[English] 日本語
Yorodumi
- PDB-5o9a: Crystal structure of the GluA2 ligand-binding domain (S1S2J-L504Y... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o9a
TitleCrystal structure of the GluA2 ligand-binding domain (S1S2J-L504Y-N775S) in complex with glutamate and BPAM121 at 1.78 A resolution
ComponentsGlutamate receptor 2,Glutamate receptor 2
KeywordsMEMBRANE PROTEIN / AMPA receptor / Ligand-binding domain / positive allosteric modulator / signaling protein / Ionotropic glutamate receptor / GLUA2 / GLUR2 / L504Y-N775S
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / 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 / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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. ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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 II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7M6 / CITRIC ACID / GLUTAMIC ACID / DI(HYDROXYETHYL)ETHER / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsLaulumaa, S. / Rovinskaja, K. / Frydenvang, K.A. / Kastrup, J.S.
CitationJournal: J. Med. Chem. / Year: 2018
Title: 7-Phenoxy-Substituted 3,4-Dihydro-2H-1,2,4-benzothiadiazine 1,1-Dioxides as Positive Allosteric Modulators of alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptors with Nanomolar Potency.
Authors: Goffin, E. / Drapier, T. / Larsen, A.P. / Geubelle, P. / Ptak, C.P. / Laulumaa, S. / Rovinskaja, K. / Gilissen, J. / Tullio, P. / Olsen, L. / Frydenvang, K. / Pirotte, B. / Hanson, J. / ...Authors: Goffin, E. / Drapier, T. / Larsen, A.P. / Geubelle, P. / Ptak, C.P. / Laulumaa, S. / Rovinskaja, K. / Gilissen, J. / Tullio, P. / Olsen, L. / Frydenvang, K. / Pirotte, B. / Hanson, J. / Oswald, R.E. / Kastrup, J.S. / Francotte, P.
History
DepositionJun 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 17, 2024Group: 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)121,36842
Polymers117,2074
Non-polymers4,16138
Water20,8971160
1
A: Glutamate receptor 2,Glutamate receptor 2
B: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,48420
Polymers58,6032
Non-polymers1,88018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-112 kcal/mol
Surface area24850 Å2
MethodPISA
2
C: Glutamate receptor 2,Glutamate receptor 2
D: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,88422
Polymers58,6032
Non-polymers2,28120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-146 kcal/mol
Surface area24320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.308, 98.408, 121.787
Angle α, β, γ (deg.)90.000, 90.530, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 5:15 or resseq 17:20 or (resid...
21(chain B and (resseq 5:15 or resseq 17:20 or (resid...
31(chain D and (resseq 5:15 or resseq 17:20 or (resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRPROPRO(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA5 - 155 - 15
12VALVALLYSLYS(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA17 - 2017 - 20
13HISHISHISHIS(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA2323
14GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
15GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
16GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
17GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
18GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
19GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
110GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
111GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
112GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
113GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
114GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
115GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
116GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
117GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
118GLYGLYSERSER(chain A and (resseq 5:15 or resseq 17:20 or (resid...AA1 - 2631 - 263
21THRTHRPROPRO(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB5 - 155 - 15
22VALVALLYSLYS(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB17 - 2017 - 20
23HISHISHISHIS(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB2323
24GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
25GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
26GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
27GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
28GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
29GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
210GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
211GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
212GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
213GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
214GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
215GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
216GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
217GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
218GLYGLYGLYGLY(chain B and (resseq 5:15 or resseq 17:20 or (resid...BB1 - 2641 - 264
31THRTHRPROPRO(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD5 - 155 - 15
32VALVALLYSLYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD17 - 2017 - 20
33HISHISHISHIS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2323
34ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
35ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
36ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
37ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
38ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
39ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
310ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
311ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
312ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
313ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
314ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
315ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
316ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
317ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261
318ALAALACYSCYS(chain D and (resseq 5:15 or resseq 17:20 or (resid...DD2 - 2612 - 261

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Glutamate receptor 2,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.: 4 / Mutation: L504Y,N775S
Source method: isolated from a genetically manipulated source
Details: Native GluA2 is a membrane protein. The crystallized protein is a double mutant (L540Y, N775S) of the ligand-binding domain of GluA2. Transmembrane regions were replaced with a Gly-Thr ...Details: Native GluA2 is a membrane protein. The crystallized protein is a double mutant (L540Y, N775S) of the ligand-binding domain of GluA2. Transmembrane regions were replaced with a Gly-Thr linker (residues 117-118). Gly1 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P19491

-
Non-polymers , 9 types, 1198 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Formula: SO4
#3: Chemical
ChemComp-7M6 / 7-chloro-4-(2-fluoroethyl)-2,3-dihydro-1,2,4-benzothiadiazine 1,1-dioxide


Mass: 264.704 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C9H10ClFN2O2S
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1160 / 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: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 18% PEG4000, 0.23 M lithium sulfate, 0.1 M phosphate citrate pH 4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.78→121.782 Å / Num. all: 106755 / Num. obs: 106755 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 15.47 Å2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.074 / Rsym value: 0.063 / Net I/av σ(I): 10.4 / Net I/σ(I): 14.7 / Num. measured all: 395853
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.78-1.883.60.377256042155820.2330.4450.3773.5100
1.88-1.993.70.249354342146820.1510.2920.2495.3100
1.99-2.133.70.1554.851284138090.0940.1820.1558100
2.13-2.33.70.1057.148006128750.0630.1230.10511.3100
2.3-2.523.70.082944383118740.050.0960.08213.7100
2.52-2.813.70.061240212107280.0360.070.0617.9100
2.81-3.253.80.04315.93553394560.0260.0510.04323.9100
3.25-3.983.70.03219.93016380580.0190.0380.03232.4100
3.98-5.633.70.02620.92323562100.0160.0310.02636.8100
5.63-49.2043.60.026201265334810.0160.0310.0263499.8

-
Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TKD

3tkd


Resolution: 1.78→49.204 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 17.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1789 5325 4.99 %
Rwork0.1534 101384 -
obs0.1547 106709 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.84 Å2 / Biso mean: 22.4654 Å2 / Biso min: 5.63 Å2
Refinement stepCycle: final / Resolution: 1.78→49.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8178 0 199 1186 9563
Biso mean--41.23 29.23 -
Num. residues----1054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058868
X-RAY DIFFRACTIONf_angle_d0.78612010
X-RAY DIFFRACTIONf_chiral_restr0.0491304
X-RAY DIFFRACTIONf_plane_restr0.0051490
X-RAY DIFFRACTIONf_dihedral_angle_d15.8165450
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3712X-RAY DIFFRACTION4.403TORSIONAL
12B3712X-RAY DIFFRACTION4.403TORSIONAL
13D3712X-RAY DIFFRACTION4.403TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.78-1.80020.27311470.22634323579100
1.8002-1.82140.25011840.217834243608100
1.8214-1.84360.22281320.197833563488100
1.8436-1.8670.23641910.191633213512100
1.867-1.89150.20971820.190234223604100
1.8915-1.91740.19821520.186633313483100
1.9174-1.94480.19971730.189733873560100
1.9448-1.97390.21731780.184234063584100
1.9739-2.00470.20191760.176933293505100
2.0047-2.03760.21391860.169733603546100
2.0376-2.07270.18431720.157533673539100
2.0727-2.11040.19022030.154333223525100
2.1104-2.1510.18342250.1533793604100
2.151-2.19490.14971690.145233163485100
2.1949-2.24260.17691620.144934463608100
2.2426-2.29480.19021890.147433103499100
2.2948-2.35220.18041780.146933983576100
2.3522-2.41580.1751790.145733493528100
2.4158-2.48690.17621790.147834353614100
2.4869-2.56710.17241760.14833153491100
2.5671-2.65890.17621940.146833983592100
2.6589-2.76530.1931750.144733663541100
2.7653-2.89120.16141610.148433783539100
2.8912-3.04360.18192050.155633633568100
3.0436-3.23420.18361890.14533733562100
3.2342-3.48390.15371600.138634153575100
3.4839-3.83440.15311830.134433913574100
3.8344-4.38890.13471780.121234143592100
4.3889-5.52840.14661740.132534113585100
5.5284-49.22280.22391730.18923470364399
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)
12.1731-0.22920.0982.02630.27551.9456-0.05710.32230.1682-0.15370.04950.0294-0.05610.06760.02280.1313-0.0175-0.01730.10170.0130.06728.930926.540324.6711
22.3426-0.10210.59490.9970.46213.5005-0.11660.27290.1778-0.25460.16810.0268-0.3670.1871-0.01720.1849-0.0651-0.02140.14530.04430.11958.131931.686522.4919
32.88960.84580.01233.09270.55552.1461-0.0980.0193-0.3412-0.10910.0675-0.17360.27550.12940.0630.0897-0.00180.01930.1127-0.02340.088314.682616.850831.763
42.72390.63750.24510.68630.19480.6443-0.0261-0.074-0.03650.0154-0.0035-0.01540.01510.0540.03330.09720.012-0.00790.06520.00610.0463.909320.380639.4679
53.24210.5937-0.04872.8361-0.72433.87360.0463-0.285-0.22250.2671-0.0738-0.13340.2543-0.05190.02050.19970.0019-0.01250.06050.02570.1003-4.30188.240144.0692
62.03010.29450.50393.77750.81271.84270.0812-0.199-0.29310.019-0.0011-0.01480.6332-0.12480.00220.20840.001-0.00410.08050.02170.1254-3.27373.788641.5509
73.45530.60270.48543.7191-0.24552.776-0.03670.0882-0.0898-0.13770.0481-0.03490.1299-0.15060.00160.0964-0.007-0.00230.0787-0.010.0416-9.267915.953132.7976
86.06121.17934.61780.41961.20667.4588-0.0371-0.27880.2302-0.0165-0.11990.1173-0.2569-0.52810.09340.14990.0244-0.00650.0851-0.01530.1452-11.617120.528436.8308
93.51990.2456-0.14132.54110.32181.7461-0.00140.0070.18360.0509-0.0227-0.1453-0.16310.14650.02870.1109-0.0117-0.02080.0975-0.01210.047913.705832.428739.5142
106.0994.44651.72964.13311.26941.8442-0.19440.01480.5971-0.11160.0050.4834-0.1503-0.16640.19650.16960.0223-0.03690.1025-0.00830.1761-5.217534.780831.4429
111.9762-0.33740.14881.89020.0371.57880.0306-0.123-0.02890.1144-0.0402-0.06090.03040.23960.0030.0927-0.01270.00390.1871-0.00510.08098.910830.092970.5916
121.9016-0.3162-0.14711.809-0.40961.80310.0011-0.09530.25310.0396-0.018-0.0151-0.22490.11680.03170.1179-0.0317-0.01010.1297-0.02530.1098.795440.339157.1352
131.3679-0.351-0.52813.69760.50772.31380.2830.05710.4976-0.11620.00520.7486-0.4083-0.2505-0.22520.36940.02290.09570.1572-0.01680.4317-5.167652.155853.5174
144.0454-1.3164-1.22512.37260.15512.15170.0582-0.19560.2082-0.0027-0.04550.4935-0.0488-0.23730.00150.1468-0.0432-0.00910.1272-0.04640.2363-2.651837.678156.9725
154.9584-0.8075-1.64522.42930.18022.7186-0.092-0.1565-0.08430.05890.01480.3220.1567-0.25640.1030.1004-0.0117-0.00770.15380.00520.08570.603623.665559.111
162.1767-0.02320.39641.8329-0.02691.4685-0.10850.22-0.2024-0.18880.0728-0.0070.1736-0.15840.04840.1331-0.03380.0250.1257-0.01730.1012-9.570419.962484.6026
172.95240.72320.03993.5047-0.55592.4338-0.08760.0080.2912-0.09880.10520.1409-0.2729-0.14020.01740.06440.0179-0.01840.11270.03640.0857-15.840732.367592.4356
181.99470.8003-0.2270.81050.05860.98650.0318-0.09620.08120.053-0.02880.0163-0.05070.05590.00320.07860.0199-0.00210.07720.01150.057-2.025733.7527102.2695
191.75080.3499-0.90724.22850.09843.02610.0501-0.17970.2729-0.0560.01710.03-0.70840.1085-0.02170.13980.00340.01090.1031-0.02140.10631.888945.4827102.2621
203.08360.6237-0.45133.96980.24653.1232-0.05940.07040.0568-0.16480.08690.0201-0.08310.1373-0.01450.0567-0.0019-0.0050.10520.00850.04597.962533.480993.416
217.40850.8186-6.39940.1088-0.93258.3417-0.0142-0.2876-0.1844-0.0283-0.09-0.06420.1510.53680.07430.10910.0322-0.00350.09310.02090.143410.351628.613497.7008
223.2477-0.32630.99143.5911-0.72212.4886-0.0252-0.1226-0.3175-0.1520.03040.20790.256-0.2069-0.00590.1113-0.01510.02910.10240.01460.0733-14.699717.1572100.3095
234.44092.4896-1.30762.1311-0.56111.9774-0.3532-0.1688-0.8447-0.12370.025-0.56420.29260.23570.30450.19050.04970.07570.14410.02290.24724.073314.557592.28
242.00680.1572-0.33892.33820.36531.82730.0492-0.13190.04960.2085-0.02490.09910.0468-0.2363-0.00390.1076-0.01220.01330.17260.03380.0933-10.855916.0813131.105
253.8732-0.96011.74072.5041-1.86347.2532-0.0299-0.08080.08220.21610.04380.0555-0.2762-0.1825-0.00890.0937-0.0082-0.00220.0829-0.02370.0868-10.701921.7356131.3769
263.5876-0.59510.00534.86720.09672.3461-0.0654-0.0805-0.4271-0.01690.05670.22370.4935-0.28080.02920.13-0.06980.02620.16890.06620.1396-17.06986.9232122.1429
271.9463-0.44590.44782.76980.99510.6627-0.0353-0.2618-0.08380.0829-0.13530.27420.2197-0.31950.11830.102-0.04790.00740.17390.02560.1183-16.158711.8389119.5395
281.6903-0.61460.7011.0112-0.38431.2026-0.0431-0.0273-0.1375-0.2385-0.1038-0.19830.3350.13370.04230.17420.02330.06550.14310.06320.1641-1.78039.4835113.7569
291.417-0.28930.13741.28140.1580.35140.48820.2342-0.5633-1.0319-0.2603-0.15210.63930.15940.14720.74460.2523-0.0530.12260.10210.31862.1818-3.8374112.3432
307.7987-3.1817-0.47367.01712.53725.5346-0.0682-0.9925-0.40730.0414-0.002-0.43680.23790.17930.1060.1909-0.00840.00540.25340.11510.22918.0438-0.9217126.5183
312.2481-1.4065-0.12922.6612-0.92741.20210.0798-0.16060.1089-0.1201-0.1987-0.51410.10750.37630.090.16360.03520.06020.23680.0980.28167.42469.5175120.3405
323.05660.2251-0.2283.2886-0.55531.4711-0.0361-0.00330.031-0.13840.06530.3373-0.015-0.31920.00170.0884-0.0031-0.01850.14090.01360.0548-15.335122.0464114.5471
337.0824-2.25022.41563.2592-0.34272.8217-0.2217-0.18750.25720.07770.1043-0.5199-0.21140.50.20260.1066-0.0284-0.01420.2170.00590.15093.239824.3856123.7666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 22 )A1 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 47 )A23 - 47
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 79 )A48 - 79
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 123 )A80 - 123
5X-RAY DIFFRACTION5chain 'A' and (resid 124 through 152 )A124 - 152
6X-RAY DIFFRACTION6chain 'A' and (resid 153 through 173 )A153 - 173
7X-RAY DIFFRACTION7chain 'A' and (resid 174 through 202 )A174 - 202
8X-RAY DIFFRACTION8chain 'A' and (resid 203 through 217 )A203 - 217
9X-RAY DIFFRACTION9chain 'A' and (resid 218 through 243 )A218 - 243
10X-RAY DIFFRACTION10chain 'A' and (resid 244 through 263 )A244 - 263
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 47 )B1 - 47
12X-RAY DIFFRACTION12chain 'B' and (resid 48 through 123 )B48 - 123
13X-RAY DIFFRACTION13chain 'B' and (resid 124 through 187 )B124 - 187
14X-RAY DIFFRACTION14chain 'B' and (resid 188 through 230 )B188 - 230
15X-RAY DIFFRACTION15chain 'B' and (resid 231 through 264 )B231 - 264
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 47 )C1 - 47
17X-RAY DIFFRACTION17chain 'C' and (resid 48 through 79 )C48 - 79
18X-RAY DIFFRACTION18chain 'C' and (resid 80 through 152 )C80 - 152
19X-RAY DIFFRACTION19chain 'C' and (resid 153 through 173 )C153 - 173
20X-RAY DIFFRACTION20chain 'C' and (resid 174 through 202 )C174 - 202
21X-RAY DIFFRACTION21chain 'C' and (resid 203 through 217 )C203 - 217
22X-RAY DIFFRACTION22chain 'C' and (resid 218 through 243 )C218 - 243
23X-RAY DIFFRACTION23chain 'C' and (resid 244 through 263 )C244 - 263
24X-RAY DIFFRACTION24chain 'D' and (resid 2 through 22 )D2 - 22
25X-RAY DIFFRACTION25chain 'D' and (resid 23 through 47 )D23 - 47
26X-RAY DIFFRACTION26chain 'D' and (resid 48 through 79 )D48 - 79
27X-RAY DIFFRACTION27chain 'D' and (resid 80 through 93 )D80 - 93
28X-RAY DIFFRACTION28chain 'D' and (resid 94 through 123 )D94 - 123
29X-RAY DIFFRACTION29chain 'D' and (resid 124 through 173 )D124 - 173
30X-RAY DIFFRACTION30chain 'D' and (resid 174 through 187 )D174 - 187
31X-RAY DIFFRACTION31chain 'D' and (resid 188 through 217 )D188 - 217
32X-RAY DIFFRACTION32chain 'D' and (resid 218 through 243 )D218 - 243
33X-RAY DIFFRACTION33chain 'D' and (resid 244 through 261 )D244 - 261

+
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