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- PDB-24mc: Structure of oocyte cytoplasmic lattices -

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Entry
Database: PDB / ID: 24mc
TitleStructure of oocyte cytoplasmic lattices
Components
  • (F-box and WD-40 domain protein ...) x 2
  • (NACHT, LRR and PYD domains-containing protein ...) x 2
  • E3 ubiquitin-protein ligase UHRF1
  • Expressed sequence C85627
  • Inactive protein-arginine deiminase type-6
  • Isoform 2 of KH domain-containing protein 3
  • NLR family, pyrin domain containing 4F
  • Oocyte-expressed protein homolog
  • S-phase kinase-associated protein 1
  • Transducin-like enhancer protein 6
  • Tubulin alpha-1C chain
  • Tubulin beta-2A chain
  • Ubiquitin-conjugating enzyme E2 D3
  • Zinc finger BED domain-containing protein 3
KeywordsCELL CYCLE / oocytes cytoplasmic lattices
Function / homology
Function and homology information


regulation of translation by machinery localization / Prolactin receptor signaling / Signaling by BMP / subcortical maternal complex / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / establishment of organelle localization / Chromatin modifying enzymes / protein storage ...regulation of translation by machinery localization / Prolactin receptor signaling / Signaling by BMP / subcortical maternal complex / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / establishment of organelle localization / Chromatin modifying enzymes / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / cortical granule exocytosis / embryonic process involved in female pregnancy / endoplasmic reticulum localization / ooplasm / Carboxyterminal post-translational modifications of tubulin / Intraflagellar transport / establishment or maintenance of apical/basal cell polarity / SCF-beta-TrCP mediated degradation of Emi1 / COPI-independent Golgi-to-ER retrograde traffic / E3 ubiquitin ligases ubiquitinate target proteins / Downregulation of SMAD2/3:SMAD4 transcriptional activity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cytoplasm organization / Regulation of BACH1 activity / histone H3K18 ubiquitin ligase activity / histone H3K14 ubiquitin ligase activity / histone H3 ubiquitin ligase activity / PINK1-PRKN Mediated Mitophagy / Inactivation of CSF3 (G-CSF) signaling / SCF(Skp2)-mediated degradation of p27/p21 / histone H3K23 ubiquitin ligase activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / COPI-mediated anterograde transport / spermatogonial cell division / Regulation of TNFR1 signaling / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Kinesins / histone H3 reader activity / Regulation of RUNX2 expression and activity / cortical granule / Degradation of GLI1 by the proteasome / Cyclin D associated events in G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / IKK complex recruitment mediated by RIP1 / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / PKR-mediated signaling / Aggrephagy / RHO GTPases activate IQGAPs / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / Degradation of beta-catenin by the destruction complex / Activation of NF-kappaB in B cells / Recycling pathway of L1 / Iron uptake and transport / The role of GTSE1 in G2/M progression after G2 checkpoint / COPI-dependent Golgi-to-ER retrograde traffic / apical cortex / positive regulation of meiotic nuclear division / regulation of RNA stability / positive regulation of embryonic development / chromosomal DNA methylation maintenance following DNA replication / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / Hedgehog 'off' state / RHO GTPases Activate Formins / F-box domain binding / Separation of Sister Chromatids / Downstream TCR signaling / Recruitment of NuMA to mitotic centrosomes / hemi-methylated DNA-binding / regulation of establishment of protein localization / Peroxisomal protein import / GLI3 is processed to GLI3R by the proteasome / PcG protein complex / Regulation of PLK1 Activity at G2/M Transition / Neddylation / embryonic pattern specification / (E3-independent) E2 ubiquitin-conjugating enzyme / mitochondrion localization / establishment of spindle localization / embryonic cleavage / MHC class II antigen presentation / gap junction / flagellated sperm motility / regulation of epithelial cell proliferation / maintenance of protein location in nucleus / Cul7-RING ubiquitin ligase complex / intermediate filament cytoskeleton / methyl-CpG binding / Antigen processing: Ubiquitination & Proteasome degradation / protein K11-linked ubiquitination / fertilization
Similarity search - Function
Zinc finger BED domain-containing protein 2/3 / : / BED zinc finger / KH-like RNA-binding domain / : / KH-like RNA-binding domain / Groucho/transducin-like enhancer / : / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 ...Zinc finger BED domain-containing protein 2/3 / : / BED zinc finger / KH-like RNA-binding domain / : / KH-like RNA-binding domain / Groucho/transducin-like enhancer / : / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily / Protein-arginine deiminase (PAD) / Protein-arginine deiminase (PAD) N-terminal domain / Protein-arginine deiminase (PAD) middle domain / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / A Receptor for Ubiquitination Targets / NOD2, winged helix domain / NOD2 winged helix domain / F-box domain profile. / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / F-box-like / DAPIN domain / PAAD/DAPIN/Pyrin domain / F-box-like domain superfamily / PAAD/DAPIN/Pyrin domain / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / K Homology domain, type 1 superfamily / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / PUA-like superfamily / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / PHD-finger / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Beta tubulin / Death-like domain superfamily / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Zinc finger PHD-type signature. / Zinc finger C2H2 superfamily / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / SKP1/BTB/POZ domain superfamily / Ring finger / Cupredoxin / Zinc finger PHD-type profile. / Leucine-rich repeat / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Leucine-rich repeat domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / Tubulin alpha-1C chain / Expressed sequence C85627 / NACHT, LRR and PYD domains-containing protein 14 / Tubulin beta-2A chain / F-box and WD-40 domain protein 21 / F-box and WD-40 domain protein 19 ...ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / Tubulin alpha-1C chain / Expressed sequence C85627 / NACHT, LRR and PYD domains-containing protein 14 / Tubulin beta-2A chain / F-box and WD-40 domain protein 21 / F-box and WD-40 domain protein 19 / Inactive protein-arginine deiminase type-6 / E3 ubiquitin-protein ligase UHRF1 / Oocyte-expressed protein homolog / KH domain-containing protein 3 / Zinc finger BED domain-containing protein 3 / NACHT, LRR and PYD domains-containing protein 5 / S-phase kinase-associated protein 1 / Transducin-like enhancer protein 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLiu, Q. / Gui, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The structure of oocytes cytoplasmic lattice
Authors: Liu, Q. / Gui, M.
History
DepositionMar 10, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 20, 2026Group: Data collection / Structure summary / Category: em_admin / em_entity_assembly / struct
Item: _em_admin.last_update / _em_admin.title ..._em_admin.last_update / _em_admin.title / _em_entity_assembly.name / _struct.title
Revision 2.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Experimental summary / Source and taxonomy / Data content type: EM metadata / EM metadata / Category: em_admin / em_entity_assembly / Data content type: EM metadata / EM metadata / EM metadata
Item: _em_admin.last_update / _em_admin.title / _em_entity_assembly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
m: F-box and WD-40 domain protein 19
p: F-box and WD-40 domain protein 21
A: Inactive protein-arginine deiminase type-6
B: Inactive protein-arginine deiminase type-6
C: Inactive protein-arginine deiminase type-6
D: Inactive protein-arginine deiminase type-6
E: Inactive protein-arginine deiminase type-6
F: Inactive protein-arginine deiminase type-6
G: Inactive protein-arginine deiminase type-6
H: Inactive protein-arginine deiminase type-6
I: Inactive protein-arginine deiminase type-6
K: Inactive protein-arginine deiminase type-6
M: NLR family, pyrin domain containing 4F
N: Oocyte-expressed protein homolog
O: Isoform 2 of KH domain-containing protein 3
P: NACHT, LRR and PYD domains-containing protein 5
Q: Transducin-like enhancer protein 6
R: NLR family, pyrin domain containing 4F
S: NACHT, LRR and PYD domains-containing protein 5
T: Transducin-like enhancer protein 6
U: Oocyte-expressed protein homolog
V: Zinc finger BED domain-containing protein 3
W: Tubulin beta-2A chain
X: Tubulin alpha-1C chain
Y: Tubulin alpha-1C chain
Z: Tubulin beta-2A chain
a: Ubiquitin-conjugating enzyme E2 D3
b: E3 ubiquitin-protein ligase UHRF1
c: Ubiquitin-conjugating enzyme E2 D3
d: E3 ubiquitin-protein ligase UHRF1
e: NACHT, LRR and PYD domains-containing protein 14
f: NACHT, LRR and PYD domains-containing protein 14
h: S-phase kinase-associated protein 1
n: Expressed sequence C85627
j: S-phase kinase-associated protein 1
l: S-phase kinase-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,339,06855
Polymers2,333,95036
Non-polymers5,11819
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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F-box and WD-40 domain protein ... , 2 types, 2 molecules mp

#1: Protein F-box and WD-40 domain protein 19


Mass: 53657.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8C2W8
#2: Protein F-box and WD-40 domain protein 21


Mass: 54517.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BI38

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Protein , 12 types, 30 molecules ABCDEFGHIKMRNUOQTVWZXYacbdhjln

#3: Protein
Inactive protein-arginine deiminase type-6 / Arginine deiminase-like protein / Egg and embryo abundant PAD / ePAD / P75 / Peptidylarginine ...Arginine deiminase-like protein / Egg and embryo abundant PAD / ePAD / P75 / Peptidylarginine deiminase VI / Protein-arginine deiminase type VI / Protein-arginine deiminase type-6


Mass: 76854.109 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8K3V4
#4: Protein NLR family, pyrin domain containing 4F


Mass: 108001.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: L7N1W9
#5: Protein Oocyte-expressed protein homolog / Factor located in oocytes permitting embryonic development / Floped / Oocyte- and embryo-specific ...Factor located in oocytes permitting embryonic development / Floped / Oocyte- and embryo-specific protein 19 / mOEP19 / STAT3 downstream gene and differentiation regulator


Mass: 18481.295 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CWE6
#6: Protein Isoform 2 of KH domain-containing protein 3 / Protein Filia


Mass: 37854.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CWU5
#8: Protein Transducin-like enhancer protein 6 / Groucho-related protein 6


Mass: 65187.332 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9WVB3
#9: Protein Zinc finger BED domain-containing protein 3 / Axin-interacting protein


Mass: 25643.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D0L1
#10: Protein Tubulin beta-2A chain


Mass: 49953.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q7TMM9
#11: Protein Tubulin alpha-1C chain / Alpha-tubulin 6 / Alpha-tubulin isotype M-alpha-6 / Tubulin alpha-6 chain


Mass: 49962.172 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P68373, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#12: Protein Ubiquitin-conjugating enzyme E2 D3 / (E3-independent) E2 ubiquitin-conjugating enzyme D3 / E2 ubiquitin-conjugating enzyme D3 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D3 / E2 ubiquitin-conjugating enzyme D3 / Ubiquitin carrier protein D3 / Ubiquitin-conjugating enzyme E2(17)KB 3 / Ubiquitin-conjugating enzyme E2-17 kDa 3 / Ubiquitin-protein ligase D3


Mass: 16706.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P61079, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#13: Protein E3 ubiquitin-protein ligase UHRF1


Mass: 88436.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8VDF2
#15: Protein S-phase kinase-associated protein 1 / Cyclin-A/CDK2-associated protein p19 / S-phase kinase-associated protein 1A / p19A / p19skp1


Mass: 18693.992 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9WTX5
#16: Protein Expressed sequence C85627 / F-box and WD-40 domain protein 18


Mass: 54205.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q3TSA9

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NACHT, LRR and PYD domains-containing protein ... , 2 types, 4 molecules PSef

#7: Protein NACHT, LRR and PYD domains-containing protein 5 / Maternal antigen that embryos require / Mater protein / Ooplasm-specific protein 1 / OP1


Mass: 131468.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9R1M5
#14: Protein NACHT, LRR and PYD domains-containing protein 14 / NALP-iota / Germ cell specific leucine-rich repeat NTPase


Mass: 113527.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6B966

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Non-polymers , 4 types, 19 molecules

#17: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#18: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#19: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Structure of oocyte cytoplasmic lattices / Type: COMPLEX / Entity ID: #1-#16 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 288673 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008141962
ELECTRON MICROSCOPYf_angle_d1.186192318
ELECTRON MICROSCOPYf_dihedral_angle_d7.36418674
ELECTRON MICROSCOPYf_chiral_restr0.06221621
ELECTRON MICROSCOPYf_plane_restr0.00924525

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