[English] 日本語
Yorodumi
- PDB-5tzw: CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A IN COMPLEX WITH 1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tzw
TitleCRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A IN COMPLEX WITH 1-[(3,4-difluorophenyl)carbonyl]-3,3-difluoro-5-{5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl}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 / ventricular septum development / 3',5'-cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of cGMP-mediated signaling / 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 cAMP / cellular response to transforming growth factor beta stimulus / cAMP-mediated signaling / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / synaptic membrane / positive regulation of inflammatory response / cellular response to mechanical stimulus / 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-7P4 / cGMP-dependent 3',5'-cyclic phosphodiesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 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 22, 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 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)162,60416
Polymers160,6724
Non-polymers1,93212
Water19,9971110
1
A: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6514
Polymers40,1681
Non-polymers4833
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)40,6514
Polymers40,1681
Non-polymers4833
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)40,6514
Polymers40,1681
Non-polymers4833
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)40,6514
Polymers40,1681
Non-polymers4833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.806, 72.997, 91.000
Angle α, β, γ (deg.)109.220, 90.960, 91.070
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): baculovirus insect cell Hi5
References: UniProt: O00408, 3',5'-cyclic-nucleotide phosphodiesterase
#2: Chemical
ChemComp-7P4 / [(5S)-3,3-difluoro-5-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl](3,4-difluorophenyl)methanone


Mass: 393.338 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C18H15F4N5O
#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.: 1110 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
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: Sep 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.59→68.91 Å / Num. obs: 173341 / % possible obs: 95.2 % / Redundancy: 2 % / Biso Wilson estimate: 17.38 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 9.2
Reflection shellResolution: 1.59→1.63 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.669 / % possible all: 77.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.21 Å68.91 Å
Translation8.21 Å68.91 Å

-
Processing

Software
NameVersionClassification
xia2data scaling
PHASER2.6.1phasing
PHENIX(1.10.1-2155_1692: ???)refinement
PDB_EXTRACT3.2data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→68.907 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.15
RfactorNum. reflection% reflection
Rfree0.2246 8491 4.92 %
Rwork0.1884 --
obs0.1902 172516 94.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.92 Å2 / Biso mean: 27.2027 Å2 / Biso min: 8.55 Å2
Refinement stepCycle: final / Resolution: 1.59→68.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11045 0 0 1110 12155
Biso mean---33.48 -
Num. residues----1348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711344
X-RAY DIFFRACTIONf_angle_d0.85515330
X-RAY DIFFRACTIONf_chiral_restr0.0461627
X-RAY DIFFRACTIONf_plane_restr0.0051983
X-RAY DIFFRACTIONf_dihedral_angle_d17.9834177
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 (%)
1.59-1.60810.37911930.35273995418870
1.6081-1.6270.35842690.33854601487079
1.627-1.64690.35792970.33935331562893
1.6469-1.66770.35922750.32995363563894
1.6677-1.68960.34893190.31665480579994
1.6896-1.71280.38862640.32325415567994
1.7128-1.73730.32792840.30775478576295
1.7373-1.76320.3082900.28785445573595
1.7632-1.79080.31722760.2785512578895
1.7908-1.82010.30873050.26925503580895
1.8201-1.85150.30562800.25495492577295
1.8515-1.88520.28552530.2445514576795
1.8852-1.92140.28252700.23635585585596
1.9214-1.96070.25892700.22535499576996
1.9607-2.00330.24522720.21865573584596
2.0033-2.04990.24842540.21235563581796
2.0499-2.10120.22792660.19375646591296
2.1012-2.1580.22982730.18335591586496
2.158-2.22150.21162810.17335565584697
2.2215-2.29320.20883060.17095552585897
2.2932-2.37510.19733340.16825517585197
2.3751-2.47020.21123110.1685584589597
2.4702-2.58270.21572810.16755658593997
2.5827-2.71880.21572850.16945602588797
2.7188-2.88920.21313120.16445627593997
2.8892-3.11230.20693180.16645621593997
3.1123-3.42550.19982910.15645624591598
3.4255-3.92110.17282970.14865659595698
3.9211-4.940.15422960.13955656595298
4.94-68.97150.22282690.17135774604399
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.24530.37160.61392.33730.73842.17240.0256-0.1903-0.18050.1304-0.01190.05910.1779-0.0231-0.00010.116-0.03850.02220.17360.04030.1399-10.6683-14.8036-0.6761
22.15990.04240.32620.94120.10810.97850.027-0.0344-0.047-0.04680.00780.02030.03340.0076-0.03480.0919-0.01250.00560.0657-00.0667-0.3092-4.8861-8.085
32.5004-0.8528-0.4442.18740.05491.5814-0.0860.02410.4586-0.22280.04710.0572-0.40810.086-0.00750.1863-0.0070.01020.09060.01730.1691-3.87048.4871-10.8448
43.4678-1.57021.63384.3447-2.28714.53750.007-0.15090.2541-0.06430.03950.1671-0.2266-0.1555-0.04220.1030.00540.02220.0734-0.040.1401-8.37998.5221-3.8914
51.5414-0.1314-2.04172.21570.54673.48240.0349-0.66860.01840.1662-0.0068-0.08560.07060.5382-0.04440.1691-0.0164-0.04410.3107-0.01150.129112.892-1.24758.9241
61.9162-0.34340.68941.87240.00452.2091-0.0952-0.18360.50160.2178-0.033-0.1667-0.30290.29860.09620.2283-0.0405-0.01190.2215-0.04020.15998.54989.38417.589
77.5605-1.35715.25390.5844-0.81083.6328-0.08-0.5320.31530.140.0179-0.0887-0.1196-0.18540.05410.33280.02990.03870.4358-0.09950.19888.73415.105821.4392
81.6789-0.5260.16162.621-1.1013.40530.0330.0114-0.2573-0.1605-0.1552-0.11050.42360.28980.10160.20850.06990.00820.1473-0.03850.207626.4336-18.3787-38.6036
95.8779-3.17832.98783.6494-1.9913.40210.1508-0.0968-0.50970.10040.080.15510.3299-0.0034-0.22390.184-0.0035-0.01190.0715-0.00440.150415.5038-14.5979-32.0178
103.0606-0.0324-0.37011.54350.14222.06670.0582-0.10530.03740.0264-0.008-0.0011-0.05310.0095-0.05420.13630.0163-0.00080.04620.00380.073517.6699-3.0471-32.801
112.3532-0.11360.93551.7897-0.22313.30540.0476-0.2425-0.16670.18510.0137-0.1220.09750.2443-0.04440.1470.01390.01360.1420.00910.108625.6502-4.6136-22.6761
123.43030.79680.48232.57140.18661.4781-0.02650.01220.2632-0.12340.099-0.1608-0.35630.0612-0.06110.1881-0.00180.02570.08480.01510.119124.71688.2966-39.2688
139.0203-1.4636-4.75521.56420.20523.25940.08660.6073-0.2201-0.0836-0.20270.10490.0932-0.42240.12260.21030.0218-0.05860.2545-0.03640.13952.0664-3.8067-45.9222
143.21830.66860.27470.86440.25540.99470.02020.54040.4661-0.17820.0170.1392-0.2186-0.2415-0.03610.24780.0473-0.00460.23140.07150.17558.74576.1666-48.2137
158.43441.53335.31690.57811.00383.278-0.17230.2512-0.1577-0.14960.14770.0128-0.21750.01860.05270.31130.02850.03790.38640.04870.14546.7675-0.7593-60.513
161.3114-0.0689-0.24471.6291-0.41292.51050.07560.155-0.3299-0.1657-0.1453-0.34740.32170.56760.06010.19270.07690.02590.2439-0.02780.275953.3946-45.6957-37.6332
176.23781.8379-0.02916.4524-0.62471.60620.06490.0320.0808-0.0621-0.0271-0.7385-0.28650.77120.02570.1752-0.08940.01440.3299-0.03130.219156.4049-33.8399-32.299
186.0408-1.88570.3081.2757-1.06671.86360.0012-0.034-0.09440.07560.08370.0495-0.0868-0.1613-0.08830.1321-0.023-0.00520.0904-0.00930.120233.6636-39.0767-26.8505
194.3985-1.87512.06012.6912-0.99784.3978-0.1-0.4378-0.02490.21010.1321-0.1979-0.09970.2328-0.01190.1251-0.02310.00990.2033-0.03460.152251.727-38.275-21.1396
201.8160.62220.36482.40270.32731.11470.2828-0.0020.38760.02540.0189-0.2982-0.82120.0306-0.1390.3996-0.04760.1070.1497-0.04260.251647.7789-24.4453-36.334
217.02171.2137-2.35352.3408-1.25023.1888-0.01270.6083-0.3584-0.2125-0.0610.20750.2799-0.7850.1090.2221-0.0226-0.06960.3252-0.08270.187330.6798-41.373-46.681
223.13940.66810.19952.09870.12493.26290.28480.30110.2166-0.1441-0.17930.2032-0.2641-0.5731-0.11190.30820.09240.02390.2815-0.02830.146533.2039-30.2243-46.7331
236.12313.32455.42972.21932.57564.9807-0.09920.20860.0735-0.29930.04430.0388-0.2441-0.01810.03330.33060.05390.04410.3744-0.01660.162534.0753-35.6956-60.1193
243.0044-0.3425-1.20192.0824-0.77121.5238-0.1668-0.5719-0.47770.34420.1330.49760.3356-0.35330.03540.2736-0.08810.06360.51460.13940.303915.2825-41.476711.7941
251.15190.11250.37241.35960.6741.29960.14-0.3346-0.42430.071-0.12570.30630.2197-0.3563-0.00330.1802-0.06690.00160.24170.08030.281819.0271-42.93840.1602
262.57220.0070.23980.90670.15751.01710.0581-0.0143-0.2158-0.057-0.01530.09790.0254-0.0856-0.03440.108-0.0088-0.01370.09530.02540.129227.7189-37.032-8.79
275.72033.335.29523.34533.09595.0366-0.18130.3532-0.0067-0.260.14780.286-0.2853-0.00120.03920.16910.01440.010.21640.03140.19921.0798-33.2915-14.4363
289.0226-6.28920.35426.36540.21250.79890.0444-0.00130.5102-0.0543-0.0056-0.3718-0.07-0.024-0.05090.14460.00230.01390.20230.01850.165128.1845-17.5548-3.4622
293.0168-2.01652.11424.4015-3.10454.53020.085-0.1695-0.0084-0.14220.00690.13090.0865-0.0484-0.0540.0608-0.01010.01470.14160.00590.100720.7441-24.1451-1.8428
306.8992-1.298-2.53572.57850.88433.5199-0.0333-0.5653-0.32130.19360.04280.02620.26510.15320.02770.16910.0048-0.04240.23810.06560.141440.6091-36.258910.801
313.8475-1.73681.19391.79760.06881.73570.0026-0.42960.1140.06770.1092-0.1339-0.05690.1283-0.11370.1553-0.01220.010.22460.02820.109837.8102-25.08978.5766
325.498-2.05264.83421.1557-1.52724.3635-0.1617-0.38110.02190.20340.14130.0019-0.1578-0.15370.00740.22770.03790.03450.40670.00250.145837.053-28.18422.5343
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 750 )A636 - 750
3X-RAY DIFFRACTION3chain 'A' and (resid 751 through 786 )A751 - 786
4X-RAY DIFFRACTION4chain 'A' and (resid 787 through 815 )A787 - 815
5X-RAY DIFFRACTION5chain 'A' and (resid 816 through 839 )A816 - 839
6X-RAY DIFFRACTION6chain 'A' and (resid 840 through 878 )A840 - 878
7X-RAY DIFFRACTION7chain 'A' and (resid 879 through 917 )A879 - 917
8X-RAY DIFFRACTION8chain 'B' and (resid 578 through 635 )B578 - 635
9X-RAY DIFFRACTION9chain 'B' and (resid 636 through 657 )B636 - 657
10X-RAY DIFFRACTION10chain 'B' and (resid 658 through 738 )B658 - 738
11X-RAY DIFFRACTION11chain 'B' and (resid 739 through 768 )B739 - 768
12X-RAY DIFFRACTION12chain 'B' and (resid 769 through 815 )B769 - 815
13X-RAY DIFFRACTION13chain 'B' and (resid 816 through 840 )B816 - 840
14X-RAY DIFFRACTION14chain 'B' and (resid 841 through 878 )B841 - 878
15X-RAY DIFFRACTION15chain 'B' and (resid 879 through 916 )B879 - 916
16X-RAY DIFFRACTION16chain 'C' and (resid 589 through 675 )C589 - 675
17X-RAY DIFFRACTION17chain 'C' and (resid 676 through 695 )C676 - 695
18X-RAY DIFFRACTION18chain 'C' and (resid 696 through 738 )C696 - 738
19X-RAY DIFFRACTION19chain 'C' and (resid 739 through 768 )C739 - 768
20X-RAY DIFFRACTION20chain 'C' and (resid 769 through 815 )C769 - 815
21X-RAY DIFFRACTION21chain 'C' and (resid 816 through 839 )C816 - 839
22X-RAY DIFFRACTION22chain 'C' and (resid 840 through 878 )C840 - 878
23X-RAY DIFFRACTION23chain 'C' and (resid 879 through 916 )C879 - 916
24X-RAY DIFFRACTION24chain 'D' and (resid 590 through 611 )D590 - 611
25X-RAY DIFFRACTION25chain 'D' and (resid 612 through 674 )D612 - 674
26X-RAY DIFFRACTION26chain 'D' and (resid 675 through 750 )D675 - 750
27X-RAY DIFFRACTION27chain 'D' and (resid 751 through 768 )D751 - 768
28X-RAY DIFFRACTION28chain 'D' and (resid 769 through 786 )D769 - 786
29X-RAY DIFFRACTION29chain 'D' and (resid 787 through 815 )D787 - 815
30X-RAY DIFFRACTION30chain 'D' and (resid 816 through 839 )D816 - 839
31X-RAY DIFFRACTION31chain 'D' and (resid 840 through 878 )D840 - 878
32X-RAY DIFFRACTION32chain '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