[English] 日本語
Yorodumi
- PDB-6aek: Crystal structure of ENPP1 in complex with pApG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6aek
TitleCrystal structure of ENPP1 in complex with pApG
ComponentsEctonucleotide pyrophosphatase/phosphodiesterase 1, isoform CRA_d
KeywordsIMMUNOSUPPRESSANT / Enzyme / Phoshodiesterase / cGAMP / cGAS-STING / cyclic GMP-AMP
Function / homology
Function and homology information


articular cartilage development / microglial cell migration / cellular response to sodium phosphate / Vitamin B2 (riboflavin) metabolism / vascular associated smooth muscle cell migration / post-embryonic forelimb morphogenesis / vascular associated smooth muscle cell proliferation / ligamentous ossification / hematopoietic stem cell migration to bone marrow / bone trabecula formation ...articular cartilage development / microglial cell migration / cellular response to sodium phosphate / Vitamin B2 (riboflavin) metabolism / vascular associated smooth muscle cell migration / post-embryonic forelimb morphogenesis / vascular associated smooth muscle cell proliferation / ligamentous ossification / hematopoietic stem cell migration to bone marrow / bone trabecula formation / organic phosphonate metabolic process / inorganic diphosphate transport / tooth mineralization / GTP diphosphatase activity / cyclic-GMP-AMP hydrolase activity / plasma cell differentiation / vitamin D3 metabolic process / UTP diphosphatase activity / dinucleotide phosphatase activity / coenzyme A diphosphatase activity / coenzyme A catabolic process / nucleotide diphosphatase / basal dendrite / B-1 B cell homeostasis / phosphodiesterase I / fat pad development / mucus secretion / middle ear morphogenesis / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / endochondral bone morphogenesis / nucleoside triphosphate catabolic process / bone growth / response to vitamin B6 / pyrophosphatase activity / central nervous system myelination / sensory perception of temperature stimulus / diphosphate metabolic process / response to Gram-positive bacterium / inhibition of non-skeletal tissue mineralization / endochondral ossification / microglia differentiation / cementum mineralization / magnesium ion homeostasis / biomineral tissue development / nucleoside triphosphate diphosphatase activity / bone mineralization involved in bone maturation / sensory perception of mechanical stimulus / artery development / response to sodium phosphate / melanocyte differentiation / ATP diphosphatase activity / negative regulation of glycogen biosynthetic process / response to platelet-derived growth factor / phosphate ion homeostasis / hormone metabolic process / negative regulation of D-glucose import across plasma membrane / negative regulation of bone mineralization / collagen-activated signaling pathway / bone remodeling / morphogenesis of an epithelium / inflammatory response to antigenic stimulus / adult walking behavior / defense response to protozoan / bone resorption / regulation of bone mineralization / negative regulation of ossification / aorta development / phosphoric diester hydrolase activity / intracellular phosphate ion homeostasis / smoothened signaling pathway / phosphate-containing compound metabolic process / cartilage development / apical dendrite / odontogenesis / oligodendrocyte apoptotic process / axon regeneration / phosphodiesterase I activity / bone mineralization / scavenger receptor activity / negative regulation of fat cell differentiation / response to dietary excess / exonuclease activity / skin development / spinal cord development / response to ATP / multicellular organism growth / protein poly-ADP-ribosylation / fibroblast growth factor receptor signaling pathway / adipose tissue development / polysaccharide binding / vasculogenesis / macrophage differentiation / phosphatase activity / T cell differentiation / 3',5'-cyclic-AMP phosphodiesterase activity / determination of adult lifespan / response to magnesium ion / fat cell differentiation / neuron apoptotic process / osteoclast differentiation
Similarity search - Function
Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase ...Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / His-Me finger superfamily / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / ADENOSINE MONOPHOSPHATE / Ectonucleotide pyrophosphatase/phosphodiesterase family member 1 / Ectonucleotide pyrophosphatase/phosphodiesterase family member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKato, K. / Nishimasu, H. / Hirano, S. / Hirano, H. / Ishitani, R. / Nureki, O.
CitationJournal: Nat Commun / Year: 2018
Title: Structural insights into cGAMP degradation by Ecto-nucleotide pyrophosphatase phosphodiesterase 1.
Authors: Kato, K. / Nishimasu, H. / Oikawa, D. / Hirano, S. / Hirano, H. / Kasuya, G. / Ishitani, R. / Tokunaga, F. / Nureki, O.
History
DepositionAug 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.0May 29, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id
Revision 3.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 4.0Jul 1, 2026Group: Advisory / Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ectonucleotide pyrophosphatase/phosphodiesterase 1, isoform CRA_d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,53322
Polymers84,8161
Non-polymers2,71721
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint6 kcal/mol
Surface area28330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.486, 94.071, 74.680
Angle α, β, γ (deg.)90.00, 96.86, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Ectonucleotide pyrophosphatase/phosphodiesterase 1, isoform CRA_d / Ectonucleotide pyrophosphatase/phosphodiesterase family member 1


Mass: 84816.156 Da / Num. of mol.: 1 / Mutation: T238A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Enpp1, mCG_9001 / Production host: Homo sapiens (human) / References: UniProt: G3X9S2, UniProt: P06802*PLUS

-
Sugars , 2 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 7 types, 339 molecules

#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsProtease recognition site

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 17% PEG3350, 0.1 M Bis-Tris propane, pH 7.5, 0.2 M NaBr and 0.1 M MgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→47 Å / Num. obs: 69252 / % possible obs: 100 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 10
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.662 / Num. unique obs: 69203

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GTW

4gtw


Resolution: 1.8→47 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.83
RfactorNum. reflection% reflection
Rfree0.208 3432 4.96 %
Rwork0.1831 --
obs0.1843 69203 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5806 0 160 322 6288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066156
X-RAY DIFFRACTIONf_angle_d0.8518402
X-RAY DIFFRACTIONf_dihedral_angle_d13.4743659
X-RAY DIFFRACTIONf_chiral_restr0.053920
X-RAY DIFFRACTIONf_plane_restr0.0061068
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82470.39541360.37872654X-RAY DIFFRACTION100
1.8247-1.85070.3461460.33752586X-RAY DIFFRACTION100
1.8507-1.87840.37391310.31752686X-RAY DIFFRACTION100
1.8784-1.90770.31811370.28482573X-RAY DIFFRACTION100
1.9077-1.9390.26351310.26572636X-RAY DIFFRACTION100
1.939-1.97240.29361560.25712594X-RAY DIFFRACTION100
1.9724-2.00830.26371360.23452609X-RAY DIFFRACTION100
2.0083-2.04690.2381340.22182598X-RAY DIFFRACTION100
2.0469-2.08870.26931350.21522669X-RAY DIFFRACTION100
2.0887-2.13410.24081510.21122589X-RAY DIFFRACTION100
2.1341-2.18380.24991470.20512624X-RAY DIFFRACTION100
2.1838-2.23840.22051300.19442585X-RAY DIFFRACTION100
2.2384-2.29890.21551330.19552649X-RAY DIFFRACTION100
2.2989-2.36650.25491290.19392640X-RAY DIFFRACTION100
2.3665-2.44290.2251320.18582615X-RAY DIFFRACTION100
2.4429-2.53020.26211200.19982650X-RAY DIFFRACTION100
2.5302-2.63150.22921480.19262625X-RAY DIFFRACTION100
2.6315-2.75130.24251330.19192626X-RAY DIFFRACTION100
2.7513-2.89630.20781380.19452647X-RAY DIFFRACTION100
2.8963-3.07770.22971350.19282618X-RAY DIFFRACTION100
3.0777-3.31530.20311260.18392646X-RAY DIFFRACTION100
3.3153-3.64880.19111580.17052647X-RAY DIFFRACTION100
3.6488-4.17650.16411480.14432636X-RAY DIFFRACTION100
4.1765-5.26090.1481320.13352647X-RAY DIFFRACTION100
5.2609-47.05150.1531300.1512722X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9475-0.11940.29632.37190.19361.2782-0.0744-0.2085-0.05090.39430.1931-0.3930.07770.0005-0.08630.2250.0598-0.03670.2777-0.02450.248418.1524-0.748823.2666
21.7422-0.62380.8692.3303-0.90222.9999-0.00590.3435-0.0202-0.71670.19430.04370.1173-0.2617-0.16930.4995-0.12040.01090.3438-0.02640.2574.9156-6.4612-16.4815
32.5483-0.71060.86732.5608-0.95223.2079-0.08040.40380.362-0.87340.1265-0.0748-0.47420.08780.01680.7213-0.15760.00460.39560.02250.28795.5437.3937-20.9227
41.2255-0.1081-0.00242.5952-0.14412.6998-0.07940.09370.0974-0.54520.1588-0.2384-0.26180.0306-0.06060.2985-0.07420.06820.2185-0.01870.205811.92074.1477-5.7234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 170 through 576 )
2X-RAY DIFFRACTION2chain 'A' and (resid 577 through 668 )
3X-RAY DIFFRACTION3chain 'A' and (resid 669 through 733 )
4X-RAY DIFFRACTION4chain 'A' and (resid 734 through 903 )

+
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