[English] 日本語
Yorodumi
- PDB-3kg2: AMPA subtype ionotropic glutamate receptor in complex with compet... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kg2
TitleAMPA subtype ionotropic glutamate receptor in complex with competitive antagonist ZK 200775
ComponentsGlutamate receptor 2
Keywordsmembrane protein / transport protein / ion channel / Cell membrane / Glycoprotein / Ion transport / Membrane / Postsynaptic cell membrane / Receptor / RNA editing / Synapse / Transmembrane / Transport / tetramer
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / extracellularly glutamate-gated ion channel activity ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / cellular response to glycine / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / response to fungicide / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / regulation of synaptic transmission, glutamatergic / ionotropic glutamate receptor binding / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / synaptic transmission, glutamatergic / synaptic membrane / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / establishment of protein localization / modulation of chemical synaptic transmission / terminal bouton / Schaffer collateral - CA1 synapse / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / dendrite / synapse / protein-containing complex binding / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
Helix Hairpins - #70 / Response regulator / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. ...Helix Hairpins - #70 / Response regulator / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-ZK1 / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsSobolevsky, A.I. / Rosconi, M.P. / Gouaux, E.
CitationJournal: Nature / Year: 2009
Title: X-ray structure, symmetry and mechanism of an AMPA-subtype glutamate receptor.
Authors: Sobolevsky, A.I. / Rosconi, M.P. / Gouaux, E.
History
DepositionOct 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3May 27, 2015Group: Refinement description
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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.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 2.1Oct 13, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate receptor 2
B: Glutamate receptor 2
C: Glutamate receptor 2
D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)372,48012
Polymers368,1724
Non-polymers4,3078
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25170 Å2
ΔGint-194 kcal/mol
Surface area135070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.715, 109.848, 161.130
Angle α, β, γ (deg.)85.32, 84.75, 78.92
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
13
23
14
24
34
44
15
25
35
45
16
26
36
46
17
27
37
47
18
28
19
29
110
210
310
410
111
211
311
411
112
212
312
412
113
213
313
413

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and resid 10:306
211chain B and resid 10:306
311chain C and resid 10:306
411chain D and resid 10:306
112chain A and resid 307:311
212chain D and resid 307:311
113chain B and resid 307:311
213chain C and resid 307:311
114chain A and resid 312:381
214chain B and resid 312:381
314chain C and resid 312:381
414chain D and resid 312:381
115chain A and resid 396:503
215chain B and resid 396:503
315chain C and resid 396:503
415chain D and resid 396:503
116chain A and resid 513:544
216chain B and resid 513:544
316chain C and resid 513:544
416chain D and resid 513:544
117chain A and resid 568:621
217chain B and resid 568:621
317chain C and resid 568:621
417chain D and resid 568:621
118chain A and resid 622:634
218chain C and resid 622:634
119chain B and resid 622:634
219chain D and resid 622:634
1110chain A and resid 635:773
2110chain B and resid 635:773
3110chain C and resid 635:773
4110chain D and resid 635:773
1111chain A and resid 775:780
2111chain B and resid 775:780
3111chain C and resid 775:780
4111chain D and resid 775:780
1112chain A and resid 788:817
2112chain B and resid 788:817
3112chain C and resid 788:817
4112chain D and resid 788:817
1113chain A and resid 818
2113chain B and resid 818
3113chain C and resid 818
4113chain D and resid 818

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13

-
Components

#1: Protein
Glutamate receptor 2 / GluR-2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / AMPA-selective glutamate receptor 2


Mass: 92043.039 Da / Num. of mol.: 4 / Fragment: sequence database residues 25-847
Mutation: N241E, N385D, N392Q, K410A, E413A, M414A, E416A, and C589A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P19491
#2: Polysaccharide beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-ZK1 / {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid / [[3,4-Dihydro-7-(4-morpholinyl)-2,3-dioxo-6-(trifluorom ethyl)-1(2H)-quinoxalinyl]methyl]phosphonic acid


Mass: 409.254 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H15F3N3O6P / Comment: antagonist, medication*YM
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 4.25 Å3/Da / Density % sol: 71.08 %
Crystal growTemperature: 277 K / Details: Under paraffin oil, temperature 277K / PH range: 6.0-6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2008
Details: VERTICALLY COLLIMATING PREMIRROR, LN2 COOLED DOUBLE- CRYSTAL SILICON (111) MONOCHROMATOR, TOROIDAL FOCUSING M2 MIRROR
RadiationMonochromator: DOUBLE-CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 69301 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 136.41 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 17.2
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 2.08 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3H5V and 1FTL

3h5v

1ftl


Resolution: 3.6→49.89 Å / SU ML: 0.01 / σ(F): 1.96 / Phase error: 33.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.296 3483 5.03 %
Rwork0.286 --
obs0.287 69301 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.87 Å2 / ksol: 0.21 e/Å3
Displacement parametersBiso mean: 192.72 Å2
Baniso -1Baniso -2Baniso -3
1--15.6279 Å2-1.4252 Å235.0738 Å2
2--14.5974 Å2-13.3631 Å2
3---1.0304 Å2
Refinement stepCycle: LAST / Resolution: 3.6→49.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22400 0 286 0 22686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223200
X-RAY DIFFRACTIONf_angle_d0.44231770
X-RAY DIFFRACTIONf_dihedral_angle_d9.6967414
X-RAY DIFFRACTIONf_chiral_restr0.0273788
X-RAY DIFFRACTIONf_plane_restr0.0024032
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2209X-RAY DIFFRACTIONPOSITIONAL
12B2209X-RAY DIFFRACTIONPOSITIONAL0.005
13C2209X-RAY DIFFRACTIONPOSITIONAL0.004
14D2209X-RAY DIFFRACTIONPOSITIONAL0.004
21A28X-RAY DIFFRACTIONPOSITIONAL
22D28X-RAY DIFFRACTIONPOSITIONAL0.003
31B28X-RAY DIFFRACTIONPOSITIONAL
32C28X-RAY DIFFRACTIONPOSITIONAL0.004
41A498X-RAY DIFFRACTIONPOSITIONAL
42B498X-RAY DIFFRACTIONPOSITIONAL0.005
43C498X-RAY DIFFRACTIONPOSITIONAL0.004
44D498X-RAY DIFFRACTIONPOSITIONAL0.004
51A793X-RAY DIFFRACTIONPOSITIONAL
52B793X-RAY DIFFRACTIONPOSITIONAL0.004
53C793X-RAY DIFFRACTIONPOSITIONAL0.004
54D793X-RAY DIFFRACTIONPOSITIONAL0.004
61A254X-RAY DIFFRACTIONPOSITIONAL
62B254X-RAY DIFFRACTIONPOSITIONAL0.002
63C254X-RAY DIFFRACTIONPOSITIONAL0.003
64D254X-RAY DIFFRACTIONPOSITIONAL0.003
71A310X-RAY DIFFRACTIONPOSITIONAL
72B310X-RAY DIFFRACTIONPOSITIONAL0.007
73C310X-RAY DIFFRACTIONPOSITIONAL0.006
74D310X-RAY DIFFRACTIONPOSITIONAL0.006
81A95X-RAY DIFFRACTIONPOSITIONAL
82C95X-RAY DIFFRACTIONPOSITIONAL0.133
91B95X-RAY DIFFRACTIONPOSITIONAL
92D95X-RAY DIFFRACTIONPOSITIONAL0.022
101A995X-RAY DIFFRACTIONPOSITIONAL
102B995X-RAY DIFFRACTIONPOSITIONAL0.005
103C995X-RAY DIFFRACTIONPOSITIONAL0.004
104D995X-RAY DIFFRACTIONPOSITIONAL0.004
111A29X-RAY DIFFRACTIONPOSITIONAL
112B29X-RAY DIFFRACTIONPOSITIONAL0.023
113C29X-RAY DIFFRACTIONPOSITIONAL0.007
114D29X-RAY DIFFRACTIONPOSITIONAL0.013
121A217X-RAY DIFFRACTIONPOSITIONAL
122B217X-RAY DIFFRACTIONPOSITIONAL0.003
123C217X-RAY DIFFRACTIONPOSITIONAL0.004
124D217X-RAY DIFFRACTIONPOSITIONAL0.004
131A27X-RAY DIFFRACTIONPOSITIONAL
132B27X-RAY DIFFRACTIONPOSITIONAL0.003
133C27X-RAY DIFFRACTIONPOSITIONAL0.003
134D27X-RAY DIFFRACTIONPOSITIONAL0.002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6029-3.65230.45641270.42574X-RAY DIFFRACTION94
3.6523-3.70440.43551400.38982589X-RAY DIFFRACTION100
3.7044-3.75970.36511380.37322669X-RAY DIFFRACTION99
3.7597-3.81840.34591330.37182647X-RAY DIFFRACTION99
3.8184-3.8810.38631450.36672623X-RAY DIFFRACTION99
3.881-3.94790.36081420.36622653X-RAY DIFFRACTION98
3.9479-4.01970.36461460.35232586X-RAY DIFFRACTION99
4.0197-4.09690.2791530.33752605X-RAY DIFFRACTION98
4.0969-4.18050.32991330.32562601X-RAY DIFFRACTION98
4.1805-4.27140.34721680.32072612X-RAY DIFFRACTION98
4.2714-4.37070.3241270.29522626X-RAY DIFFRACTION99
4.3707-4.47990.30251420.29182616X-RAY DIFFRACTION99
4.4799-4.6010.28911350.27882661X-RAY DIFFRACTION99
4.601-4.73630.32021320.27862625X-RAY DIFFRACTION99
4.7363-4.8890.33091370.26312615X-RAY DIFFRACTION99
4.889-5.06360.26871450.26692669X-RAY DIFFRACTION99
5.0636-5.26610.2831510.27282613X-RAY DIFFRACTION99
5.2661-5.50550.28681440.27892650X-RAY DIFFRACTION100
5.5055-5.79530.26391320.28072667X-RAY DIFFRACTION100
5.7953-6.15780.28121240.28592679X-RAY DIFFRACTION100
6.1578-6.63230.2981270.25362664X-RAY DIFFRACTION100
6.6323-7.29790.28821430.25472656X-RAY DIFFRACTION100
7.2979-8.34960.24411420.22882670X-RAY DIFFRACTION100
8.3496-10.50350.20751380.1982667X-RAY DIFFRACTION100
10.5035-49.89230.27581390.30092581X-RAY DIFFRACTION97
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)
14.18660.8276-2.76563.5819-0.63384.4906-0.4393-0.4141-0.20530.11490.13890.36730.4525-0.0347-0.00011.17550.1172-0.0940.9922-0.07651.2748-54.2082-14.6743-29.0048
27.02021.8649-0.41233.78530.48651.6963-0.0033-0.062-0.12820.2306-0.08140.13330.0655-0.1767-00.96970.052-0.14261.086-0.10241.0511-59.824417.1572-15.8351
32.1580.53190.20522.2389-0.20644.1410.1953-0.9780.4810.9470.15880.3133-1.39370.4532-02.0145-0.12120.02632.2069-0.30131.5458-13.173261.071512.9931
42.91410.54811.05032.89310.42166.061-0.1626-1.4817-0.64421.1121-0.31810.15780.361-0.051-0.00021.10270.05760.06492.19480.19411.476-14.474226.245914.5404
54.2372.1328-0.67422.6953-0.27992.2275-0.35050.76750.1015-0.47250.26380.36040.0866-0.105-0.00011.4698-0.0416-0.11471.1687-0.03431.2136-18.6299.7851-65.4644
63.2927-0.3844-1.47911.77160.23363.61820.22180.62430.154-0.5232-0.09170.1772-0.4164-0.14140.00011.6782-0.0561-0.01440.890.04871.4563-15.039459.3039-53.7743
72.85730.2634-0.76822.44510.583.4729-0.08910.064-0.2942-0.18680.2535-0.58140.00031.1697-0.00011.5273-0.29390.11111.3939-0.13781.50736.973855.7359-39.5385
83.73880.68640.41781.7212-0.4822.34710.01850.1997-0.6461-0.4386-0.3051-0.55210.68610.559801.51680.1737-0.02531.30650.02021.30695.15664.2517-54.9975
94.24120.2272-0.83883.07350.09932.5848-0.18441.07250.1563-0.90050.2728-0.5289-0.08650.6428-01.91780.01860.16362.20260.27281.182324.604240.143-98.5753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 10:381A10 - 381
2X-RAY DIFFRACTION2chain B and resid 10:381B10 - 381
3X-RAY DIFFRACTION3chain C and resid 10:381C10 - 381
4X-RAY DIFFRACTION4chain D and resid 10:381D10 - 381
5X-RAY DIFFRACTION5chain A and (resid 396:503 or resid 635:773)A396 - 503
6X-RAY DIFFRACTION5chain A and (resid 396:503 or resid 635:773)A635 - 773
7X-RAY DIFFRACTION6chain B and (resid 396:503 or resid 635:773)B396 - 503
8X-RAY DIFFRACTION6chain B and (resid 396:503 or resid 635:773)B635 - 773
9X-RAY DIFFRACTION7chain C and (resid 396:503 or resid 635:773)C396 - 503
10X-RAY DIFFRACTION7chain C and (resid 396:503 or resid 635:773)C635 - 773
11X-RAY DIFFRACTION8chain D and (resid 396:503 or resid 635:773)D396 - 503
12X-RAY DIFFRACTION8chain D and (resid 396:503 or resid 635:773)D635 - 773
13X-RAY DIFFRACTION9resid 513:544 or resid 568:634 or resid 788:8170

+
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