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- PDB-3qlu: Crystal structure of the GluK2/GluK5 (GluR6/KA2) ATD dimer assembly -

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Basic information

Entry
Database: PDB / ID: 3qlu
TitleCrystal structure of the GluK2/GluK5 (GluR6/KA2) ATD dimer assembly
Components(Glutamate receptor, ionotropic kainate ...) x 2
KeywordsMEMBRANE PROTEIN / Glycosylation
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 / mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity ...regulation of synaptic vesicle fusion to presynaptic active zone membrane / protein retention in ER lumen / chemical synaptic transmission, postsynaptic / mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding / receptor clustering / modulation of excitatory postsynaptic potential / regulation of JNK cascade / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / neuronal action potential / behavioral fear response / regulation of postsynaptic membrane potential / positive regulation of synaptic transmission / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / monoatomic ion transmembrane transport / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / hippocampal mossy fiber to CA3 synapse / regulation of membrane potential / SNARE binding / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / establishment of localization in cell / PDZ domain binding / cellular response to glucose stimulus / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / terminal bouton / SH3 domain binding / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynaptic density / axon / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / 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 2 / Glutamate receptor ionotropic, kainate 5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.906 Å
AuthorsKumar, J. / Mayer, M.L.
CitationJournal: Neuron / Year: 2011
Title: Structure and assembly mechanism for heteromeric kainate receptors.
Authors: Kumar, J. / Schuck, P. / Mayer, M.L.
History
DepositionFeb 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 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 1.4Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor, ionotropic kainate 5
B: Glutamate receptor, ionotropic kainate 5
C: Glutamate receptor, ionotropic kainate 2
D: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,94523
Polymers177,2434
Non-polymers3,70219
Water1086
1
A: Glutamate receptor, ionotropic kainate 5
C: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,42611
Polymers88,6212
Non-polymers1,8059
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-4 kcal/mol
Surface area32250 Å2
MethodPISA
2
B: Glutamate receptor, ionotropic kainate 5
D: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,51912
Polymers88,6212
Non-polymers1,89710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint8 kcal/mol
Surface area33000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.626, 139.548, 195.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21D
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ILEILELYSLYSchain C and (resseq 10:104 or resseq 114:174 or resseq...CC10 - 10410 - 104
121PHEPHEPROPROchain C and (resseq 10:104 or resseq 114:174 or resseq...CC114 - 174114 - 174
131LYSLYSSERSERchain C and (resseq 10:104 or resseq 114:174 or resseq...CC181 - 266181 - 266
141GLYGLYGLNGLNchain C and (resseq 10:104 or resseq 114:174 or resseq...CC279 - 305279 - 305
151PHEPHETHRTHRchain C and (resseq 10:104 or resseq 114:174 or resseq...CC324 - 383324 - 383
211ILEILELYSLYSchain D and (resseq 10:104 or resseq 114:174 or resseq...DD10 - 10410 - 104
221PHEPHEPROPROchain D and (resseq 10:104 or resseq 114:174 or resseq...DD114 - 174114 - 174
231LYSLYSSERSERchain D and (resseq 10:104 or resseq 114:174 or resseq...DD181 - 266181 - 266
241GLYGLYGLNGLNchain D and (resseq 10:104 or resseq 114:174 or resseq...DD279 - 305279 - 305
251PHEPHETHRTHRchain D and (resseq 10:104 or resseq 114:174 or resseq...DD324 - 383324 - 383
112LEULEUILEILEchain A and (resseq 2:10 or resseq 22:37 or resseq...AA2 - 102 - 10
122ARGARGGLUGLUchain A and (resseq 2:10 or resseq 22:37 or resseq...AA22 - 3722 - 37
132ALAALAHISHISchain A and (resseq 2:10 or resseq 22:37 or resseq...AA40 - 9840 - 98
142SERSERARGARGchain A and (resseq 2:10 or resseq 22:37 or resseq...AA118 - 172118 - 172
152ASPASPARGARGchain A and (resseq 2:10 or resseq 22:37 or resseq...AA179 - 270179 - 270
162TYRTYRLEULEUchain A and (resseq 2:10 or resseq 22:37 or resseq...AA278 - 356278 - 356
212LEULEUILEILEchain B and (resseq 2:10 or resseq 22:37 or resseq...BB2 - 102 - 10
222ARGARGGLUGLUchain B and (resseq 2:10 or resseq 22:37 or resseq...BB22 - 3722 - 37
232ALAALAHISHISchain B and (resseq 2:10 or resseq 22:37 or resseq...BB40 - 9840 - 98
242SERSERARGARGchain B and (resseq 2:10 or resseq 22:37 or resseq...BB118 - 172118 - 172
252ASPASPARGARGchain B and (resseq 2:10 or resseq 22:37 or resseq...BB179 - 270179 - 270
262TYRTYRLEULEUchain B and (resseq 2:10 or resseq 22:37 or resseq...BB278 - 356278 - 356

NCS ensembles :
ID
1
2

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Components

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Glutamate receptor, ionotropic kainate ... , 2 types, 4 molecules ABCD

#1: Protein Glutamate receptor, ionotropic kainate 5 / 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-IRES_EGFP / Cell line (production host): HEK 293 GNTI(-) / Production host: Homo Sapiens (human) / References: UniProt: Q63273
#2: Protein Glutamate receptor, ionotropic kainate 2 / Glutamate receptor 6 / GluR-6 / GluR6


Mass: 44823.172 Da / Num. of mol.: 2 / Mutation: A213N,G215S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur6, Grik2 / Plasmid: PRK-IRES_EGFP / Cell line (production host): HEK 293 GNTI(-) / Production host: Homo Sapiens (human) / References: UniProt: P42260

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Sugars , 1 types, 16 molecules

#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.: 16
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

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Non-polymers , 3 types, 9 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.15 M Ammonium Sulfate; 0.1 M Tris; 18% PEG 4K, pH 8.20, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 24, 2009
RadiationMonochromator: Si(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 40232 / Num. obs: 40232 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 41.4 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 11.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3850 / % possible all: 97.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OM0 and 3H6H
Resolution: 2.906→29.97 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 1991 5.01 %random
Rwork0.1971 ---
all0.2 39761 --
obs0.2 39761 98.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 13.214 Å2 / ksol: 0.363 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.9131 Å20 Å2-0 Å2
2--6.0228 Å20 Å2
3----4.1097 Å2
Refinement stepCycle: LAST / Resolution: 2.906→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11749 0 232 6 11987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612268
X-RAY DIFFRACTIONf_angle_d0.91816626
X-RAY DIFFRACTIONf_dihedral_angle_d13.7874549
X-RAY DIFFRACTIONf_chiral_restr0.0491926
X-RAY DIFFRACTIONf_plane_restr0.0042094
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C2616X-RAY DIFFRACTIONPOSITIONAL0.028
12D2616X-RAY DIFFRACTIONPOSITIONAL0.028
21A2376X-RAY DIFFRACTIONPOSITIONAL0.043
22B2376X-RAY DIFFRACTIONPOSITIONAL0.043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9064-2.9790.35361280.26752392X-RAY DIFFRACTION89
2.979-3.05950.34511330.26142593X-RAY DIFFRACTION97
3.0595-3.14950.37541440.2472665X-RAY DIFFRACTION98
3.1495-3.2510.28091360.23472647X-RAY DIFFRACTION98
3.251-3.3670.28251310.21142679X-RAY DIFFRACTION99
3.367-3.50170.26411280.20222735X-RAY DIFFRACTION99
3.5017-3.66080.28761330.19572703X-RAY DIFFRACTION100
3.6608-3.85340.23281370.17752715X-RAY DIFFRACTION100
3.8534-4.09430.21911580.16332707X-RAY DIFFRACTION100
4.0943-4.40950.21361420.1512723X-RAY DIFFRACTION100
4.4095-4.85150.21231470.13272729X-RAY DIFFRACTION100
4.8515-5.54970.20421630.15412767X-RAY DIFFRACTION100
5.5497-6.97740.26421530.19372796X-RAY DIFFRACTION100
6.9774-29.97120.21391580.19292919X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.3427-0.2687-0.07130.419-0.56161.0259-0.01020.2949-0.35450.0015-0.2837-0.2982-0.07850.2080.190.0646-0.0358-0.04370.17180.07630.144814.61467.774626.3172
22.10990.27750.18930.72850.21431.0166-0.38840.1016-0.22320.02310.18870.0356-0.13070.32050.12660.0186-0.03910.00950.00830.00080.12390.45223.0417.6521
31.04291.01590.35490.887-0.24452.1125-0.0117-0.0424-0.31780.09430.0373-0.2775-0.3143-0.1191-0.03480.0996-0.0246-0.00750.03530.04780.1344.662625.3132-3.558
40.7483-0.60650.21340.9644-0.85751.098-0.00670.02910.23860.1497-0.12360.2383-0.24860.14350.01550.0642-0.0345-0.04940.03310.00750.06387.524818.30122.6754
50.82670.30990.52950.6310.25831.0826-0.1320.0216-0.0673-0.05810.1518-0.0845-0.0149-0.0886-0.13360.051-0.0075-0.04670.09080.00440.122133.7478-2.753229.9242
60.70220.0256-0.61730.29780.00361.3607-0.04180.0448-0.02280.11490.09050.0640.085-0.2401-0.06470.0730.02860.02790.117-0.02250.086645.2972-11.732851.2242
72.1162-0.0783-1.25111.40710.5360.55060.07410.29780.02280.419-0.20890.22830.1938-0.34770.12180.2-0.09760.02990.25740.00770.059336.7708-23.215857.94
80.3714-0.0880.92940.8195-0.28460.8242-0.0521-0.3904-0.09040.1985-0.00580.0326-0.266-0.17990.02840.02140.03060.04570.1183-0.05730.116333.47430.291645.6937
91.40250.25330.41230.5439-0.44270.9359-0.2674-0.20960.1444-0.27920.0928-0.07390.2982-0.14550.11270.3377-0.05910.06360.0489-0.01260.0446-8.1159-14.030.7416
100.44060.1550.0720.96790.09580.45050.11040.1345-0.14570.0852-0.04760.04740.0303-0.2118-0.02670.0275-0.0420.00750.110.0340.0937-21.95649.9418-10.3106
110.585-0.10750.33530.0197-0.9550.6237-0.01020.3917-0.3473-0.4632-0.16720.42820.39790.3165-0.01310.2498-0.11730.0120.1251-0.05480.0112-8.7723-9.5818-12.0899
120.7185-0.86930.47351.3182-0.11710.1852-0.089-0.02620.202-0.11450.0231-0.29110.22060.0930.05550.2776-0.03680.10420.0001-0.00910.108352.5705-28.31920.8831
130.6629-0.3905-0.14650.25620.41190.22160.0184-0.1355-0.18940.0846-0.1713-0.08540.10630.01240.07580.1380.04890.01260.15170.05640.116365.4942-29.809647.6003
140.6464-0.14180.26220.31880.26470.7814-0.1386-0.1286-0.45450.08180.13170.05430.68960.11890.04050.36350.01590.11660.01920.01670.308553.4008-38.861428.9885
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:53)A3 - 53
2X-RAY DIFFRACTION2(chain A and resid 54:120)A54 - 120
3X-RAY DIFFRACTION3(chain A and resid 121:247) or (chain G and resid 1)A121 - 247
4X-RAY DIFFRACTION3(chain A and resid 121:247) or (chain G and resid 1)A1 - 394
5X-RAY DIFFRACTION4(chain A and resid 248:375) or (chain G and resid 2:5)A248 - 375
6X-RAY DIFFRACTION4(chain A and resid 248:375) or (chain G and resid 2:5)A2 - 398
7X-RAY DIFFRACTION5(chain B and resid 3:105)B3 - 105
8X-RAY DIFFRACTION6(chain B and resid 110:153)B110 - 153
9X-RAY DIFFRACTION7(chain B and resid 154:231) or (chain H and resid 1)B154 - 231
10X-RAY DIFFRACTION7(chain B and resid 154:231) or (chain H and resid 1)B1 - 394
11X-RAY DIFFRACTION8(chain B and resid 232:382) or (chain H and resid 2:6)B232 - 382
12X-RAY DIFFRACTION8(chain B and resid 232:382) or (chain H and resid 2:6)B2 - 398
13X-RAY DIFFRACTION9(chain C and resid 2:119) or (chain I and resid 1) or (chain E)C2 - 119
14X-RAY DIFFRACTION9(chain C and resid 2:119) or (chain I and resid 1) or (chain E)C1 - 396
15X-RAY DIFFRACTION9(chain C and resid 2:119) or (chain I and resid 1) or (chain E)E0
16X-RAY DIFFRACTION10(chain C and resid 120:267)C120 - 267
17X-RAY DIFFRACTION11(chain C and resid 278:383) or (chain I and resid 3:4)C278 - 383
18X-RAY DIFFRACTION11(chain C and resid 278:383) or (chain I and resid 3:4)C3 - 398
19X-RAY DIFFRACTION12(chain D and resid 2:120) or (chain J and resid 1) or (chain F)D2 - 120
20X-RAY DIFFRACTION12(chain D and resid 2:120) or (chain J and resid 1) or (chain F)D1 - 396
21X-RAY DIFFRACTION12(chain D and resid 2:120) or (chain J and resid 1) or (chain F)B - F0
22X-RAY DIFFRACTION13(chain D and resid 121:268) or (chain J and resid 2)D121 - 268
23X-RAY DIFFRACTION13(chain D and resid 121:268) or (chain J and resid 2)D2 - 397
24X-RAY DIFFRACTION14(chain D and resid 279:383) or (chain J and resid 3)D279 - 383
25X-RAY DIFFRACTION14(chain D and resid 279:383) or (chain J and resid 3)D3 - 398

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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

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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

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