[English] 日本語
Yorodumi
- PDB-6gkt: X-ray structure of a non-autocrystallizing galectin-10 variant, G... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gkt
TitleX-ray structure of a non-autocrystallizing galectin-10 variant, Gal10-Tyr69Glu
ComponentsGalectin-10
KeywordsSUGAR BINDING PROTEIN / Non-autocrystallizing / mutant / galectin-10
Function / homology
Function and homology information


regulation of activated T cell proliferation / regulation of T cell cytokine production / T cell apoptotic process / regulation of T cell anergy / : / carbohydrate binding / collagen-containing extracellular matrix / identical protein binding / cytosol
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Galectin-10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsVerstraete, K. / Verschueren, K. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Belgium
CitationJournal: Science / Year: 2019
Title: Protein crystallization promotes type 2 immunity and is reversible by antibody treatment.
Authors: Emma K Persson / Kenneth Verstraete / Ines Heyndrickx / Elien Gevaert / Helena Aegerter / Jean-Michel Percier / Kim Deswarte / Koen H G Verschueren / Ann Dansercoer / Delphine Gras / Pascal ...Authors: Emma K Persson / Kenneth Verstraete / Ines Heyndrickx / Elien Gevaert / Helena Aegerter / Jean-Michel Percier / Kim Deswarte / Koen H G Verschueren / Ann Dansercoer / Delphine Gras / Pascal Chanez / Claus Bachert / Amanda Gonçalves / Hanne Van Gorp / Hans De Haard / Christophe Blanchetot / Michael Saunders / Hamida Hammad / Savvas N Savvides / Bart N Lambrecht /
Abstract: Although spontaneous protein crystallization is a rare event in vivo, Charcot-Leyden crystals (CLCs) consisting of galectin-10 (Gal10) protein are frequently observed in eosinophilic diseases, such ...Although spontaneous protein crystallization is a rare event in vivo, Charcot-Leyden crystals (CLCs) consisting of galectin-10 (Gal10) protein are frequently observed in eosinophilic diseases, such as asthma. We found that CLCs derived from patients showed crystal packing and Gal10 structure identical to those of Gal10 crystals grown in vitro. When administered to the airways, crystalline Gal10 stimulated innate and adaptive immunity and acted as a type 2 adjuvant. By contrast, a soluble Gal10 mutein was inert. Antibodies directed against key epitopes of the CLC crystallization interface dissolved preexisting CLCs in patient-derived mucus within hours and reversed crystal-driven inflammation, goblet-cell metaplasia, immunoglobulin E (IgE) synthesis, and bronchial hyperreactivity (BHR) in a humanized mouse model of asthma. Thus, protein crystals may promote hallmark features of asthma and are targetable by crystal-dissolving antibodies.
History
DepositionMay 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Galectin-10
B: Galectin-10
C: Galectin-10
D: Galectin-10
E: Galectin-10
F: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,47616
Polymers99,7986
Non-polymers1,67810
Water11,620645
1
A: Galectin-10
B: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9116
Polymers33,2662
Non-polymers6454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Galectin-10
D: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5664
Polymers33,2662
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Galectin-10
F: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9996
Polymers33,2662
Non-polymers7334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.823, 93.296, 93.068
Angle α, β, γ (deg.)90.00, 108.94, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Galectin-10 / Gal-10 / Charcot-Leyden crystal protein / CLC / Eosinophil lysophospholipase / Lysolecithin acylhydrolase


Mass: 16632.971 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Recombinant human galectin-10-Tyr69Glu was produced with an N-terminal cleavable His-tag (MASTTHHHHHHDTDIPTTGGGSRPDDDDKENLYFQG). The His-tag was removed by TEV-cleavage before crystallization.
Source: (gene. exp.) Homo sapiens (human) / Gene: CLC, LGALS10, LGALS10A / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05315
#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 3 Å3/Da / Density % sol: 58.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium citrate pH 5.1 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 68207 / % possible obs: 99 % / Redundancy: 6.9 % / Biso Wilson estimate: 39.7 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.15 / Net I/σ(I): 9.33
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 10924 / CC1/2: 0.36 / Rrim(I) all: 2.27 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LCL
Resolution: 2.1→42 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.166 / SU Rfree Blow DPI: 0.144 / SU Rfree Cruickshank DPI: 0.142
RfactorNum. reflection% reflectionSelection details
Rfree0.204 3368 4.94 %RANDOM
Rwork0.172 ---
obs0.174 68187 99.1 %-
Displacement parametersBiso mean: 51.83 Å2
Baniso -1Baniso -2Baniso -3
1--8.5691 Å20 Å2-0.7405 Å2
2--5.0708 Å20 Å2
3---3.4983 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: 1 / Resolution: 2.1→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6766 0 112 648 7526
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017029HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.129460HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2509SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes186HARMONIC2
X-RAY DIFFRACTIONt_gen_planes979HARMONIC5
X-RAY DIFFRACTIONt_it7029HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.03
X-RAY DIFFRACTIONt_other_torsion17.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion871SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7608SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 237 4.7 %
Rwork0.217 4804 -
all0.218 5041 -
obs--99.12 %
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)
12.3312-0.2063-0.73391.4140.09143.3036-0.0416-0.21740.05360.1928-0.043-0.10770.22850.4540.08450.03320.0775-0.0473-0.04680.03190.00483.991611.836446.0434
21.7814-0.05670.93710.7425-0.46552.0055-0.0649-0.0252-0.0862-0.38180.0705-0.08590.2543-0.0725-0.00560.0560.00170.0231-0.0805-0.0066-0.0243-4.63237.258334.4094
32.29730.2841.11132.3693-1.17324.2988-0.0475-0.18110.06050.33910.1318-0.1561-0.1121-0.0655-0.08430.00980.0284-0.0174-0.06660.00090.0136-4.819919.068744.6524
41.1150.62431.09893.16140.95413.1276-0.12140.09390.16560.0818-0.04180.1595-0.1813-0.33750.16320.03950.02960.0028-0.00850.00990.0027-10.029723.315938.6966
52.83612.02681.52210-2.27294.1148-0.11470.22730.006-0.2324-0.02530.04420.0835-0.09840.14-0.0001-0.02530.0473-0.05440.0031-0.0731-6.230912.918327.3259
60.7874-1.3651-1.14030.1442-0.76681.5402-0.03470.26460.1227-0.1059-0.0442-0.2140.05920.32370.07890.0340.00750.02760.00620.03710.05254.702917.873533.0724
70.96430.1032-0.19921.8801-0.02541.8656-0.07870.03210.19140.00580.0715-0.2221-0.2393-0.00480.00720.00660.0252-0.0103-0.0791-0.00360.0164-0.178221.268240.3176
81.2888-1.6365-0.80080.3983-1.20231.69-0.12010.09390.1947-0.02380.029-0.36180.16120.21350.0911-0.01970.0308-0.0394-0.11820.03080.07568.414812.094840.4876
90.39720.7713-0.99752.33860.4513.5824-0.0845-0.0789-0.2015-0.12440.01590.26160.11460.26370.0686-0.06770.01360.0077-0.20860.0629-0.0572-20.677-6.63644.4911
100.1007-0.23880.27432.1820.43470.606-0.0613-0.25890.0380.0654-0.07710.1197-0.1518-0.08650.13830.07570.01430.0398-0.0590.0292-0.0287-18.78247.172650.369
112.3470.2377-1.53564.07020.09223.8469-0.14360.3545-0.0658-0.42690.18210.2935-0.0335-0.1791-0.03850.0753-0.0373-0.0256-0.06120.05820.0027-22.82971.254736.4582
122.77220.29850.36660.7809-1.23712.5476-0.13250.02210.4667-0.12180.07810.5325-0.2906-0.21880.05440.03840.0115-0.0464-0.16250.08130.0493-26.289410.944540.6374
133.0279-0.1076-0.79751.7331-1.6563-0.90170.0697-0.1666-0.08680.2950.02880.6309-0.0092-0.1085-0.0986-0.02980.01770.0445-0.10670.06280.0889-31.76031.521448.4202
140.91351.032-0.44471.5205-0.31341.5714-0.1140.15380.2282-0.320.19810.4651-0.1396-0.1272-0.08410.0159-0.0058-0.0352-0.10220.05760.0602-28.6510.664139.6204
150.30061.186-0.13831.84350.9128-0.1303-0.0257-0.1546-0.05330.2912-0.08840.2844-0.08720.04330.1141-0.02160.00590.0509-0.00520.03870.0349-25.6739-6.412849.7218
163.91951.07970.35443.35911.49114.29770.1241-0.09640.2987-0.5006-0.10150.0353-0.4690.5284-0.02260.0002-0.01830.0408-0.02660.0501-0.1555-30.457811.536672.717
176.9230.7986-1.7972.22790.25482.58260.0099-0.1978-0.1416-0.1064-0.0418-0.07420.04390.46580.0319-0.02560.0212-0.00480.05070.0107-0.0926-31.16222.656979.0628
18-0.1191-0.54121.9752.3804-1.65891.51410.0395-0.0167-0.19020.05070.0411-0.05340.11460.059-0.08060.03480.03980.03880.02890.05590.0125-33.2094-6.560983.7288
193.4852-1.53261.25571.1522-0.41941.59740.15050.026-0.20090.03240.082-0.1532-0.19850.3603-0.2324-0.0594-0.04010.07990.16840.0044-0.1661-17.11756.642274.514
200.7831.5925-0.22332.1356-0.50763.87420.05630.383-0.1653-0.26560.01420.12130.12750.4782-0.07040.02980.08090.04890.1189-0.0111-0.0621-26.55692.224166.0022
210.01340.56360.29761.0861-0.67772.45170.1086-0.0375-0.3195-0.3562-0.0589-0.09990.33790.4592-0.0497-0.02570.0683-0.005-0.0094-0.0282-0.0339-32.2066-0.260173.166
221.244-2.47930.1050.5077-0.41430.98720.08490.09120.0196-0.137-0.0385-0.0019-0.19630.1358-0.04640.0238-0.01990.02050.00720.0179-0.115-34.535111.467367.039
232.67640.7441-1.32082.19811.73323.47740.04090.16470.192-0.2272-0.0854-0.1319-0.3707-0.0710.04450.2355-0.1801-0.0789-0.15010.0567-0.0567-27.049828.233992.5538
24-0.49291.19260.29783.28780.51762.4504-0.06660.02820.1397-0.0468-0.06130.2299-0.11740.05920.1279-0.0825-0.0211-0.041-0.0731-0.05780.0334-34.522314.993493.046
25-0.0798-1.20360.18782.370.93543.71820.03480.33820.0058-0.37850.0088-0.004-0.41780.6911-0.0437-0.0245-0.15270.04510.1346-0.0232-0.0933-19.532219.599192.2665
263.34441.51933.22892.79711.51074.5230.05130.2859-0.44880.09260.1711-0.41190.30960.6735-0.2225-0.11940.02490.01530.0237-0.032-0.0267-23.330510.347597.142
27-0.10811.0806-0.44420.87680.79524.94270.0656-0.16890.00790.0145-0.2640.1154-0.29140.33620.19840.0144-0.0478-0.0008-0.0468-0.0098-0.0246-27.869720.3399104.4945
281.69450.67490.46542.91550.6672.2986-0.15210.0677-0.0603-0.11910.0624-0.4046-0.16010.59860.0898-0.047-0.08670.03350.05340-0.0352-20.613720.473998.8427
291.72221.3495-0.48021.97250.38260.18280.11920.0550.11890.0121-0.2060.0658-0.26780.0540.08680.1192-0.0917-0.0749-0.13030.0269-0.0311-30.774128.268499.1114
304.8122-0.15340.24342.4819-1.05452.5659-0.0276-0.5209-0.0669-0.02580.12220.1980.2699-0.1587-0.09460.0321-0.06590.01660.02710.1253-0.0449-0.5866-1.973973.9842
312.0179-2.86771.79240.48560.36892.5378-0.0959-0.34780.24440.0654-0.07750.0647-0.1587-0.46290.1734-0.06640.0902-0.0272-0.0451-0.0094-0.10560.527611.076565.8986
326.3077-0.97092.33091.98450.32894.55580.1222-0.4073-0.3910.17080.0235-0.08730.4076-0.0203-0.14570.02490.0306-0.0873-0.08670.06870.01389.4541-1.584768.4697
33-0.02242.6883-0.55910.7412-0.89293.44870.00410.1150.0328-0.04530.0058-0.1756-0.081-0.0254-0.00990.00890.039-0.0578-0.07550.03620.07418.88537.860458.4334
343.3878-3.291-1.58360.55020.7334-1.35990.0414-0.0474-0.1713-0.0569-0.0307-0.22410.05850.1377-0.01070.08530.1073-0.118-0.0549-0.01620.12617.5079-4.85662.6426
351.1839-0.53312.3782.7358-3.16343.9715-0.03890.00970.0937-0.15580.0209-0.13120.0521-0.2930.01790.0080.0134-0.0709-0.129-0.029-0.03912.171210.615256.5707
363.85862.04582.40980.5119-0.14252.58390.037-0.1826-0.1138-0.01760.16850.28140.3473-0.3795-0.20550.0486-0.0257-0.0674-0.03430.06510.0016-2.7242-1.466559.7441
372.48881.42570.43940.6004-2.07040.895-0.03170.041-0.5488-0.0450.0128-0.13810.4977-0.04520.01890.17660.068-0.1169-0.2117-0.0032-0.01244.4883-7.577360.0653
38-1.3856-1.07411.708200.19632.7973-0.0219-0.3038-0.06750.0665-0.03480.06760.1105-0.04530.0568-0.03130.013-0.0528-0.02490.05950.02436.66643.10171.8158
392.10980.7545-0.33071.11031.00881.8198-0.1021-0.36780.0405-0.02550.21890.18250.1567-0.499-0.11680.0041-0.0124-0.03090.05860.0991-0.0457-6.8717-1.325269.1582
404.3901-2.3643-1.63011.77742.26574.243-0.0237-0.50490.51960.2246-0.0392-0.0023-0.4501-0.09160.0629-0.02590.0743-0.1063-0.0614-0.13520.020913.239423.845781.8504
413.6701-1.44330.59275.6115-0.21171.5186-0.0035-0.11860.5187-0.3611-0.16310.3174-0.2656-0.11980.16660.01050.0991-0.1089-0.1616-0.05330.018115.739618.94270.3828
421.4968-0.79230.37885.40210.04332.71370.0436-0.03970.6188-0.51680.10560.0667-0.4567-0.1903-0.1493-0.06810.0362-0.0456-0.15930.04390.062321.582119.2168.0084
430.58281.31.41442.62783.37020.9021-0.1535-0.48320.50670.0760.0393-0.2326-0.08330.20510.1142-0.06260.0232-0.0628-0.0655-0.15270.194724.822324.540279.4815
440.9844-0.7372-0.10350.45791.15942.77540.0534-0.28350.5377-0.2099-0.1361-0.2657-0.51440.05160.0826-0.01380.0601-0.1108-0.2629-0.07470.205518.897527.107872.6318
45-0.4033-1.55780.51850.19520.29710.4033-0.0319-0.23610.17060.01610.0418-0.0387-0.0374-0.0548-0.0098-0.03280.0463-0.0127-0.0102-0.14480.041813.561921.881584.5403
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|2 - A|17 }
2X-RAY DIFFRACTION2{ A|18 - A|34 }
3X-RAY DIFFRACTION3{ A|35 - A|57 }
4X-RAY DIFFRACTION4{ A|58 - A|75 }
5X-RAY DIFFRACTION5{ A|76 - A|87 }
6X-RAY DIFFRACTION6{ A|88 - A|106 }
7X-RAY DIFFRACTION7{ A|107 - A|129 }
8X-RAY DIFFRACTION8{ A|130 - A|141 }
9X-RAY DIFFRACTION9{ B|2 - B|17 }
10X-RAY DIFFRACTION10{ B|18 - B|34 }
11X-RAY DIFFRACTION11{ B|35 - B|57 }
12X-RAY DIFFRACTION12{ B|58 - B|87 }
13X-RAY DIFFRACTION13{ B|88 - B|106 }
14X-RAY DIFFRACTION14{ B|107 - B|129 }
15X-RAY DIFFRACTION15{ B|130 - B|141 }
16X-RAY DIFFRACTION16{ C|2 - C|34 }
17X-RAY DIFFRACTION17{ C|35 - C|65 }
18X-RAY DIFFRACTION18{ C|66 - C|75 }
19X-RAY DIFFRACTION19{ C|76 - C|87 }
20X-RAY DIFFRACTION20{ C|88 - C|106 }
21X-RAY DIFFRACTION21{ C|107 - C|129 }
22X-RAY DIFFRACTION22{ C|130 - C|139 }
23X-RAY DIFFRACTION23{ D|2 - D|17 }
24X-RAY DIFFRACTION24{ D|18 - D|34 }
25X-RAY DIFFRACTION25{ D|35 - D|57 }
26X-RAY DIFFRACTION26{ D|58 - D|87 }
27X-RAY DIFFRACTION27{ D|88 - D|106 }
28X-RAY DIFFRACTION28{ D|107 - D|129 }
29X-RAY DIFFRACTION29{ D|130 - D|141 }
30X-RAY DIFFRACTION30{ E|2 - E|17 }
31X-RAY DIFFRACTION31{ E|18 - E|34 }
32X-RAY DIFFRACTION32{ E|35 - E|57 }
33X-RAY DIFFRACTION33{ E|58 - E|65 }
34X-RAY DIFFRACTION34{ E|66 - E|75 }
35X-RAY DIFFRACTION35{ E|76 - E|87 }
36X-RAY DIFFRACTION36{ E|88 - E|106 }
37X-RAY DIFFRACTION37{ E|107 - E|122 }
38X-RAY DIFFRACTION38{ E|123 - E|129 }
39X-RAY DIFFRACTION39{ E|130 - E|141 }
40X-RAY DIFFRACTION40{ F|2 - F|26 }
41X-RAY DIFFRACTION41{ F|27 - F|65 }
42X-RAY DIFFRACTION42{ F|66 - F|87 }
43X-RAY DIFFRACTION43{ F|88 - F|106 }
44X-RAY DIFFRACTION44{ F|107 - F|129 }
45X-RAY DIFFRACTION45{ F|130 - F|138 }

+
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