[English] 日本語
Yorodumi
- PDB-9w2m: Cryo-EM structure of the Cytoplasmic lattice(CPL) from mouse oocyte -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9w2m
TitleCryo-EM structure of the Cytoplasmic lattice(CPL) from mouse oocyte
Components
  • (Tubulin beta- ...) x 2
  • E3 ubiquitin-protein ligase UHRF1
  • FBXW24
  • Inactive protein-arginine deiminase type-6
  • Isoform 4 of NACHT, LRR and PYD domains-containing protein 5
  • KH domain-containing protein 3
  • NACHT, LRR and PYD domains-containing protein 14
  • NLR family, pyrin domain containing 4F
  • Oocyte-expressed protein homolog
  • S-phase kinase-associated protein 1
  • Transducin-like enhancer protein 6
  • Ubiquitin-conjugating enzyme E2 D3
  • Zinc finger BED domain-containing protein 3
KeywordsSTRUCTURAL PROTEIN / Cytoplasmic lattice / Maternal complex / Cryo-EM structure / Protein assembly
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 / SCF-beta-TrCP mediated degradation of Emi1 / Chromatin modifying enzymes ...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 / SCF-beta-TrCP mediated degradation of Emi1 / Chromatin modifying enzymes / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / cortical granule exocytosis / E3 ubiquitin ligases ubiquitinate target proteins / endoplasmic reticulum localization / Carboxyterminal post-translational modifications of tubulin / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Intraflagellar transport / Regulation of BACH1 activity / establishment or maintenance of apical/basal cell polarity / ooplasm / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / COPI-independent Golgi-to-ER retrograde traffic / PINK1-PRKN Mediated Mitophagy / SCF(Skp2)-mediated degradation of p27/p21 / Inactivation of CSF3 (G-CSF) signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Regulation of TNFR1 signaling / histone H3 ubiquitin ligase activity / cytoplasm organization / Regulation of RUNX2 expression and activity / 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 / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / IKK complex recruitment mediated by RIP1 / COPI-mediated anterograde transport / Aggrephagy / spermatogonial cell division / Kinesins / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cortical granule / Resolution of Sister Chromatid Cohesion / Iron uptake and transport / Degradation of beta-catenin by the destruction complex / PKR-mediated signaling / Activation of NF-kappaB in B cells / The role of GTSE1 in G2/M progression after G2 checkpoint / RHO GTPases activate IQGAPs / Recycling pathway of L1 / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / positive regulation of meiotic nuclear division / COPI-dependent Golgi-to-ER retrograde traffic / apical cortex / RHO GTPases Activate Formins / Downstream TCR signaling / Separation of Sister Chromatids / regulation of RNA stability / positive regulation of embryonic development / F-box domain binding / Hedgehog 'off' state / hemi-methylated DNA-binding / Peroxisomal protein import / Recruitment of NuMA to mitotic centrosomes / regulation of establishment of protein localization / GLI3 is processed to GLI3R by the proteasome / Regulation of PLK1 Activity at G2/M Transition / PcG protein complex / Neddylation / embryonic pattern specification / protein K6-linked ubiquitination / (E3-independent) E2 ubiquitin-conjugating enzyme / embryonic brain development / MHC class II antigen presentation / embryonic cleavage / flagellated sperm motility / mitochondrion localization / gap junction / establishment of spindle localization / Cul7-RING ubiquitin ligase complex / regulation of epithelial cell proliferation / intermediate filament cytoskeleton / ubiquitin ligase activator activity / maintenance of protein location in nucleus / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of epithelial cell apoptotic process / methyl-CpG binding / histone H3K9me2/3 reader activity / protein K11-linked ubiquitination / fertilization / positive regulation of axon guidance
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 / UHRF1/2-like ...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 / NOD2, winged helix domain / NOD2 winged helix domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / DAPIN domain / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation 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 / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Death-like domain superfamily / 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 / Leucine-rich repeat domain superfamily / Zinc finger, FYVE/PHD-type / 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 / Ubiquitin-like domain superfamily / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / NACHT, LRR and PYD domains-containing protein 14 / Tubulin beta-2A chain / Inactive protein-arginine deiminase type-6 / E3 ubiquitin-protein ligase UHRF1 / Oocyte-expressed protein homolog / Tubulin beta-2B chain ...ADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / NACHT, LRR and PYD domains-containing protein 14 / Tubulin beta-2A chain / Inactive protein-arginine deiminase type-6 / E3 ubiquitin-protein ligase UHRF1 / Oocyte-expressed protein homolog / Tubulin beta-2B chain / 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: 4.2 Å
AuthorsLiu, S.X. / Xue, J.C. / Zhang, Y. / Liu, Y.S. / Gao, H.S. / Shen, E.Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070628 China
National Natural Science Foundation of China (NSFC)32271258 China
CitationJournal: To Be Published
Title: Cryo-EM structure of the Cytoplasmic lattice(CPL) from mouse oocyte
Authors: Liu, S.X. / Xue, J.C. / Zhang, Y. / Liu, Y.S. / Gao, H.S. / Shen, E.Z.
History
DepositionJul 28, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: Inactive protein-arginine deiminase type-6
C: Oocyte-expressed protein homolog
D: KH domain-containing protein 3
E: NLR family, pyrin domain containing 4F
H: Oocyte-expressed protein homolog
I: NLR family, pyrin domain containing 4F
J: FBXW24
K: S-phase kinase-associated protein 1
O: Ubiquitin-conjugating enzyme E2 D3
Q: E3 ubiquitin-protein ligase UHRF1
R: Zinc finger BED domain-containing protein 3
Z: Inactive protein-arginine deiminase type-6
c: Oocyte-expressed protein homolog
d: KH domain-containing protein 3
e: NLR family, pyrin domain containing 4F
h: Oocyte-expressed protein homolog
i: NLR family, pyrin domain containing 4F
j: FBXW24
k: S-phase kinase-associated protein 1
o: Ubiquitin-conjugating enzyme E2 D3
q: E3 ubiquitin-protein ligase UHRF1
r: Zinc finger BED domain-containing protein 3
z: Inactive protein-arginine deiminase type-6
2: Inactive protein-arginine deiminase type-6
3: Inactive protein-arginine deiminase type-6
4: Inactive protein-arginine deiminase type-6
5: Inactive protein-arginine deiminase type-6
6: Inactive protein-arginine deiminase type-6
7: Inactive protein-arginine deiminase type-6
8: Inactive protein-arginine deiminase type-6
9: Inactive protein-arginine deiminase type-6
12: Inactive protein-arginine deiminase type-6
N: NACHT, LRR and PYD domains-containing protein 14
P: E3 ubiquitin-protein ligase UHRF1
L: Tubulin beta-2A chain
M: Tubulin beta-2B chain
A: Isoform 4 of NACHT, LRR and PYD domains-containing protein 5
B: Transducin-like enhancer protein 6
F: Isoform 4 of NACHT, LRR and PYD domains-containing protein 5
G: Transducin-like enhancer protein 6
n: NACHT, LRR and PYD domains-containing protein 14
p: E3 ubiquitin-protein ligase UHRF1
l: Tubulin beta-2A chain
m: Tubulin beta-2B chain
a: Isoform 4 of NACHT, LRR and PYD domains-containing protein 5
b: Transducin-like enhancer protein 6
f: Isoform 4 of NACHT, LRR and PYD domains-containing protein 5
g: Transducin-like enhancer protein 6
11: Inactive protein-arginine deiminase type-6
19: Inactive protein-arginine deiminase type-6
15: Inactive protein-arginine deiminase type-6
16: Inactive protein-arginine deiminase type-6
14: Inactive protein-arginine deiminase type-6
13: Inactive protein-arginine deiminase type-6
17: Inactive protein-arginine deiminase type-6
18: Inactive protein-arginine deiminase type-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,656,58364
Polymers3,653,10156
Non-polymers3,4828
Water00
1


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

-
Components

-
Protein , 12 types, 52 molecules 1Zz23456789121119151614131718CHchDdEIei...

#1: 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.: 20 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8K3V4
#2: 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: 14294.582 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CWE6
#3: Protein KH domain-containing protein 3 / Protein Filia


Mass: 15250.954 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CWU5
#4: Protein
NLR family, pyrin domain containing 4F


Mass: 107564.766 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: L7N1W9
#5: Protein FBXW24


Mass: 53469.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#6: 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.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9WTX5
#7: 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
#8: Protein
E3 ubiquitin-protein ligase UHRF1 / Nuclear protein 95 / Nuclear zinc finger protein Np95 / RING-type E3 ubiquitin transferase UHRF1 / ...Nuclear protein 95 / Nuclear zinc finger protein Np95 / RING-type E3 ubiquitin transferase UHRF1 / Ubiquitin-like PHD and RING finger domain-containing protein 1 / mUhrf1 / Ubiquitin-like-containing PHD and RING finger domains protein 1


Mass: 88436.805 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q8VDF2, RING-type E3 ubiquitin transferase
#9: Protein Zinc finger BED domain-containing protein 3 / Axin-interacting protein


Mass: 6370.292 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D0L1
#10: Protein NACHT, LRR and PYD domains-containing protein 14 / NALP-iota / Germ cell specific leucine-rich repeat NTPase


Mass: 110368.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6B966
#13: Protein
Isoform 4 of NACHT, LRR and PYD domains-containing protein 5 / Maternal antigen that embryos require / Mater protein / Ooplasm-specific protein 1 / OP1


Mass: 109296.773 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9R1M5
#14: Protein
Transducin-like enhancer protein 6 / Groucho-related protein 6


Mass: 49005.340 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9WVB3

-
Tubulin beta- ... , 2 types, 4 molecules LlMm

#11: 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
#12: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CWF2

-
Non-polymers , 2 types, 8 molecules

#15: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#16: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: mouse oocyte cytoplasmic lattices (CPL) / Type: COMPLEX / Entity ID: #1-#14 / Source: NATURAL
Molecular weightValue: 2 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
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: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 676923 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003239117
ELECTRON MICROSCOPYf_angle_d0.625323918
ELECTRON MICROSCOPYf_dihedral_angle_d5.27131542
ELECTRON MICROSCOPYf_chiral_restr0.04436426
ELECTRON MICROSCOPYf_plane_restr0.00441567

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more