[English] 日本語
Yorodumi
- PDB-3om1: Crystal structure of the GluK5 (KA2) ATD dimer at 1.7 Angstrom Re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3om1
TitleCrystal structure of the GluK5 (KA2) ATD dimer at 1.7 Angstrom Resolution
ComponentsGlutamate receptor ionotropic, kainate 5
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of synaptic vesicle fusion to presynaptic active zone membrane / protein retention in ER lumen / chemical synaptic transmission, postsynaptic / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / glutamate receptor activity / receptor clustering / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / regulation of postsynaptic membrane potential ...regulation of synaptic vesicle fusion to presynaptic active zone membrane / protein retention in ER lumen / chemical synaptic transmission, postsynaptic / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / glutamate receptor activity / receptor clustering / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / regulation of postsynaptic membrane potential / monoatomic ion transmembrane transport / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / establishment of localization in cell / PDZ domain binding / regulation of membrane potential / cellular response to glucose stimulus / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / SH3 domain binding / positive regulation of neuron apoptotic process / presynaptic membrane / chemical synaptic transmission / postsynaptic membrane / perikaryon / axon / neuronal cell body / glutamatergic synapse / dendrite / endoplasmic reticulum / identical protein binding / membrane / plasma membrane
Similarity search - Function
Response regulator / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region ...Response regulator / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamate receptor ionotropic, kainate 5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.677 Å
AuthorsKumar, J. / Mayer, M.L.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: Crystal Structures of the Glutamate Receptor Ion Channel GluK3 and GluK5 Amino-Terminal Domains.
Authors: Kumar, J. / Mayer, M.L.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2009
Title: The N-terminal domain of GluR6-subtype glutamate receptor ion channels.
History
DepositionAug 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 24, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_name_com / entity_src_gen / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.type / _entity.pdbx_description ..._chem_comp.type / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / struct_asym / struct_conn / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 2.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate receptor ionotropic, kainate 5
B: Glutamate receptor ionotropic, kainate 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,44516
Polymers87,5962
Non-polymers2,84914
Water10,971609
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-19 kcal/mol
Surface area31240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.344, 65.635, 113.772
Angle α, β, γ (deg.)90.00, 95.72, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Glutamate receptor ionotropic, kainate 5 / GluK5 / Glutamate receptor KA-2 / KA2


Mass: 43798.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik5 / Plasmid: pRK / Cell line (production host): HEK 293 GNTI(-) / Production host: Homo Sapiens (human) / References: UniProt: Q63273

-
Sugars , 2 types, 10 molecules

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


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 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.: 8
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 , 3 types, 613 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.1 M BICINE, 20% PEG 8K, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Sep 22, 2009 / Details: double-crystal Si(220)
RadiationMonochromator: double-crystal monochromator Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.677→30 Å / Num. all: 91506 / Num. obs: 91506 / % possible obs: 96.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 22.47 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 18.1
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.4 / Num. unique all: 7006 / % possible all: 77.3

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OM0

3om0


Resolution: 1.677→29.894 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1963 4410 4.99 %Random
Rwork0.1682 ---
all0.1696 88368 --
obs0.1696 88368 96.12 %-
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.478 Å2 / ksol: 0.418 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.183 Å20 Å2-7.3888 Å2
2---5.7739 Å20 Å2
3----3.4091 Å2
Refinement stepCycle: LAST / Resolution: 1.677→29.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5714 0 182 609 6505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066154
X-RAY DIFFRACTIONf_angle_d1.0778363
X-RAY DIFFRACTIONf_dihedral_angle_d15.4422366
X-RAY DIFFRACTIONf_chiral_restr0.061988
X-RAY DIFFRACTIONf_plane_restr0.0051055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.677-1.69590.3208920.26741795X-RAY DIFFRACTION63
1.6959-1.71580.2631220.2492226X-RAY DIFFRACTION76
1.7158-1.73670.30331380.23322337X-RAY DIFFRACTION81
1.7367-1.75870.24411200.22862481X-RAY DIFFRACTION85
1.7587-1.78190.22461570.21432552X-RAY DIFFRACTION89
1.7819-1.80630.25171200.21122714X-RAY DIFFRACTION94
1.8063-1.83210.22441550.20482811X-RAY DIFFRACTION97
1.8321-1.85940.21991420.19932871X-RAY DIFFRACTION99
1.8594-1.88850.20841300.19482893X-RAY DIFFRACTION100
1.8885-1.91940.28861650.19552893X-RAY DIFFRACTION100
1.9194-1.95250.22561440.19062900X-RAY DIFFRACTION100
1.9525-1.9880.20811570.18042938X-RAY DIFFRACTION100
1.988-2.02620.21941310.17762868X-RAY DIFFRACTION100
2.0262-2.06760.20511390.17252924X-RAY DIFFRACTION100
2.0676-2.11250.18871550.16792914X-RAY DIFFRACTION100
2.1125-2.16170.19821710.16482852X-RAY DIFFRACTION100
2.1617-2.21570.20571490.16182931X-RAY DIFFRACTION100
2.2157-2.27560.23351380.16092956X-RAY DIFFRACTION100
2.2756-2.34250.2221460.16672894X-RAY DIFFRACTION100
2.3425-2.41810.18761640.16352881X-RAY DIFFRACTION100
2.4181-2.50450.20811640.16742897X-RAY DIFFRACTION100
2.5045-2.60470.22211700.16072880X-RAY DIFFRACTION100
2.6047-2.72320.20411520.16682940X-RAY DIFFRACTION100
2.7232-2.86660.20461640.16742903X-RAY DIFFRACTION100
2.8666-3.04610.18641410.16512951X-RAY DIFFRACTION100
3.0461-3.2810.22261410.17572930X-RAY DIFFRACTION100
3.281-3.61070.1621440.16562922X-RAY DIFFRACTION100
3.6107-4.1320.17011740.14542929X-RAY DIFFRACTION100
4.132-5.20140.13551680.12652951X-RAY DIFFRACTION100
5.2014-29.89890.21611570.19143024X-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)
10.8071-0.51750.45661.9685-0.50921.68920.0450.066-0.0124-0.14170.03440.20480.1256-0.0277-0.07310.1592-0.00840.00530.1480.01280.181211.856-10.676942.0472
20.4818-0.4364-0.20220.9026-0.37820.5071-0.00050.00430.06940.037-0.1042-0.1234-0.01660.04030.08510.16750.02370.0270.1830.01880.210441.1509-12.413632.1963
31.28660.1253-0.19170.95750.49361.22320.02090.1515-0.3168-0.0008-0.01930.06760.1865-0.0110.01330.21360.03090.01970.191-0.02210.261138.0613-26.351530.0681
40.93120.00140.02581.4026-0.20210.530.1185-0.0201-0.1106-0.0655-0.11470.15670.1289-0.0501-0.00640.1887-0.01840.01260.16120.00020.162215.0265-16.525849.6518
52.0677-0.5099-1.21870.30960.24641.0355-0.0816-0.2074-0.0720.0667-0.0023-0.02460.02120.12050.08520.1959-0.00420.00420.1515-0.01090.143230.5812-13.095250.0543
60.89690.2146-0.10611.1468-0.65551.44540.0759-0.0651-0.0207-0.0154-0.02080.05070.0176-0.1027-0.04590.1937-0.0214-0.02260.18280.00580.14716.13876.472513.4854
70.43580.376-0.03411.9656-0.71120.98240.0776-0.0191-0.08810.1522-0.1937-0.12540.05070.1230.08410.1872-0.0355-0.05030.20950.04280.219845.18683.780724.3168
81.0114-0.13420.33460.3789-0.40161.0075-0.025-0.06790.3660.1183-0.1546-0.0298-0.3051-0.01320.2040.2347-0.0218-0.07810.1501-0.02590.279942.913417.311922.0003
90.7510.50460.40740.8950.17890.79380.01320.0450.0577-0.2302-0.01510.063-0.0112-0.06220.00030.2040.0219-0.02890.1654-0.01440.131320.898310.60094.8528
104.3490.0862.12512.0428-0.66311.43350.00640.48560.0735-0.3525-0.18170.0454-0.02990.2220.12950.26140.0466-0.01710.2389-0.03870.165639.92148.70696.49
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:119)A3 - 119
2X-RAY DIFFRACTION2(chain A and resid 120:176) or (chain A and resid 178:180)A120 - 176
3X-RAY DIFFRACTION2(chain A and resid 120:176) or (chain A and resid 178:180)A178 - 180
4X-RAY DIFFRACTION3(chain A and resid 181:249) or (chain N and resid 1) or (chain D and resid 1)A181 - 249
5X-RAY DIFFRACTION3(chain A and resid 181:249) or (chain N and resid 1) or (chain D and resid 1)N1
6X-RAY DIFFRACTION3(chain A and resid 181:249) or (chain N and resid 1) or (chain D and resid 1)D1
7X-RAY DIFFRACTION4(chain A and resid 250:325) or (chain N and resid 2:4)A250 - 325
8X-RAY DIFFRACTION4(chain A and resid 250:325) or (chain N and resid 2:4)N2 - 4
9X-RAY DIFFRACTION5(chain A and resid 326:376) or (chain N and resid 5)A326 - 376
10X-RAY DIFFRACTION5(chain A and resid 326:376) or (chain N and resid 5)N5
11X-RAY DIFFRACTION6(chain B and resid 2:35) or (chain B and resid 41:107) or (chain B and resid 109:119)B2 - 35
12X-RAY DIFFRACTION6(chain B and resid 2:35) or (chain B and resid 41:107) or (chain B and resid 109:119)B41 - 107
13X-RAY DIFFRACTION6(chain B and resid 2:35) or (chain B and resid 41:107) or (chain B and resid 109:119)B109 - 119
14X-RAY DIFFRACTION7(chain B and resid 120:175) or (chain B and resid 177:197)B120 - 175
15X-RAY DIFFRACTION7(chain B and resid 120:175) or (chain B and resid 177:197)B177 - 197
16X-RAY DIFFRACTION8(chain B and resid 198:252) or (chain N and resid 6) or (chain F and resid 1)B198 - 252
17X-RAY DIFFRACTION8(chain B and resid 198:252) or (chain N and resid 6) or (chain F and resid 1)N6
18X-RAY DIFFRACTION8(chain B and resid 198:252) or (chain N and resid 6) or (chain F and resid 1)F1
19X-RAY DIFFRACTION9(chain B and resid 253:344) or (chain N and resid 7:9)B253 - 344
20X-RAY DIFFRACTION9(chain B and resid 253:344) or (chain N and resid 7:9)N7 - 9
21X-RAY DIFFRACTION10(chain B and resid 345:375) or (chain N and resid 10)B345 - 375
22X-RAY DIFFRACTION10(chain B and resid 345:375) or (chain N and resid 10)N10

+
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://pdbjlvh1.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