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- EMDB-49223: Viral protein DP71L in complex with phosphorylated eIF2alpha (NTD... -

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Basic information

Entry
Database: EMDB / ID: EMD-49223
TitleViral protein DP71L in complex with phosphorylated eIF2alpha (NTD) and protein phosphatase 1A (D64A), stabilized by G-actin/DNAseI
Map data
Sample
  • Complex: PP1A holo-phosphatase complex with viral protein DP71L, G-actin, DNAseI, and substrate phospho-eIF2alpha (2-187)
    • Protein or peptide: Protein DP71L
    • Protein or peptide: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Deoxyribonuclease-1
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 1
  • Ligand: MANGANESE (II) ION
  • Ligand: CALCIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsPhosphatase / complex / ISR / TRANSLATION
Function / homology
Function and homology information


regulation of macromolecule metabolic process / regulation of neutrophil mediated cytotoxicity / regulation of primary metabolic process / zymogen granule / regulation of acute inflammatory response / protein serine/threonine phosphatase inhibitor activity / regulation of glycogen catabolic process / translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot ...regulation of macromolecule metabolic process / regulation of neutrophil mediated cytotoxicity / regulation of primary metabolic process / zymogen granule / regulation of acute inflammatory response / protein serine/threonine phosphatase inhibitor activity / regulation of glycogen catabolic process / translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / response to kainic acid / deoxyribonuclease I / Cellular response to mitochondrial stress / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / PTW/PP1 phosphatase complex / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / negative regulation of translational initiation in response to stress / PERK-mediated unfolded protein response / protein phosphatase type 1 complex / PERK regulates gene expression / glycogen granule / eukaryotic translation initiation factor 2 complex / deoxyribonuclease I activity / symbiont-mediated suppression of host translation initiation / protein phosphatase 1 binding / neutrophil activation involved in immune response / cadherin binding involved in cell-cell adhesion / regulation of translational initiation in response to stress / eukaryotic 48S preinitiation complex / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / DNA catabolic process / regulation of canonical Wnt signaling pathway / Formation of the ternary complex, and subsequently, the 43S complex / cytoskeletal motor activator activity / dephosphorylation / histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / branching morphogenesis of an epithelial tube / glycogen metabolic process / Ribosomal scanning and start codon recognition / protein serine/threonine phosphatase activity / myosin heavy chain binding / protein-serine/threonine phosphatase / Translation initiation complex formation / tropomyosin binding / Triglyceride catabolism / entrainment of circadian clock by photoperiod / Maturation of hRSV A proteins / troponin I binding / filamentous actin / mesenchyme migration / phosphatase activity / actin filament bundle / telomere maintenance in response to DNA damage / actin filament bundle assembly / phosphoprotein phosphatase activity / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / Response of EIF2AK4 (GCN2) to amino acid deficiency / DARPP-32 events / transition metal ion binding / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of glycogen biosynthetic process / ribonucleoprotein complex binding / stress fiber / mitophagy / skeletal muscle fiber development / protein dephosphorylation / titin binding / actin filament polymerization / translation initiation factor activity / stress granule assembly / cellular response to amino acid starvation / response to endoplasmic reticulum stress / Downregulation of TGF-beta receptor signaling / adherens junction / filopodium / actin filament / translational initiation / lung development / circadian regulation of gene expression / response to lead ion / regulation of circadian rhythm / PKR-mediated signaling / ABC-family proteins mediated transport / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic stress granule
Similarity search - Function
Protein phosphatase 1, regulatory subunit 15A/B, C-terminal / : / Phosphatase-1 catalytic subunit binding region / Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / Serine-threonine protein phosphatase, N-terminal ...Protein phosphatase 1, regulatory subunit 15A/B, C-terminal / : / Phosphatase-1 catalytic subunit binding region / Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / Eukaryotic translation initiation factor 2 alpha subunit / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / S1 domain profile. / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Actin / S1 domain / Actin family / Actin / ATPase, nucleotide binding domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Deoxyribonuclease-1 / Eukaryotic translation initiation factor 2 subunit 1 / Protein DP71L / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human) / African swine fever virus / Oryctolagus cuniculus (rabbit) / Bos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsReineke LC / Dalwadi U / Croll T / Arthur C / Lee DJ / Frost A / Costa-Mattioli M
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: bioRxiv / Year: 2025
Title: Harnessing the Evolution of Proteostasis Networks to Reverse Cognitive Dysfunction.
Abstract: The integrated stress response (ISR) is a highly conserved network essential for maintaining cellular homeostasis and cognitive function. Here, we investigated how persistent ISR activation impacts ...The integrated stress response (ISR) is a highly conserved network essential for maintaining cellular homeostasis and cognitive function. Here, we investigated how persistent ISR activation impacts cognitive performance, primarily focusing on a PPP1R15B genetic variant associated with intellectual disability. By generating a novel mouse model that mimics this human condition, we revealed that this variant destabilizes the PPP1R15B•PP1 phosphatase complex, resulting in chronic ISR activation, impaired protein synthesis, and deficits in long-term memory. Importantly, we found that the cognitive and synaptic deficits in mice are directly due to ISR activation. Leveraging insights from evolutionary biology, we characterized DP71L, a viral orthologue of PPP1R15B, through detailed molecular and structural analyses, uncovering its mechanism of action as a potent pan-ISR inhibitor. Remarkably, we found that DP71L not only buffers cognitive decline associated with a wide array of conditions-including Down syndrome, Alzheimer's disease and aging-but also enhances long-term synaptic plasticity and memory in healthy mice. These findings highlight the promise of utilizing evolutionary insight to inform innovative therapeutic strategies.
History
DepositionFeb 13, 2025-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49223.png

Downloads & links

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Map

FileDownload / File: emd_49223.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 320 pix.
= 297.152 Å		0.93 Å/pix.
x 320 pix.
= 297.152 Å		0.93 Å/pix.
x 320 pix.
= 297.152 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9286 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0275
Minimum - Maximum-0.0049355794 - 0.30359018
Average (Standard dev.)0.00081813097 (±0.0029707311)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 297.152 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : PP1A holo-phosphatase complex with viral protein DP71L, G-actin, ...

EntireName: PP1A holo-phosphatase complex with viral protein DP71L, G-actin, DNAseI, and substrate phospho-eIF2alpha (2-187)
Components
  • Complex: PP1A holo-phosphatase complex with viral protein DP71L, G-actin, DNAseI, and substrate phospho-eIF2alpha (2-187)
    • Protein or peptide: Protein DP71L
    • Protein or peptide: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Deoxyribonuclease-1
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 1
  • Ligand: MANGANESE (II) ION
  • Ligand: CALCIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: PP1A holo-phosphatase complex with viral protein DP71L, G-actin, ...

SupramoleculeName: PP1A holo-phosphatase complex with viral protein DP71L, G-actin, DNAseI, and substrate phospho-eIF2alpha (2-187)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 140 KDa

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Macromolecule #1: Protein DP71L

MacromoleculeName: Protein DP71L / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 8.43573 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGGRRRKKRT NDVKHVRFAA AVEVWEADDI ERKGPWEQAA VDRFRFQRRI ASVEELLSAV LLRQKKLLEQ Q

UniProtKB: Protein DP71L

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Macromolecule #2: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit

MacromoleculeName: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein-serine/threonine phosphatase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.514039 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSDSEKLNLD SIIGRLLEVQ GSRPGKNVQL TENEIRGLCL KSREIFLSQP ILLELEAPLK ICGAIHGQYY DLLRLFEYGG FPPESNYLF LGDYVDRGKQ SLETICLLLA YKIKYPENFF LLRGNHECAS INRIYGFYDE CKRRYNIKLW KTFTDCFNCL P IAAIVDEK ...String:
MSDSEKLNLD SIIGRLLEVQ GSRPGKNVQL TENEIRGLCL KSREIFLSQP ILLELEAPLK ICGAIHGQYY DLLRLFEYGG FPPESNYLF LGDYVDRGKQ SLETICLLLA YKIKYPENFF LLRGNHECAS INRIYGFYDE CKRRYNIKLW KTFTDCFNCL P IAAIVDEK IFCCHGGLSP DLQSMEQIRR IMRPTDVPDQ GLLCDLLWSD PDKDVQGWGE NDRGVSFTFG AEVVAKFLHK HD LDLICRA HQVVEDGYEF FAKRQLVTLF SAPNYCGEFD NAGAMMSVDE TLMCSFQILK PADKNKGKYG QFSGLNPGGR PIT PPRNSA KAKK

UniProtKB: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit

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Macromolecule #3: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 42.096953 KDa
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSSSL EK SYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQK EIT ALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #4: Deoxyribonuclease-1

MacromoleculeName: Deoxyribonuclease-1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: deoxyribonuclease I
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 31.374436 KDa
SequenceString: MRGTRLMGLL LALAGLLQLG LSLKIAAFNI RTFGETKMSN ATLASYIVRI VRRYDIVLIQ EVRDSHLVAV GKLLDYLNQD DPNTYHYVV SEPLGRNSYK ERYLFLFRPN KVSVLDTYQY DDGCESCGND SFSREPAVVK FSSHSTKVKE FAIVALHSAP S DAVAEINS ...String:
MRGTRLMGLL LALAGLLQLG LSLKIAAFNI RTFGETKMSN ATLASYIVRI VRRYDIVLIQ EVRDSHLVAV GKLLDYLNQD DPNTYHYVV SEPLGRNSYK ERYLFLFRPN KVSVLDTYQY DDGCESCGND SFSREPAVVK FSSHSTKVKE FAIVALHSAP S DAVAEINS LYDVYLDVQQ KWHLNDVMLM GDFNADCSYV TSSQWSSIRL RTSSTFQWLI PDSADTTATS TNCAYDRIVV AG SLLQSSV VPGSAAPFDF QAAYGLSNEM ALAISDHYPV EVTLT

UniProtKB: Deoxyribonuclease-1

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Macromolecule #5: Eukaryotic translation initiation factor 2 subunit 1

MacromoleculeName: Eukaryotic translation initiation factor 2 subunit 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.817863 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PGLSCRFYQH KFPEVEDVVM VNVRSIAEMG AYVSLLEYNN IEGMILLSEL (SEP)RRRIRSINK LIRIGRNECV VVIRVD KEK GYIDLSKRRV SPEEAIKCED KFTKSKTVYS ILRHVAEVLE YTKDEQLESL FQRTAWVFDD KYKRPGYGAY DAFKHAV SD PSILDSLDLN EDEREVLINN INRRLTPQ

UniProtKB: Eukaryotic translation initiation factor 2 subunit 1

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Macromolecule #6: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #8: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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

Concentration5.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMKClPotassium chloride
1.0 mMMnCl2Manganese chloride
0.2 mMATPAdenosine triphosphate
0.2 mMTCEPtris(2-carboxyethyl)phosphine
1.0 mMCaCl2Calcium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 25 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.045 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV / Details: 3.5 uL volume, -5 blot force, 1.5 blot time.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 5236 / 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: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
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: 1315944
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 309745
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final 3D classificationNumber classes: 80 / Avg.num./class: 7290 / Software - Name: cryoSPARC (ver. 4.6.0)
Details: A final 2D classification was carried out to exclude poorly aligning or noisy particles.

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9nb9:
Viral protein DP71L in complex with phosphorylated eIF2alpha (NTD) and protein phosphatase 1A (D64A), stabilized by G-actin/DNAseI

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