[English] 日本語
Yorodumi
- PDB-5tza: CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A WITH 3-{5-methyl-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tza
TitleCRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A WITH 3-{5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl-1-[(naphthalene-2-yl)carbonyl]piperidine
ComponentscGMP-dependent 3',5'-cyclic phosphodiesterase
KeywordsHydrolase/Hydrolase Inhibitor / phosphodiesterase / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


regulation of cGMP-mediated signaling / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / cellular response to macrophage colony-stimulating factor stimulus / cellular response to cGMP / negative regulation of cAMP-mediated signaling / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of vascular permeability / heart valve development / cellular response to granulocyte macrophage colony-stimulating factor stimulus / negative regulation of vascular permeability ...regulation of cGMP-mediated signaling / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / cellular response to macrophage colony-stimulating factor stimulus / cellular response to cGMP / negative regulation of cAMP-mediated signaling / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of vascular permeability / heart valve development / cellular response to granulocyte macrophage colony-stimulating factor stimulus / negative regulation of vascular permeability / regulation of mitochondrion organization / establishment of endothelial barrier / aorta development / cGMP-mediated signaling / ventricular septum development / 3',5'-cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of cGMP-mediated signaling / TPR domain binding / cGMP catabolic process / phosphate ion binding / cGMP effects / monocyte differentiation / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / regulation of cAMP-mediated signaling / cAMP binding / cellular response to transforming growth factor beta stimulus / cellular response to cAMP / cAMP-mediated signaling / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / synaptic membrane / cellular response to mechanical stimulus / positive regulation of inflammatory response / cellular response to xenobiotic stimulus / presynaptic membrane / G alpha (s) signalling events / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrial matrix / positive regulation of gene expression / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / GAF domain ...Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7OG / cGMP-dependent 3',5'-cyclic phosphodiesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsXu, R. / Aertgeerts, K.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Design and Synthesis of Novel and Selective Phosphodiesterase 2 (PDE2a) Inhibitors for the Treatment of Memory Disorders.
Authors: Gomez, L. / Massari, M.E. / Vickers, T. / Freestone, G. / Vernier, W. / Ly, K. / Xu, R. / McCarrick, M. / Marrone, T. / Metz, M. / Yan, Y.G. / Yoder, Z.W. / Lemus, R. / Broadbent, N.J. / ...Authors: Gomez, L. / Massari, M.E. / Vickers, T. / Freestone, G. / Vernier, W. / Ly, K. / Xu, R. / McCarrick, M. / Marrone, T. / Metz, M. / Yan, Y.G. / Yoder, Z.W. / Lemus, R. / Broadbent, N.J. / Barido, R. / Warren, N. / Schmelzer, K. / Neul, D. / Lee, D. / Andersen, C.B. / Sebring, K. / Aertgeerts, K. / Zhou, X. / Tabatabaei, A. / Peters, M. / Breitenbucher, J.G.
History
DepositionNov 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Mar 29, 2017Group: Data collection
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cGMP-dependent 3',5'-cyclic phosphodiesterase
B: cGMP-dependent 3',5'-cyclic phosphodiesterase
C: cGMP-dependent 3',5'-cyclic phosphodiesterase
D: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,51716
Polymers160,6724
Non-polymers1,84512
Water21,2941182
1
A: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6294
Polymers40,1681
Non-polymers4613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6294
Polymers40,1681
Non-polymers4613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6294
Polymers40,1681
Non-polymers4613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6294
Polymers40,1681
Non-polymers4613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.799, 73.444, 91.614
Angle α, β, γ (deg.)109.360, 91.170, 91.140
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
cGMP-dependent 3',5'-cyclic phosphodiesterase / Cyclic GMP-stimulated phosphodiesterase / cGSPDE


Mass: 40168.051 Da / Num. of mol.: 4 / Fragment: catalytic domain, UNP residues 323-663
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE2A / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5
References: UniProt: O00408, 3',5'-cyclic-nucleotide phosphodiesterase
#2: Chemical
ChemComp-7OG / [(3S)-3-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl](naphthalen-2-yl)methanone


Mass: 371.435 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C22H21N5O
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Zn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1182 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 / Details: 17-19% PEG3350, 0.2M MgCl2, 0.1M Tris, pH 8.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 11, 2016
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.38→55.77 Å / Num. obs: 142086 / % possible obs: 61.6 % / Redundancy: 2.6 % / Biso Wilson estimate: 17.04 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 10.8
Reflection shellResolution: 1.38→1.42 Å / Redundancy: 2.1 % / Rmerge(I) obs: 1.056 / % possible all: 3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.06 Å55.77 Å
Translation8.06 Å55.77 Å

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.5phasing
PHENIXphenix.refine: 1.9_1692refinement
PDB_EXTRACT3.2data extraction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→55.765 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.99
RfactorNum. reflection% reflection
Rfree0.1965 7160 5.05 %
Rwork0.1646 --
obs0.1662 141759 93.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.25 Å2 / Biso mean: 23.6972 Å2 / Biso min: 7.32 Å2
Refinement stepCycle: final / Resolution: 1.7→55.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11083 0 0 1183 12266
Biso mean---29.03 -
Num. residues----1352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711356
X-RAY DIFFRACTIONf_angle_d1.08415330
X-RAY DIFFRACTIONf_chiral_restr0.0451637
X-RAY DIFFRACTIONf_plane_restr0.0061985
X-RAY DIFFRACTIONf_dihedral_angle_d13.4094192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.71930.26491450.21423012315763
1.7193-1.73960.25341630.21183323348670
1.7396-1.76080.24142000.21083729392978
1.7608-1.78310.26582340.20874441467593
1.7831-1.80650.22542260.20964583480995
1.8065-1.83130.24592350.20144606484195
1.8313-1.85740.25012410.19094570481196
1.8574-1.88520.23422420.19994560480296
1.8852-1.91460.24142470.19534536478396
1.9146-1.9460.21162540.18764572482696
1.946-1.97960.2192500.184607485796
1.9796-2.01560.20982490.17914570481996
2.0156-2.05440.21992500.17434593484396
2.0544-2.09630.21072440.17334598484296
2.0963-2.14190.20292480.16654660490897
2.1419-2.19170.18582200.16324571479196
2.1917-2.24650.19072430.16134682492597
2.2465-2.30720.2052430.16714615485897
2.3072-2.37510.19812740.15844572484697
2.3751-2.45180.19062550.16514648490397
2.4518-2.53940.19332580.16664675493397
2.5394-2.64110.21012460.16894591483797
2.6411-2.76130.19992440.16774659490397
2.7613-2.90690.18942190.17424684490398
2.9069-3.0890.2162540.17384657491198
3.089-3.32750.19192640.15724688495298
3.3275-3.66230.18672710.154651492298
3.6623-4.19210.17423010.13554614491598
4.1921-5.28090.14061890.13264736492598
5.2809-55.79520.1842510.16314596484796
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)
10.92350.50470.30692.04470.65611.4830.0398-0.1362-0.13850.1548-0.06090.05940.0825-0.07960.02480.1186-0.03860.01310.15630.03480.138-7.9803-12.67690.7153
21.19710.08660.13020.82610.01980.7980.02610.0338-0.0412-0.07120.00360.0223-0.01470.0016-0.0360.1154-0.01150.00760.08620.00060.08181.6501-1.9433-7.9264
36.1331-2.85710.60274.2565-0.6381.8292-0.0584-0.10940.94-0.08310.0071-0.1865-0.5710.0689-0.01050.2948-0.0243-0.00070.122-0.03560.21980.527518.5965-2.8262
42.8267-1.23641.87783.8259-2.36463.97310.0002-0.14580.2037-0.10570.01830.207-0.1556-0.2294-0.0460.13020.00190.0130.0916-0.02970.1209-5.611210.6209-2.4506
53.546-0.72770.66461.65980.16541.48720.0136-0.22280.20890.1446-0.008-0.154-0.17320.1455-0.03790.178-0.0438-0.00470.165-0.01010.101412.95947.42379.6128
66.0757-1.5025.46020.5203-0.95194.2106-0.1052-0.36240.07410.1910.0846-0.0394-0.1384-0.10620.02560.3115-0.0090.03620.3877-0.04660.170910.63217.360422.9581
71.7961-0.51520.19282.2306-1.04793.0930.08120.0278-0.2877-0.0851-0.0578-0.12060.32150.2062-0.02040.20530.0636-0.00760.1461-0.05780.211129.1805-16.1224-37.1965
85.2658-3.45382.93553.5826-2.14723.0230.064-0.0101-0.41160.15770.12040.0790.3058-0.0194-0.18430.20150.0082-0.03030.0906-0.01430.168118.2297-12.3846-30.6995
92.03150.6519-0.43822.4408-0.04362.54430.04710.0164-0.0963-0.09040.0214-0.22520.01390.3484-0.06640.13580.0456-0.00080.1218-0.02850.137830.3684-3.2402-36.783
103.6975-0.21840.12872.42680.33062.9534-0.0202-0.21630.20780.27020.00280.296-0.253-0.3201-0.00290.17350.02270.02620.1422-0.00650.120410.68121.5929-26.1285
111.7381-0.26360.46271.84440.04312.10830.1168-0.1693-0.19150.16260.0283-0.06680.16690.2464-0.09220.16620.0183-0.01330.13970.00340.117828.3471-2.4237-21.2263
126.47642.1307-1.30052.1874-0.51921.3319-0.03190.13220.5969-0.02680.19220.0736-0.4552-0.0321-0.20190.29780.01430.02330.11390.00460.170424.279515.8299-37.9261
135.89192.72392.25694.0672.0392.88140.08590.06420.010.00870.0642-0.2412-0.0920.1457-0.12060.13660.02260.02740.08260.01170.10929.45547.141-37.5593
145.8673-0.735-2.53061.5431-0.13852.4510.08610.39-0.0943-0.0686-0.09920.09050.0789-0.24190.03910.16540.0259-0.0550.2577-0.02280.12474.8939-1.5172-44.5958
151.86880.46820.14680.84750.67230.7270.20580.66810.3882-0.1315-0.08270.0871-0.2612-0.2662-0.05840.23760.0713-0.00370.27520.07760.155111.55598.4895-46.8014
166.34371.27424.85510.54540.90012.9747-0.01310.2899-0.0885-0.17220.04540.02-0.00790.067-0.0460.33590.04810.02720.41950.02510.142610.34541.6434-59.2265
171.0560.4226-0.22961.357-0.85871.9824-0.03170.0819-0.4031-0.1925-0.1669-0.4580.34970.57630.08920.18410.09360.03710.2745-0.01140.317256.0408-43.8395-36.1984
185.59242.6838-0.0115.08420.14371.31520.101-0.03310.06490.1198-0.0037-0.6259-0.24240.80140.01380.1593-0.0661-0.010.386-0.0410.253659.1037-31.9808-30.7298
195.5753-1.4379-1.80391.1607-0.62112.56790.0155-0.0743-0.05310.05470.07730.0506-0.067-0.0866-0.10590.1049-0.0115-0.01650.0802-0.0110.106733.0059-36.2808-26.5415
203.05470.44070.3691.28810.33142.08480.0856-0.2517-0.3310.1427-0.0238-0.17560.10340.2355-0.03120.1123-0.0046-0.01650.14750.00410.152249.1922-41.008-20.5606
217.9038-0.47145.88272.65260.31956.5907-0.1228-0.76010.04260.26150.1936-0.2891-0.22720.0758-0.00950.1502-0.0290.01590.3098-0.06620.161652.78-31.7796-20.9104
225.27841.04411.12592.46710.52212.04880.16410.08920.9446-0.07630.0581-0.0479-0.7590.1782-0.13820.3710.00410.11050.1721-0.05360.286145.9848-18.4314-34.7197
233.18311.17611.22493.63840.60182.50050.1734-0.1140.31790.2432-0.0227-0.3794-0.31770.3354-0.13810.1804-0.05210.04630.2188-0.05850.234853.4438-25.2379-34.8566
246.08560.8761-1.95531.8105-0.85222.58430.06540.7088-0.2958-0.238-0.0940.14970.1833-0.59540.13570.2008-0.0107-0.06190.2588-0.06790.158533.3889-39.4286-45.2744
254.42781.4632-0.12582.2824-0.32532.22220.1790.34230.1869-0.1382-0.02370.0954-0.1815-0.3073-0.14880.22120.06490.02480.1942-0.02110.137935.9918-28.1291-45.2686
265.09753.18474.79272.03142.40654.2958-0.12870.14350.046-0.28220.10510.0065-0.16190.0673-0.01220.28060.01250.03290.3414-0.01070.162836.9867-33.7578-58.8433
271.0177-0.0778-0.28451.29290.3621.1097-0.0536-0.2296-0.38010.1802-0.10810.37650.3801-0.16640.17680.3046-0.06520.10510.29910.07430.362917.6658-43.242810.3401
281.69810.6917-0.52081.87931.44462.1455-0.21490.0119-0.47040.1208-0.39620.52720.1253-0.50150.08820.1708-0.07440.08020.1901-0.01210.463214.8169-41.90280.363
293.29470.84781.2191.29541.14591.9011-0.0662-0.1706-0.49930.2637-0.08570.41680.3885-0.13130.01820.1916-0.03370.04810.11860.02830.304528.7502-44.9034-0.7133
300.45450.03010.13022.30650.60111.3906-0.0759-0.1222-0.21010.2235-0.06440.26980.1345-0.23880.12380.1318-0.04060.04660.17250.03870.181121.8012-34.47696.1419
312.2246-0.1337-0.0721.0230.13710.76310.0210.0629-0.1919-0.038-0.01960.11140.0114-0.08060.00360.111-0.0133-0.01130.09810.01590.130530.3212-34.9869-7.3174
324.84542.78523.99963.11672.47363.9404-0.25260.54940.0137-0.31960.17660.2588-0.28360.0090.15250.13950.0020.00170.21820.02230.183323.7089-31.2338-12.9436
337.3005-5.1205-0.20714.79040.21210.10920.09980.17570.3756-0.1174-0.1178-0.2512-0.08650.0126-0.01060.1166-0.0090.00140.12020.01990.134530.8205-15.4327-2.0578
343.4485-2.79412.77285.008-3.98035.17470.0688-0.0227-0.0278-0.051-0.02880.19180.0005-0.0251-0.00990.0708-0.01720.00850.095-0.00620.115723.3341-22.0389-0.3943
352.3203-1.10210.39341.69770.11851.0724-0.0342-0.3333-0.0410.18050.0985-0.09040.03390.1171-0.06130.1533-0.012-0.01980.18750.02950.106341.4741-27.265110.9013
365.4754-1.87475.28540.8348-1.45384.5157-0.0804-0.38230.01210.15960.1122-0.04340.0304-0.0575-0.03890.25690.03850.01220.3659-0.00530.176939.6294-26.160724.17
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 576 through 635 )A576 - 635
2X-RAY DIFFRACTION2chain 'A' and (resid 636 through 768 )A636 - 768
3X-RAY DIFFRACTION3chain 'A' and (resid 769 through 786 )A769 - 786
4X-RAY DIFFRACTION4chain 'A' and (resid 787 through 815 )A787 - 815
5X-RAY DIFFRACTION5chain 'A' and (resid 816 through 878 )A816 - 878
6X-RAY DIFFRACTION6chain 'A' and (resid 879 through 916 )A879 - 916
7X-RAY DIFFRACTION7chain 'B' and (resid 578 through 635 )B578 - 635
8X-RAY DIFFRACTION8chain 'B' and (resid 636 through 657 )B636 - 657
9X-RAY DIFFRACTION9chain 'B' and (resid 658 through 695 )B658 - 695
10X-RAY DIFFRACTION10chain 'B' and (resid 696 through 738 )B696 - 738
11X-RAY DIFFRACTION11chain 'B' and (resid 739 through 768 )B739 - 768
12X-RAY DIFFRACTION12chain 'B' and (resid 769 through 786 )B769 - 786
13X-RAY DIFFRACTION13chain 'B' and (resid 787 through 815 )B787 - 815
14X-RAY DIFFRACTION14chain 'B' and (resid 816 through 840 )B816 - 840
15X-RAY DIFFRACTION15chain 'B' and (resid 841 through 878 )B841 - 878
16X-RAY DIFFRACTION16chain 'B' and (resid 879 through 915 )B879 - 915
17X-RAY DIFFRACTION17chain 'C' and (resid 589 through 675 )C589 - 675
18X-RAY DIFFRACTION18chain 'C' and (resid 676 through 695 )C676 - 695
19X-RAY DIFFRACTION19chain 'C' and (resid 696 through 724 )C696 - 724
20X-RAY DIFFRACTION20chain 'C' and (resid 725 through 750 )C725 - 750
21X-RAY DIFFRACTION21chain 'C' and (resid 751 through 768 )C751 - 768
22X-RAY DIFFRACTION22chain 'C' and (resid 769 through 786 )C769 - 786
23X-RAY DIFFRACTION23chain 'C' and (resid 787 through 815 )C787 - 815
24X-RAY DIFFRACTION24chain 'C' and (resid 816 through 839 )C816 - 839
25X-RAY DIFFRACTION25chain 'C' and (resid 840 through 878 )C840 - 878
26X-RAY DIFFRACTION26chain 'C' and (resid 879 through 916 )C879 - 916
27X-RAY DIFFRACTION27chain 'D' and (resid 582 through 611 )D582 - 611
28X-RAY DIFFRACTION28chain 'D' and (resid 612 through 635 )D612 - 635
29X-RAY DIFFRACTION29chain 'D' and (resid 636 through 657 )D636 - 657
30X-RAY DIFFRACTION30chain 'D' and (resid 658 through 674 )D658 - 674
31X-RAY DIFFRACTION31chain 'D' and (resid 675 through 750 )D675 - 750
32X-RAY DIFFRACTION32chain 'D' and (resid 751 through 768 )D751 - 768
33X-RAY DIFFRACTION33chain 'D' and (resid 769 through 786 )D769 - 786
34X-RAY DIFFRACTION34chain 'D' and (resid 787 through 815 )D787 - 815
35X-RAY DIFFRACTION35chain 'D' and (resid 816 through 878 )D816 - 878
36X-RAY DIFFRACTION36chain 'D' and (resid 879 through 916 )D879 - 916

+
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