[English] 日本語
Yorodumi
- PDB-6hch: STRUCTURE OF GLUA2 LIGAND-BINDING DOMAIN (S1S2J-L504Y-N775S) IN C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hch
TitleSTRUCTURE OF GLUA2 LIGAND-BINDING DOMAIN (S1S2J-L504Y-N775S) IN COMPLEX WITH GLUTAMATE AND TDPAM01 AT 1.6 A RESOLUTION.
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / ampa receptor / gluA2 / ligand-binding domain / glua2-S1S2J-L504Y-N775S / signaling protein / positive allosteric modulator
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 / Schaffer collateral - CA1 synapse / terminal bouton / 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
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 ...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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-D45 / GLUTAMIC ACID / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLaulumaa, S. / Hansen, K.V. / Frydenvang, K. / Kastrup, J.S.
CitationJournal: Acs Med.Chem.Lett. / Year: 2019
Title: Crystal Structures of Potent Dimeric Positive Allosteric Modulators at the Ligand-Binding Domain of the GluA2 Receptor.
Authors: Laulumaa, S. / Hansen, K.V. / Masternak, M. / Drapier, T. / Francotte, P. / Pirotte, B. / Frydenvang, K. / Kastrup, J.S.
History
DepositionAug 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)91,55545
Polymers87,9053
Non-polymers3,65042
Water14,448802
1
A: Glutamate receptor 2
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,72427
Polymers58,6032
Non-polymers2,12125
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glutamate receptor 2
hetero molecules

C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,66236
Polymers58,6032
Non-polymers3,05834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Unit cell
Length a, b, c (Å)114.630, 163.580, 47.528
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 15 or resid 17...
21(chain B and (resid 1 through 15 or resid 17...
31(chain C and (resid 1 through 15 or resid 17...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 15 or resid 17...A1 - 15
121(chain A and (resid 1 through 15 or resid 17...A17
131(chain A and (resid 1 through 15 or resid 17...A20 - 23
141(chain A and (resid 1 through 15 or resid 17...A0
151(chain A and (resid 1 through 15 or resid 17...A1
161(chain A and (resid 1 through 15 or resid 17...A109 - 115
171(chain A and (resid 1 through 15 or resid 17...A165 - 175
181(chain A and (resid 1 through 15 or resid 17...A1 - 263
191(chain A and (resid 1 through 15 or resid 17...A1195
1101(chain A and (resid 1 through 15 or resid 17...A197
1111(chain A and (resid 1 through 15 or resid 17...A197
1121(chain A and (resid 1 through 15 or resid 17...A2
1131(chain A and (resid 1 through 15 or resid 17...A218 - 2221
1141(chain A and (resid 1 through 15 or resid 17...A223 - 23
1151(chain A and (resid 1 through 15 or resid 17...A233 - 239
1161(chain A and (resid 1 through 15 or resid 17...A241 - 245
1171(chain A and (resid 1 through 15 or resid 17...A247 - 262
211(chain B and (resid 1 through 15 or resid 17...B1 - 15
221(chain B and (resid 1 through 15 or resid 17...B17
231(chain B and (resid 1 through 15 or resid 17...B20 - 23
241(chain B and (resid 1 through 15 or resid 17...B2
251(chain B and (resid 1 through 15 or resid 17...B0
261(chain B and (resid 1 through 15 or resid 17...B78 - 106
271(chain B and (resid 1 through 15 or resid 17...B1 - 262
281(chain B and (resid 1 through 15 or resid 17...B165 - 175
291(chain B and (resid 1 through 15 or resid 17...B197
2101(chain B and (resid 1 through 15 or resid 17...B197
2111(chain B and (resid 1 through 15 or resid 17...B200 - 208
2121(chain B and (resid 1 through 15 or resid 17...B211 - 216
2131(chain B and (resid 1 through 15 or resid 17...B223 - 231
2141(chain B and (resid 1 through 15 or resid 17...B223 - 231
2151(chain B and (resid 1 through 15 or resid 17...B241 - 245
2161(chain B and (resid 1 through 15 or resid 17...B247 - 262
311(chain C and (resid 1 through 15 or resid 17...C1 - 15
321(chain C and (resid 1 through 15 or resid 17...C17
331(chain C and (resid 1 through 15 or resid 17...C20
341(chain C and (resid 1 through 15 or resid 17...C78 - 1009
351(chain C and (resid 1 through 15 or resid 17...C117 - 163
361(chain C and (resid 1 through 15 or resid 17...C165 - 175
371(chain C and (resid 1 through 15 or resid 17...C185 - 195
381(chain C and (resid 1 through 15 or resid 17...C200 - 208
391(chain C and (resid 1 through 15 or resid 17...C223 - 231
3101(chain C and (resid 1 through 15 or resid 17...C233 - 239
3111(chain C and (resid 1 through 15 or resid 17...C241 - 245
3121(chain C and (resid 1 through 15 or resid 17...C247 - 262

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Glutamate receptor 2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / ...GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2


Mass: 29301.729 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: NATIVE GLUA2 IS A MEMBRANE PROTEIN. THE CRYSTALLIZED PROTEIN IS A L540Y-N775S-MUTANT OF THE GLUA2 LIGAND-BINDING DOMAIN. TRANSMEMBRANE REGIONS ARE REPLACED WITH A GLY-THR LINKER (RESIDUES ...Details: NATIVE GLUA2 IS A MEMBRANE PROTEIN. THE CRYSTALLIZED PROTEIN IS A L540Y-N775S-MUTANT OF THE GLUA2 LIGAND-BINDING DOMAIN. TRANSMEMBRANE REGIONS ARE REPLACED WITH A GLY-THR LINKER (RESIDUES 118-119) AND GLY1-ALA2 IS A CLONING REMNANT. THE SEQUENCE MATCHES DISCONTINUOUSLY WITH REFERENCE DATABASE (413-527, 653-797).
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B / References: UniProt: P19491

-
Non-polymers , 8 types, 844 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C5H9NO4
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-D45 / 6,6'-(Ethane-1,2-diyl)bis(4-methyl-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide)


Mass: 422.522 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22N4O4S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 802 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15% PEG4000, 0.1 M zinc acetate, 0.1 M sodium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→49.24 Å / Num. all: 118901 / Num. obs: 118901 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 19.65 Å2 / Rpim(I) all: 0.028 / Rrim(I) all: 0.104 / Rsym value: 0.1 / Net I/av σ(I): 4.1 / Net I/σ(I): 13.6 / Num. measured all: 1579323
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.6-1.6913.40.850.9171750.2390.8830.85100
1.69-1.7912.70.5581.3162310.1620.5810.558100
1.79-1.9112.60.3571.8153230.1040.3720.357100
1.91-2.0712.80.2242.6142740.0650.2330.224100
2.07-2.2613.90.1463.9131520.040.1520.146100
2.26-2.5313.90.1194.4119490.0330.1240.119100
2.53-2.9213.70.0985.1105740.0270.1010.098100
2.92-3.5813.60.0746.790330.0210.0770.074100
3.58-5.0613.80.0598.870770.0170.0610.059100
5.06-49.2412.60.0637.741130.0190.0660.06399.9

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTJ

1ftj


Resolution: 1.6→49.24 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.57 / Phase error: 16.4
RfactorNum. reflection% reflection
Rfree0.1783 5882 4.95 %
Rwork0.1549 --
obs0.1561 118768 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.69 Å2 / Biso mean: 28.966 Å2 / Biso min: 10.45 Å2
Refinement stepCycle: final / Resolution: 1.6→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6135 0 215 815 7165
Biso mean--47.47 34.49 -
Num. residues----791
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3307X-RAY DIFFRACTION6.12TORSIONAL
12B3307X-RAY DIFFRACTION6.12TORSIONAL
13C3307X-RAY DIFFRACTION6.12TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.61820.22141970.205837303927
1.6182-1.63720.21141850.192837683953
1.6372-1.65720.23522200.191636513871
1.6572-1.67820.20632300.186636503880
1.6782-1.70030.20682050.182937483953
1.7003-1.72350.16681810.173837033884
1.7235-1.74820.21951800.172137353915
1.7482-1.77430.21311850.170637443929
1.7743-1.8020.20121800.182437263906
1.802-1.83150.21932190.179837343953
1.8315-1.86310.20131870.16936773864
1.8631-1.8970.19341890.16137543943
1.897-1.93350.19141850.157137283913
1.9335-1.9730.18551950.160337833978
1.973-2.01590.181750.150137123887
2.0159-2.06270.17661920.145437733965
2.0627-2.11430.191960.148436923888
2.1143-2.17150.16382000.148737933993
2.1715-2.23540.17882260.144636993925
2.2354-2.30760.16911870.143737573944
2.3076-2.390.17171920.147937823974
2.39-2.48570.17961990.151737653964
2.4857-2.59880.19352130.150737373950
2.5988-2.73580.16862130.146637633976
2.7358-2.90720.17681870.153637953982
2.9072-3.13170.17332060.152838064012
3.1317-3.44680.18311800.152938524032
3.4468-3.94530.14821820.140938714053
3.9453-4.96990.14731870.128238794066
4.9699-49.26310.19652090.190740794288
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)
10.2667-0.0747-0.02550.2045-0.1450.11-0.0134-0.01340.11970.0947-0.01120.07110.01360.028900.1314-0.00730.00310.1337-0.00120.1353-49.482.996615.3644
20.14160.0571-0.01470.09180.01410.0351-0.0080.14520.1448-0.41910.1737-0.0729-0.27980.0505-0.00040.225-0.03030.04850.25020.02330.1916-41.108681.8962-3.948
30.8454-0.14980.02570.8706-0.2070.94850.0057-0.02530.01650.0473-0.0119-0.1131-0.0510.1077-00.127-0.0074-0.00230.14570.00270.1351-36.497337.65563.2176
40.8257-0.1986-0.59630.57510.2510.8013-0.01940.0203-0.0776-0.037-0.03310.01320.0370.03500.14680.0135-0.01180.13160.00950.1431-39.131325.7919-10.8436
50.4977-0.2529-0.51750.61380.09760.5695-0.0122-0.0465-0.1641-0.0894-0.02970.02890.0997-0.086600.2268-0.0558-0.02760.1997-0.0070.2097-67.47578.23490.244
60.661-0.02730.27830.3159-0.03730.73280.0069-0.04810.0254-0.03720.00530.0221-0.03-0.104500.1494-0.0162-0.00860.1556-0.00430.1511-67.761124.78660.3009
70.9638-0.2119-0.22740.54410.11910.9420.04410.0220.31270.02390.00480.0944-0.0561-0.28510.00310.19890.00940.00210.2161-0.00050.2673-72.907632.816-14.0511
80.9031-0.04930.24960.65-0.36070.2376-0.00950.0905-0.0954-0.12840.0146-0.13820.09540.0013-0.00010.1995-0.030.01080.1605-0.0270.171-59.276417.9113-7.4915
90.53670.43580.17150.5526-0.15390.6859-0.0330.0279-0.02980.03780.0455-0.08340.01950.2799-0.00030.12360.0140.00780.2282-0.01590.1479-35.027675.439210.5401
100.1053-0.1135-0.03250.11150.03250.48670.003-0.0685-0.12160.18280.036-0.07440.16980.0925-00.17550.02150.00710.1739-0.00730.169-42.297968.757315.4768
110.4365-0.2711-0.14480.24570.20960.2399-0.0761-0.0833-0.0534-0.00320.10220.01260.43760.12660.0540.2272-0.01050.01240.12810.04390.1371-51.051861.708518.747
120.0678-0.06710.18740.21010.03030.2805-0.0394-0.0164-0.010.00250.0160.03110.0290.0244-00.131-0.00150.01090.1460.00310.1361-51.994372.352610.2683
130.59340.2824-0.22720.87210.25890.2579-0.00910.03-0.02320.041-0.02160.20090.1022-0.0081-0.00040.1406-0.00090.00840.12590.00230.1831-59.46361.4487-4.8319
140.0537-0.0049-0.09970.16170.10620.3398-0.04730.05540.00120.0988-0.02580.14290.154-0.023800.1726-0.00340.02230.13210.00170.2264-58.742355.6575-1.2464
150.33350.0061-0.07370.0853-0.01940.1158-0.003-0.0672-0.07950.0078-0.0443-0.09390.04870.0957-0.00020.14870.00460.01750.14250.00680.1287-47.23565.1374-6.8894
160.09660.1197-0.03250.2580.21250.16140.049-0.11970.0919-0.1483-0.00380.007-0.1390.12350.00010.18250.00040.00090.2160.00790.1495-50.24870.7773-9.5705
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 218 through 244 )C218 - 244
2X-RAY DIFFRACTION2chain 'C' and (resid 245 through 263 )C245 - 263
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 93 )A1 - 93
4X-RAY DIFFRACTION4chain 'A' and (resid 94 through 263 )A94 - 263
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 47 )B1 - 47
6X-RAY DIFFRACTION6chain 'B' and (resid 48 through 123 )B48 - 123
7X-RAY DIFFRACTION7chain 'B' and (resid 124 through 202 )B124 - 202
8X-RAY DIFFRACTION8chain 'B' and (resid 203 through 262 )B203 - 262
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 47 )C1 - 47
10X-RAY DIFFRACTION10chain 'C' and (resid 48 through 65 )C48 - 65
11X-RAY DIFFRACTION11chain 'C' and (resid 66 through 79 )C66 - 79
12X-RAY DIFFRACTION12chain 'C' and (resid 80 through 116 )C80 - 116
13X-RAY DIFFRACTION13chain 'C' and (resid 117 through 152 )C117 - 152
14X-RAY DIFFRACTION14chain 'C' and (resid 153 through 173 )C153 - 173
15X-RAY DIFFRACTION15chain 'C' and (resid 174 through 202 )C174 - 202
16X-RAY DIFFRACTION16chain 'C' and (resid 203 through 217 )C203 - 217

+
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