[English] 日本語
Yorodumi
- PDB-6tfm: Frizzled8 CRD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tfm
TitleFrizzled8 CRD
ComponentsFrizzled-8
KeywordsONCOPROTEIN / Wnt receptor Frizzled8 CRD
Function / homology
Function and homology information


Wnt-Frizzled-LRP5/6 complex / Regulation of FZD by ubiquitination / Asymmetric localization of PCP proteins / Wnt receptor activity / Wnt-protein binding / canonical Wnt signaling pathway / neuronal dense core vesicle / PDZ domain binding / G protein-coupled receptor activity / Wnt signaling pathway ...Wnt-Frizzled-LRP5/6 complex / Regulation of FZD by ubiquitination / Asymmetric localization of PCP proteins / Wnt receptor activity / Wnt-protein binding / canonical Wnt signaling pathway / neuronal dense core vesicle / PDZ domain binding / G protein-coupled receptor activity / Wnt signaling pathway / T cell differentiation in thymus / angiogenesis / signaling receptor binding / ubiquitin protein ligase binding / Golgi apparatus / extracellular region / plasma membrane
Similarity search - Function
Frizzled 8, cysteine-rich domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. ...Frizzled 8, cysteine-rich domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2.
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.343 Å
AuthorsZhao, Y. / Jones, E.Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/M000141/1 United Kingdom
Cancer Research UKC375/A17721 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2020
Title: Antiepileptic Drug Carbamazepine Binds to a Novel Pocket on the Wnt Receptor Frizzled-8.
Authors: Zhao, Y. / Ren, J. / Hillier, J. / Lu, W. / Jones, E.Y.
History
DepositionNov 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Frizzled-8
D: Frizzled-8
B: Frizzled-8
C: Frizzled-8


Theoretical massNumber of molelcules
Total (without water)63,2604
Polymers63,2604
Non-polymers00
Water88349
1
A: Frizzled-8


Theoretical massNumber of molelcules
Total (without water)15,8151
Polymers15,8151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Frizzled-8


Theoretical massNumber of molelcules
Total (without water)15,8151
Polymers15,8151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Frizzled-8


Theoretical massNumber of molelcules
Total (without water)15,8151
Polymers15,8151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Frizzled-8


Theoretical massNumber of molelcules
Total (without water)15,8151
Polymers15,8151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.296, 66.039, 72.666
Angle α, β, γ (deg.)90.000, 90.100, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 34 through 153 or resid 156 through 162))
21(chain B and (resid 34 through 153 or resid 156 through 162))
31(chain C and resid 34 through 162)
41chain D

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
11ALAALAARGARG(chain A and (resid 34 through 153 or resid 156 through 162))AA34 - 15310 - 129
12LEULEUGLYGLY(chain A and (resid 34 through 153 or resid 156 through 162))AA156 - 162132 - 138
21ALAALAARGARG(chain B and (resid 34 through 153 or resid 156 through 162))BC34 - 15310 - 129
22LEULEUGLYGLY(chain B and (resid 34 through 153 or resid 156 through 162))BC156 - 162132 - 138
31ALAALAGLYGLY(chain C and resid 34 through 162)CD34 - 16210 - 138
41ALAALAGLYGLYchain DDB34 - 16210 - 138

-
Components

#1: Protein
Frizzled-8 / mFz8


Mass: 15815.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fzd8 / Cell line (production host): HEK293S GNTI- / Production host: Homo sapiens (human) / References: UniProt: Q61091
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.99 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M sodium acetate, pH 5 1 M ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 2.34→72.7 Å / Num. obs: 20741 / % possible obs: 98.9 % / Redundancy: 6.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.3
Reflection shellResolution: 2.34→2.38 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1024 / CC1/2: 0.89

-
Processing

Software
NameVersionClassification
PHENIXdev_3488refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IJY

1ijy


Resolution: 2.343→72.666 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.75
RfactorNum. reflection% reflection
Rfree0.3004 1012 5.15 %
Rwork0.2432 --
obs0.246 19646 93.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 56.67 Å2 / Biso mean: 20.6271 Å2 / Biso min: 3.27 Å2
Refinement stepCycle: final / Resolution: 2.343→72.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4150 0 0 49 4199
Biso mean---12.94 -
Num. residues----513
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2532X-RAY DIFFRACTION15.108TORSIONAL
12B2532X-RAY DIFFRACTION15.108TORSIONAL
13C2532X-RAY DIFFRACTION15.108TORSIONAL
14D2532X-RAY DIFFRACTION15.108TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.343-2.46650.31651470.2842222780
2.4665-2.62110.36941280.2667243286
2.6211-2.82350.33851300.2698262593
2.8235-3.10760.31271700.2613279799
3.1076-3.55730.27981520.2452280999
3.5573-4.48170.25491470.2181284099
4.4817-72.660.30031380.2149290499
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)
10.0044-0.0327-0.00490.25080.0360.00530.0601-0.0960.01870.04880.0569-0.0591-0.00390.03850.01180.1591-0.10360.04410.3433-0.05640.165914.625-30.370257.1908
20.6131-0.21660.14760.0882-0.03460.1431-0.1774-0.12820.21650.08420.0505-0.0375-0.1558-0.0307-0.09280.16530.04310.02030.05370.00570.160410.5419-26.968546.7541
30.0273-0.02610.00160.04710.01570.01440.00550.00570.0307-0.01160.00580.0108-0.016-0.0168-0.01030.09240.0930.04680.03950.09490.086114.9368-27.496742.9079
40.3980.09280.11790.02150.02940.035-0.0031-0.1434-0.09480.04270.0065-0.01250.07130.0490.02330.16950.0664-0.08370.090.03030.036224.9286-28.46752.1586
50.0604-0.06580.00460.1258-0.06870.0666-0.0159-0.00180.0376-0.0050.0151-0.006-0.0231-0.0050.0863-0.1069-0.0378-0.2021-0.07470.0746-0.039915.4709-20.863333.3761
60.1039-0.00590.02650.0033-0.00120.007-0.00130.02690.00680.0342-0.0139-0.05470.00020.1035-0.07950.14560.0285-0.14780.26410.04020.174232.4031-24.951641.4926
70.03130.02010.01710.1117-0.04340.03870.08480.005-0.094-0.1102-0.00630.05350.1628-0.01540.11040.2818-0.0056-0.08880.11510.05280.147524.7178-36.423641.5926
80.14880.1432-0.00410.1394-0.0032-0.0002-0.0045-0.04680.08050.0035-0.01370.073-0.02160.0167-0.05180.1113-0.0969-0.00050.1567-0.01450.081265.26620.351623.4481
90.12210.05120.11240.02250.03330.2574-0.02860.00350.08770.0222-0.0131-0.0237-0.07550.04010.01650.0455-0.0485-0.0080.1025-0.05240.190260.9649-2.712727.0642
100.0271-0.0506-0.00180.09530.00310.0001-0.0076-0.0091-0.056-0.0853-0.00430.06680.0639-0.009-0.02840.1305-0.03470.02840.05630.01490.147764.8538-13.93224.1077
110.08-0.00260.03980.05730.02820.0358-0.0060.064-0.0123-0.06020.0807-0.0341-0.05120.03420.20640.1087-0.10210.04870.07180.00090.068973.5178-7.09715.183
120.0766-0.01660.01290.02430.01310.01460.0153-0.00190.0243-0.02980.02330.0095-0.00540.06580.14680.1163-0.0325-0.05130.1071-0.04860.094164.4096-3.697211.2504
130.3416-0.24870.08260.1852-0.08160.1976-0.0239-0.13040.12790.0969-0.0076-0.0135-0.0252-0.0110.09730.0709-0.0491-0.0220.0767-0.02850.033453.4044-4.113123.5826
140.0258-0.0090.01770.0081-0.00880.0148-0.01610.0588-0.0061-0.0267-0.02570.0016-0.0005-0.0104-0.29890.055-0.0346-0.00330.2607-0.02870.028362.5967-9.042.8858
150.02730.02810.00310.1294-0.04120.02660.00920.0204-0.01570.02430.0179-0.1273-0.0069-0.0064-0.00980.11520.0313-0.00630.2164-0.0460.217469.8195-14.91974.4102
160.0049-0.0089-0.00220.02410.0030.00270.02360.002-0.08180.0431-0.0108-0.03490.1217-0.01790.00160.1812-0.0647-0.02090.18270.06590.324958.4122-16.540710.6897
170.0112-0.0045-0.00690.01180.00110.0046-0.04190.0086-0.0316-0.0121-0.02160.2390.0397-0.05410.00020.1686-0.04650.03130.28390.02120.238846.156-7.356713.157
180.0219-0.01430.0040.04220.00040.00530.0602-0.04720.1652-0.05320.0293-0.0749-0.08670.00910.00030.3418-0.0190.03630.1840.04580.351554.2293.478913.2161
190.0028-0.0020.00520.0477-0.04480.04620.00470.04070.0094-0.053-0.0636-0.0455-0.01010.066-0.09270.2110.0977-0.0190.41840.14470.195539.3125-2.8157-21.063
200.0127-0.0205-0.01370.03340.02160.0143-0.00290.01830.0340.0070.00690.002-0.0250.00910.02550.09260.0111-0.05240.22670.04560.200237.29111.125-11.6731
210.031-0.0137-0.06740.0408-0.01050.2293-0.04520.0304-0.06780.0223-0.0626-0.06670.0955-0.070.00020.2631-0.14880.00520.5343-0.04910.31140.1049-9.6291-18.0832
220.31760.1244-0.04490.1252-0.05660.0253-0.02180.1508-0.00760.02450.0022-0.0356-0.0575-0.0374-0.06570.06720.0618-0.04450.19370.04420.082329.8268-7.7117-7.5016
230.04470.0064-0.01560.0174-0.00830.0132-0.0073-0.02290.00360.0121-0.0239-0.00780.0031-0.0135-0.01970.11220.0177-0.0440.2759-0.00990.207237.2191-1.6063.2093
240.01290.0093-0.0090.0119-0.00060.0104-0.0044-0.0029-0.01030.00530.00890.00160.0089-0.006-0.02820.0499-0.0647-0.00720.17170.10880.101839.6883-6.0166-6.8663
250.06560.0191-0.04890.1325-0.01580.0464-0.02660.05490.0322-0.0783-0.0039-0.04430.03080.03020.03180.1311-0.04320.050.23890.13840.092549.6293-4.9646-16.2489
260.0286-0.00430.01140.1810.05210.0208-0.0786-0.0072-0.10140.0607-0.01030.06560.07150.0308-0.14710.17380.01920.03230.1230.06060.167940.3343-10.1454.7204
270.0452-0.00880.0130.0321-0.00640.0298-0.0235-0.00960.01660-0.01090.00260-0.0038-0.04560.06620.05960.0650.1047-0.02190.238932.9236-15.42533.1132
280.03210.00290.02020.1107-0.00910.0703-0.01770.0108-0.06870.004-0.01760.00590.0732-0.01810.00340.4393-0.03610.060.20240.09460.37443.9741-17.7855-3.5808
290.03020.03810.02370.05780.05570.0924-0.0122-0.00940.00390.01970.0295-0.0272-0.0050.06150.0130.13580.01850.04760.38720.06670.166457.1098-8.9005-7.4135
300.27610.10470.20560.09820.03380.188-0.034-0.01180.17510.07550.05610.1181-0.174-0.0545-0.08130.1646-0.0031-0.00570.16460.13980.230748.83692.8428-5.4417
310.1777-0.0342-0.120.06090.06050.27640.020.05360.0028-0.0324-0.0049-0.00310.00120.01410.10360.05830.0792-0.03540.2152-0.03210.052540.1745-33.195512.469
320.01150.02250.00050.0825-0.0090.0041-0.01480.0242-0.0010.0098-0.01140.0273-0.0042-0.0083-0.00140.1279-0.01650.01290.1981-0.0710.209436.5017-30.85069.2607
330.36740.0828-0.01830.0819-0.02680.2957-0.04770.18060.098-0.04730.08340.0425-0.0717-0.07980.1130.11-0.0384-0.00530.2862-0.02320.136245.6483-23.910418.1343
340.08210.0410.00920.0232-0.00510.0884-0.0176-0.016-0.02680.00390.0062-0.00470.0074-0.0074-0.01550.10750.08050.03480.1614-0.03580.167740.991-31.437132.2517
350.05830.03660.00590.02310.00380.00110.01320.00930.0120.00090.00180.0132-0.0002-0.01180.06070.0650.08730.01630.2126-0.02250.052138.7656-27.564222.0029
360.0676-0.019-0.05760.0237-0.01150.091-0.06230.0781-0.0416-0.0366-0.00650.02020.0335-0.0624-0.12590.1018-0.0416-0.0040.1214-0.13680.045428.7977-28.889612.6368
370.8437-0.45810.80280.6873-0.71380.9408-0.0969-0.05770.0894-0.0147-0.1562-0.088-0.02070.1766-0.21160.10150.01480.01240.2967-0.03180.090137.9502-22.776533.3187
380.0001-0.00310.00060.0748-0.01410.0024-0.0110.01310.0367-0.00780.00930.0018-0.0171-0.0079-0.02080.10850.0355-0.01520.06110.06150.194145.6145-17.545431.3965
390.1577-0.0832-0.03960.125-0.06650.1064-0.00010.01260.0369-0.1158-0.0094-0.13480.0090.0018-0.07830.29960.0279-0.06570.0726-0.03620.150634.2166-15.721324.6259
400.03210.0097-0.02570.14240.01070.2676-0.0215-0.03430.01570.00340.0430.0022-0.0367-0.03380.07790.15930.0861-0.02610.2445-0.04160.057921.3633-24.662721.3068
410.62990.2555-0.11550.2131-0.02320.0269-0.0201-0.0946-0.12970.09990.0181-0.00430.20120.0792-0.02420.2592-0.0590.04410.401-0.11440.213229.494-35.47623.5079
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 40 )A33 - 40
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 83 )A41 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 92 )A84 - 92
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 107 )A93 - 107
5X-RAY DIFFRACTION5chain 'A' and (resid 108 through 137 )A108 - 137
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 147 )A138 - 147
7X-RAY DIFFRACTION7chain 'A' and (resid 148 through 162 )A148 - 162
8X-RAY DIFFRACTION8chain 'D' and (resid 34 through 48 )D34 - 48
9X-RAY DIFFRACTION9chain 'D' and (resid 49 through 53 )D49 - 53
10X-RAY DIFFRACTION10chain 'D' and (resid 54 through 61 )D54 - 61
11X-RAY DIFFRACTION11chain 'D' and (resid 62 through 78 )D62 - 78
12X-RAY DIFFRACTION12chain 'D' and (resid 79 through 92 )D79 - 92
13X-RAY DIFFRACTION13chain 'D' and (resid 93 through 107 )D93 - 107
14X-RAY DIFFRACTION14chain 'D' and (resid 108 through 124 )D108 - 124
15X-RAY DIFFRACTION15chain 'D' and (resid 125 through 130 )D125 - 130
16X-RAY DIFFRACTION16chain 'D' and (resid 131 through 137 )D131 - 137
17X-RAY DIFFRACTION17chain 'D' and (resid 138 through 148 )D138 - 148
18X-RAY DIFFRACTION18chain 'D' and (resid 149 through 162 )D149 - 162
19X-RAY DIFFRACTION19chain 'B' and (resid 33 through 40 )B33 - 40
20X-RAY DIFFRACTION20chain 'B' and (resid 41 through 48 )B41 - 48
21X-RAY DIFFRACTION21chain 'B' and (resid 49 through 61 )B49 - 61
22X-RAY DIFFRACTION22chain 'B' and (resid 62 through 78 )B62 - 78
23X-RAY DIFFRACTION23chain 'B' and (resid 79 through 83 )B79 - 83
24X-RAY DIFFRACTION24chain 'B' and (resid 84 through 92 )B84 - 92
25X-RAY DIFFRACTION25chain 'B' and (resid 93 through 107 )B93 - 107
26X-RAY DIFFRACTION26chain 'B' and (resid 108 through 124 )B108 - 124
27X-RAY DIFFRACTION27chain 'B' and (resid 125 through 130 )B125 - 130
28X-RAY DIFFRACTION28chain 'B' and (resid 131 through 137 )B131 - 137
29X-RAY DIFFRACTION29chain 'B' and (resid 138 through 148 )B138 - 148
30X-RAY DIFFRACTION30chain 'B' and (resid 149 through 162 )B149 - 162
31X-RAY DIFFRACTION31chain 'C' and (resid 33 through 48 )C33 - 48
32X-RAY DIFFRACTION32chain 'C' and (resid 49 through 53 )C49 - 53
33X-RAY DIFFRACTION33chain 'C' and (resid 54 through 78 )C54 - 78
34X-RAY DIFFRACTION34chain 'C' and (resid 79 through 83 )C79 - 83
35X-RAY DIFFRACTION35chain 'C' and (resid 84 through 92 )C84 - 92
36X-RAY DIFFRACTION36chain 'C' and (resid 93 through 107 )C93 - 107
37X-RAY DIFFRACTION37chain 'C' and (resid 108 through 124 )C108 - 124
38X-RAY DIFFRACTION38chain 'C' and (resid 125 through 130 )C125 - 130
39X-RAY DIFFRACTION39chain 'C' and (resid 131 through 137 )C131 - 137
40X-RAY DIFFRACTION40chain 'C' and (resid 138 through 148 )C138 - 148
41X-RAY DIFFRACTION41chain 'C' and (resid 149 through 162 )C149 - 162

+
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