[English] 日本語
Yorodumi
- PDB-12dl: Native structure of the cytoplasmic lattice (CPL) asymmetric unit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 12dl
TitleNative structure of the cytoplasmic lattice (CPL) asymmetric unit from mouse MII eggs
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
  • 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-4B chain
  • Ubiquitin-conjugating enzyme E2 D3
  • Zinc finger BED domain-containing protein 3
KeywordsCYTOSOLIC PROTEIN / cytoplasmic lattice / egg / filamentous 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 / 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 / ooplasm / SCF-beta-TrCP mediated degradation of Emi1 / cortical granule exocytosis / embryonic process involved in female pregnancy / endoplasmic reticulum localization / E3 ubiquitin ligases ubiquitinate target proteins / Carboxyterminal post-translational modifications of tubulin / Intraflagellar transport / Downregulation of SMAD2/3:SMAD4 transcriptional activity / establishment or maintenance of apical/basal cell polarity / Regulation of BACH1 activity / COPI-independent Golgi-to-ER retrograde traffic / PINK1-PRKN Mediated Mitophagy / Inactivation of CSF3 (G-CSF) signaling / SCF(Skp2)-mediated degradation of p27/p21 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Regulation of TNFR1 signaling / cytoplasm organization / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / histone H3K18 ubiquitin ligase activity / histone H3K14 ubiquitin ligase activity / histone H3 ubiquitin ligase activity / 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 / 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 / histone H3K23 ubiquitin ligase activity / COPI-mediated anterograde transport / Aggrephagy / spermatogonial cell division / Kinesins / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cortical granule / histone H3 reader activity / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / PKR-mediated signaling / Degradation of beta-catenin by the destruction complex / Iron uptake and transport / Activation of NF-kappaB in B cells / The role of GTSE1 in G2/M progression after G2 checkpoint / RHO GTPases activate IQGAPs / FCERI mediated NF-kB activation / Recycling pathway of L1 / CLEC7A (Dectin-1) signaling / COPI-dependent Golgi-to-ER retrograde traffic / Interleukin-1 signaling / apical cortex / positive regulation of meiotic nuclear division / RHO GTPases Activate Formins / chromosomal DNA methylation maintenance following DNA replication / regulation of RNA stability / Separation of Sister Chromatids / positive regulation of embryonic development / Downstream TCR signaling / axonemal microtubule / Hedgehog 'off' state / F-box domain binding / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Peroxisomal protein import / Anchoring of the basal body to the plasma membrane / Recruitment of NuMA to mitotic centrosomes / regulation of establishment of protein localization / AURKA Activation by TPX2 / hemi-methylated DNA-binding / GLI3 is processed to GLI3R by the proteasome / Regulation of PLK1 Activity at G2/M Transition / PcG protein complex / Neddylation / embryonic pattern specification / embryonic cleavage / (E3-independent) E2 ubiquitin-conjugating enzyme / mitochondrion localization / establishment of spindle localization / MHC class II antigen presentation / gap junction / flagellated sperm motility / regulation of epithelial cell proliferation / maintenance of protein location in nucleus
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 / F-box-like domain superfamily / DAPIN domain / PAAD/DAPIN/Pyrin domain / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / PAAD/DAPIN/Pyrin 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 C2H2 superfamily / Zinc finger PHD-type signature. / 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 / Ring finger / SKP1/BTB/POZ domain superfamily / 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
GUANOSINE-5'-TRIPHOSPHATE / NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / Tubulin beta-4B chain / Tubulin alpha-1C chain / Expressed sequence C85627 / NACHT, LRR and PYD domains-containing protein 14 / F-box and WD-40 domain protein 21 / F-box and WD-40 domain protein 19 / Inactive protein-arginine deiminase type-6 ...GUANOSINE-5'-TRIPHOSPHATE / NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / Tubulin beta-4B chain / Tubulin alpha-1C chain / Expressed sequence C85627 / NACHT, LRR and PYD domains-containing protein 14 / 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: 3.5 Å
AuthorsLi, Y. / Zheng, W. / Leem, J. / Wu, C. / Tang, S. / Mogessie, B. / Xiong, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: To Be Published
Title: Native structure of the cytoplasmic lattice (CPL) asymmetric unit from mouse MII eggs
Authors: Li, Y. / Zheng, W. / Leem, J. / Wu, C. / Tang, S. / Mogessie, B. / Xiong, Y.
History
DepositionMar 29, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 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
FA: Tubulin beta-4B chain
GB: NACHT, LRR and PYD domains-containing protein 5
GA: NACHT, LRR and PYD domains-containing protein 5
IA: Oocyte-expressed protein homolog
HB: Transducin-like enhancer protein 6
HA: Transducin-like enhancer protein 6
KA: Zinc finger BED domain-containing protein 3
LA: KH domain-containing protein 3
MA: NLR family, pyrin domain containing 4F
AC: Inactive protein-arginine deiminase type-6
AD: Inactive protein-arginine deiminase type-6
AE: Inactive protein-arginine deiminase type-6
AF: Inactive protein-arginine deiminase type-6
AG: Inactive protein-arginine deiminase type-6
AH: Inactive protein-arginine deiminase type-6
AA: Inactive protein-arginine deiminase type-6
AB: Inactive protein-arginine deiminase type-6
AI: Inactive protein-arginine deiminase type-6
AJ: Inactive protein-arginine deiminase type-6
EA: Tubulin alpha-1C chain
DA: NACHT, LRR and PYD domains-containing protein 14
DB: NACHT, LRR and PYD domains-containing protein 14
BA: E3 ubiquitin-protein ligase UHRF1
BB: E3 ubiquitin-protein ligase UHRF1
CA: Ubiquitin-conjugating enzyme E2 D3
CB: Ubiquitin-conjugating enzyme E2 D3
OA: F-box and WD-40 domain protein 19
QB: S-phase kinase-associated protein 1
QA: S-phase kinase-associated protein 1
NA: Expressed sequence C85627
QC: S-phase kinase-associated protein 1
PA: F-box and WD-40 domain protein 21
JA: Oocyte-expressed protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,137,88149
Polymers2,136,02733
Non-polymers1,85516
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 12 types, 27 molecules FAIAJAHBHAKALAMAACADAEAFAGAHAAABAIAJEABABBCACBQBQAQCNA

#1: Protein Tubulin beta-4B chain / Tubulin beta-2C chain


Mass: 49877.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P68372
#3: 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
#4: 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
#5: Protein Zinc finger BED domain-containing protein 3 / Axin-interacting protein


Mass: 25512.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D0L1
#6: Protein KH domain-containing protein 3 / Protein Filia


Mass: 48055.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CWU5
#7: Protein NLR family, pyrin domain containing 4F


Mass: 108001.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: L7N1W9
#8: 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
#9: 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.: 1 / 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
#11: Protein E3 ubiquitin-protein ligase UHRF1 / Nuclear protein 95 / Nuclear zinc finger protein Np95 / Ubiquitin-like PHD and RING finger domain- ...Nuclear protein 95 / Nuclear zinc finger protein Np95 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q8VDF2, RING-type E3 ubiquitin transferase
#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
#14: 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
#15: 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

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

#2: 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
#10: 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

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

#13: 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
#16: 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

-
Non-polymers , 4 types, 16 molecules

#17: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#18: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION

-
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: Native structure of the cytoplasmic lattice (CPL) asymmetric unit from mouse MII eggs
Type: COMPLEX / Entity ID: #1-#16 / Source: NATURAL
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

-
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: 1800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 249541 / Symmetry type: POINT
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004136180
ELECTRON MICROSCOPYf_angle_d0.569184502
ELECTRON MICROSCOPYf_dihedral_angle_d5.25217934
ELECTRON MICROSCOPYf_chiral_restr0.04420758
ELECTRON MICROSCOPYf_plane_restr0.00423626

+
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