, and EFR3A c-terminus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Complex stabilized with BS3 crosslinker
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein EFR3 homolog A

MacromoleculeName: Protein EFR3 homolog A / type: protein_or_peptide / ID: 1 / Details: EFR3A c-terminus construct (721-791) / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.366863 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MASAWSHPQF EKGGGSGGGS GGSAWSHPQF EKSGMHHHHH HHHHHGSGGS ENLYFQGAGS NTEEITFEAL KKAIDTSGME EQEKEKRRL VIEKFQKAPF EEIAAQCESK ANLLHDRLAQ ILELTIRPPP S

UniProtKB: Protein EFR3 homolog A

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Macromolecule #2: Phosphatidylinositol 4-kinase alpha

MacromoleculeName: Phosphatidylinositol 4-kinase alpha / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: 1-phosphatidylinositol 4-kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 237.102281 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAAPARGGG GGGGGGGGCS GSGSSASRGF YFNTVLSLAR SLAVQRPASL EKVQKLLCMC PVDFHGIFQL DERRRDAVIA LGIFLIESD LQHKDCVVPY LLRLLKGLPK VYWVEESTAR KGRGALPVAE SFSFCLVTLL SDVAYRDPSL RDEILEVLLQ V LHVLLGMC ...String:
MAAAPARGGG GGGGGGGGCS GSGSSASRGF YFNTVLSLAR SLAVQRPASL EKVQKLLCMC PVDFHGIFQL DERRRDAVIA LGIFLIESD LQHKDCVVPY LLRLLKGLPK VYWVEESTAR KGRGALPVAE SFSFCLVTLL SDVAYRDPSL RDEILEVLLQ V LHVLLGMC QALEIQDKEY LCKYAIPCLI GISRAFGRYS NMEESLLSKL FPKIPPHSLR VLEELEGVRR RSFNDFRSIL PS NLLTVCQ EGTLKRKTSS VSSISQVSPE RGMPPPSSPG GSAFHYFEAS CLPDGTALEP EYYFSTISSS FSVSPLFNGV TYK EFNIPL EMLRELLNLV KKIVEEAVLK SLDAIVASVM EANPSADLYY TSFSDPLYLT MFKMLRDTLY YMKDLPTSFV KEIH DFVLE QFNTSQGELQ KILHDADRIH NELSPLKLRC QANAACVDLM VWAVKDEQGA ENLCIKLSEK LQSKTSSKVI IAHLP LLIC CLQGLGRLCE RFPVVVHSVT PSLRDFLVIP SPVLVKLYKY HSQYHTVAGN DIKISVTNEH SESTLNVMSG KKSQPS MYE QLRDIAIDNI CRCLKAGLTV DPVIVEAFLA SLSNRLYISQ ESDKDAHLIP DHTIRALGHI AVALRDTPKV MEPILQI LQ QKFCQPPSPL DVLIIDQLGC LVITGNQYIY QEVWNLFQQI SVKASSVVYS ATKDYKDHGY RHCSLAVINA LANIAANI Q DEHLVDELLM NLLELFVQLG LEGKRASERA SEKGPALKAS SSAGNLGVLI PVIAVLTRRL PPIKEAKPRL QKLFRDFWL YSVLMGFAVE GSGLWPEEWY EGVCEIATKS PLLTFPSKEP LRSVLQYNSA MKNDTVTPAE LSELRSTIIN LLDPPPEVSA LINKLDFAM STYLLSVYRL EYMRVLRSTD PDRFQVMFCY FEDKAIQKDK SGMMQCVIAV ADKVFDAFLN MMADKAKTKE N EEELERHA QFLLVNFNHI HKRIRRVADK YLSGLVDKFP HLLWSGTVLK TMLDILQTLS LSLSADIHKD QPYYDIPDAP YR ITVPDTY EARESIVKDF AARCGMILQE AMKWAPTVTK SHLQEYLNKH QNWVSGLSQH TGLAMATESI LHFAGYNKQN TTL GATQLS ERPACVKKDY SNFMASLNLR NRYAGEVYGM IRFSGTTGQM SDLNKMMVQD LHSALDRSHP QHYTQAMFKL TAML ISSKD CDPQLLHHLC WGPLRMFNEH GMETALACWE WLLAGKDGVE VPFMREMAGA WHMTVEQKFG LFSAEIKEAD PLAAS EASQ PKPCPPEVTP HYIWIDFLVQ RFEIAKYCSS DQVEIFSSLL QRSMSLNIGG AKGSMNRHVA AIGPRFKLLT LGLSLL HAD VVPNATIRNV LREKIYSTAF DYFSCPPKFP TQGEKRLRED ISIMIKFWTA MFSDKKYLTA SQLVPPDNQD TRSNLDI TV GSRQQATQGW INTYPLSSGM STISKKSGMS KKTNRGSQLH KYYMKRRTLL LSLLATEIER LITWYNPLSA PELELDQA G ENSVANWRSK YISLSEKQWK DNVNLAWSIS PYLAVQLPAR FKNTEAIGNE VTRLVRLDPG AVSDVPEAIK FLVTWHTID ADAPELSHVL CWAPTDPPTG LSYFSSMYPP HPLTAQYGVK VLRSFPPDAI LFYIPQIVQA LRYDKMGYVR EYILWAASKS QLLAHQFIW NMKTNIYLDE EGHQKDPDIG DLLDQLVEEI TGSLSGPAKD FYQREFDFFN KITNVSAIIK PYPKGDERKK A CLSALSEV KVQPGCYLPS NPEAIVLDID YKSGTPMQSA AKAPYLAKFK VKRCGVSELE KEGLRCRSDS EDECSTQEAD GQ KISWQAA IFKVGDDCRQ DMLALQIIDL FKNIFQLVGL DLFVFPYRVV ATAPGCGVIE CIPDCTSRDQ LGRQTDFGMY DYF TRQYGD ESTLAFQQAR YNFIRSMAAY SLLLFLLQIK DRHNGNIMLD KKGHIIHIDF GFMFESSPGG NLGWEPDIKL TDEM VMIMG GKMEATPFKW FMEMCVRGYL AVRPYMDAVV SLVTLMLDTG LPCFRGQTIK LLKHRFSPNM TEREAANFIM KVIQS CFLS NRSRTYDMIQ YYQNDIPY

UniProtKB: Phosphatidylinositol 4-kinase alpha

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Macromolecule #3: Tetratricopeptide repeat protein 7B

MacromoleculeName: Tetratricopeptide repeat protein 7B / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 94.294109 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MATKKAGSRL ETEIERCRSE CQWERIPELV KQLSAKLIAN DDMAELLLGE SKLEQYLKEH PLRQGASPRG PKPQLTEVRK HLTAALDRG NLKSEFLQES NLIMAKLNYV EGDYKEALNI YARVGLDDLP LTAVPPYRLR VIAEAYATKG LCLEKLPISS S TSNLHVDR ...String:
MATKKAGSRL ETEIERCRSE CQWERIPELV KQLSAKLIAN DDMAELLLGE SKLEQYLKEH PLRQGASPRG PKPQLTEVRK HLTAALDRG NLKSEFLQES NLIMAKLNYV EGDYKEALNI YARVGLDDLP LTAVPPYRLR VIAEAYATKG LCLEKLPISS S TSNLHVDR EQDVITCYEK AGDIALLYLQ EIERVILSNI QNRSPKPGPA PHDQELGFFL ETGLQRAHVL YFKNGNLTRG VG RFRELLR AVETRTTQNL RMTIARQLAE ILLRGMCEQS YWNPLEDPPC QSPLDDPLRK GANTKTYTLT RRARVYSGEN IFC PQENTE EALLLLLISE SMANRDAVLS RIPEHKSDRL ISLQSASVVY DLLTIALGRR GQYEMLSECL ERAMKFAFEE FHLW YQFAL SLMAAGKSAR AVKVLKECIR LKPDDATIPL LAAKLCMGSL HWLEEAEKFA KTVVDVGEKT SEFKAKGYLA LGLTY SLQA TDASLRGMQE VLQRKALLAF QRAHSLSPTD HQAAFYLALQ LAISRQIPEA LGYVRQALQL QGDDANSLHL LALLLS AQK HYHDALNIID MALSEYPENF ILLFSKVKLQ SLCRGPDEAL LTCKHMLQIW KSCYNLTNPS DSGRGSSLLD RTIADRR QL NTITLPDFSD PETGSVHATS VAASRVEQAL SEVASSLQSS APKQGPLHPW MTLAQIWLHA AEVYIGIGKP AEATACTQ E AANLFPMSHN VLYMRGQIAE LRGSMDEARR WYEEALAISP THVKSMQRLA LILHQLGRYS LAEKILRDAV QVNSTAHEV WNGLGEVLQA QGNDAAATEC FLTALELEAS SPAVPFTIIP RVL

UniProtKB: Tetratricopeptide repeat protein 7B

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Macromolecule #4: Hyccin

MacromoleculeName: Hyccin / type: protein_or_peptide / ID: 4 / Details: Truncated construct (1-308) / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.638867 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MFTSEKGVVE EWLSEFKTLP ETSLPNYATN LKDKSSLVSS LYKVIQEPQS ELLEPVCHQL FEFYRSGEEQ LLQFTLQFLP ELIWCYLAV SASRNVHSSG CIEALLLGVY NLEIVDKQGH TKVLSFTIPS LSKPSVYHEP SSIGSMALTE SALSQHGLSK V VYSGPHPQ ...String:
MFTSEKGVVE EWLSEFKTLP ETSLPNYATN LKDKSSLVSS LYKVIQEPQS ELLEPVCHQL FEFYRSGEEQ LLQFTLQFLP ELIWCYLAV SASRNVHSSG CIEALLLGVY NLEIVDKQGH TKVLSFTIPS LSKPSVYHEP SSIGSMALTE SALSQHGLSK V VYSGPHPQ REMLTAQNRF EVLTFLLLCY NAALTYMPSV SLQSLCQICS RICVCGYPRQ HVRKYKGISS RIPVSSGFMV QM LTGIYFA FYNGEWDLAQ KALDDIIYRA QLELYPEPLL VANAIKASLP HGPMKSNKEG TRCIQVEITP T

UniProtKB: Hyccin

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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: 7
Component:
ConcentrationFormulaName
20.0 mMC3H4N2Imidazole
150.0 mMNaClSodium Chloride
5.0 %C3H8O3Glycerol
0.5 mMTCEPTris(2-carboxyethyl)phosphine

Details: Freshly prepared gel filtration buffer, filtered through 0.22um filter and degassed
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
Details: Glow discharged using the Pelco EasiGlow. 15mA Current.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force -5, blot time 1.5 s.
DetailsSample was treated with BS3 crosslinker then underwent gel filtration where fractions were taken from a peak that had an elution volume consistent with formation of the complex.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 9412 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
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: 1216317
Details: Particles were picked using the cryoSPARC template picker
CTF correctionSoftware - Name: cryoSPARC (ver. v4.2.1.) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab-initio
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 135126
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.2.1) / Details: CryoSPARC SGD-based ab initio reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.2.1)
Details: CryoSPARC - Masked Local Refinement with symmetry expanded particles (C2)
FSC plot (resolution estimation)

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