[English] 日本語
Yorodumi
- PDB-3u3y: Mouse TREX1 D200H mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3u3y
TitleMouse TREX1 D200H mutant
Components
  • 5'-D(*GP*AP*CP*G)-3'
  • Three prime repair exonuclease 1
KeywordsHYDROLASE/DNA / Rnase H fold / 3' exonuclease / homodimer / HYDROLASE-DNA complex
Function / homology
Function and homology information


immune response in brain or nervous system / adenyl deoxyribonucleotide binding / CD86 biosynthetic process / immune complex formation / cellular response to type I interferon / organ or tissue specific immune response / atrial cardiac muscle tissue development / activation of immune response / DNA synthesis involved in UV-damage excision repair / T cell antigen processing and presentation ...immune response in brain or nervous system / adenyl deoxyribonucleotide binding / CD86 biosynthetic process / immune complex formation / cellular response to type I interferon / organ or tissue specific immune response / atrial cardiac muscle tissue development / activation of immune response / DNA synthesis involved in UV-damage excision repair / T cell antigen processing and presentation / MutSalpha complex binding / retrotransposition / oligosaccharyltransferase complex / regulation of lysosome organization / regulation of fatty acid metabolic process / regulation of lipid biosynthetic process / DNA modification / MutLalpha complex binding / WW domain binding / heart process / regulation of protein complex stability / cellular response to hydroxyurea / regulation of type I interferon production / lymphoid progenitor cell differentiation / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / 3'-5'-DNA exonuclease activity / macrophage activation involved in immune response / regulation of tumor necrosis factor production / regulation of cellular respiration / inflammatory response to antigenic stimulus / DNA catabolic process / regulation of immunoglobulin production / apoptotic cell clearance / regulation of T cell activation / DNA binding, bending / DNA duplex unwinding / regulation of innate immune response / regulation of glycolytic process / DNA metabolic process / negative regulation of type I interferon-mediated signaling pathway / cellular response to organic substance / negative regulation of cGAS/STING signaling pathway / type I interferon-mediated signaling pathway / blood vessel development / nuclear replication fork / cellular response to interferon-beta / heart morphogenesis / response to UV / 3'-5' exonuclease activity / mitotic G1 DNA damage checkpoint signaling / negative regulation of innate immune response / DNA damage checkpoint signaling / generation of precursor metabolites and energy / kidney development / determination of adult lifespan / protein-DNA complex / cellular response to gamma radiation / establishment of protein localization / cellular response to reactive oxygen species / cellular response to UV / single-stranded DNA binding / cellular response to oxidative stress / regulation of inflammatory response / double-stranded DNA binding / regulation of gene expression / defense response to virus / DNA replication / adaptive immune response / protein stabilization / immune response / inflammatory response / innate immune response / DNA damage response / endoplasmic reticulum membrane / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / DNA binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Three-prime repair exonuclease 1/2 / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-BUTANEDIOL / DNA / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsBailey, S.L. / Harvey, S. / Perrino, F.W. / Hollis, T.
CitationJournal: Dna Repair / Year: 2012
Title: Defects in DNA degradation revealed in crystal structures of TREX1 exonuclease mutations linked to autoimmune disease.
Authors: Bailey, S.L. / Harvey, S. / Perrino, F.W. / Hollis, T.
History
DepositionOct 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Feb 28, 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 / struct_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Three prime repair exonuclease 1
A: Three prime repair exonuclease 1
C: 5'-D(*GP*AP*CP*G)-3'
D: 5'-D(*GP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0697
Polymers69,8994
Non-polymers1703
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-32 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.066, 57.861, 68.227
Angle α, β, γ (deg.)90.00, 108.11, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Three prime repair exonuclease 1 / 3'-5' exonuclease TREX1


Mass: 33733.453 Da / Num. of mol.: 2 / Mutation: D200H
Source method: isolated from a genetically manipulated source
Details: expressed as N-term MBP fusion protein / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trex1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91XB0, exodeoxyribonuclease III
#2: DNA chain 5'-D(*GP*AP*CP*G)-3'


Mass: 1215.843 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized DNA oligonucleotide
#3: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL / 1,4-Butanediol


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.75 Å3/Da / Density % sol: 29.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 16% PEG 4000, 0.1 M MES pH 6.0, 2% 1,4-butanediol, VAPOR DIFFUSION, temperature 298K

-
Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Oct 6, 2008 / Details: osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.28→40 Å / Num. obs: 21089 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.8

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→22.724 Å / SU ML: 0.74 / σ(F): 1.33 / Phase error: 27.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2753 1136 5.16 %random
Rwork0.2131 ---
obs0.2162 22013 99.21 %-
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.133 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.9029 Å20 Å2-2.5951 Å2
2--4.2174 Å2-0 Å2
3---3.6855 Å2
Refinement stepCycle: LAST / Resolution: 2.28→22.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3370 162 8 183 3723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073655
X-RAY DIFFRACTIONf_angle_d1.0965011
X-RAY DIFFRACTIONf_dihedral_angle_d17.2691372
X-RAY DIFFRACTIONf_chiral_restr0.057567
X-RAY DIFFRACTIONf_plane_restr0.006624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.38370.32761590.27022544X-RAY DIFFRACTION99
2.3837-2.50920.35361570.23932618X-RAY DIFFRACTION99
2.5092-2.66620.29731310.22872559X-RAY DIFFRACTION100
2.6662-2.87170.29141480.21092626X-RAY DIFFRACTION100
2.8717-3.160.28811260.20532622X-RAY DIFFRACTION100
3.16-3.61560.30421340.21982657X-RAY DIFFRACTION100
3.6156-4.54930.25361350.20692628X-RAY DIFFRACTION99
4.5493-22.72470.22491460.19652623X-RAY DIFFRACTION97
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)
12.11090.98810.18744.27690.64961.93520.267-0.0161-0.7955-0.3465-0.2817-0.13880.0651-0.16760.01650.1977-0.007-0.06340.22630.02490.356-6.6582-19.856112.2934
23.0415-0.4610.11473.9776-0.72921.68680.0388-0.2918-0.4587-0.227-0.02630.32440.1321-0.1538-0.03570.1885-0.038-0.03830.208-0.02290.1132-7.5011-7.618212.127
36.9754-1.0297-6.49570.2430.4968.3443-0.3804-0.5709-0.57480.1679-0.38020.73780.7507-0.31020.74720.3797-0.13510.07530.54210.14051.2128-0.2224-29.194524.108
44.9463-1.54952.96015.9313-1.84942.83580.43920.2019-0.31920.2928-0.4921-0.38340.36370.1978-0.08510.456-0.0256-0.11060.65430.23920.4456-1.164-21.424834.0004
50.44190.1066-1.18350.2803-0.37363.20020.2405-0.9075-0.35460.3715-0.0627-0.0739-0.0431-0.3032-0.07590.2322-0.106-0.04640.41950.07940.20046.9576-18.753118.3358
63.1863-1.737-0.24353.79140.42641.6094-0.1964-0.31590.20390.31820.00110.0267-0.0225-0.210.20160.27320.0016-0.03460.1819-0.0180.1696-5.75392.808912.803
72.9306-2.81712.10457.2051-1.0263.9421-0.4579-0.23160.43170.47280.41650.33650.3597-0.6536-0.08060.2061-0.0066-0.01020.3118-0.04020.2276-4.48775.703815.6246
86.5628-0.2956-3.39786.06414.13764.57420.21570.60980.89370.38520.0283-0.1202-0.1953-0.4331-0.08530.3891-0.0319-0.0310.26660.08180.28481.90616.05527.6238
90.2363-0.20150.11860.1978-0.17760.26720.11780.2413-0.1589-0.10360.0233-0.0230.08290.0580.19260.30010.155-0.15090.4841-0.13960.13980.7004-9.76661.3743
103.1458-0.09620.52273.19560.99751.5772-0.0328-0.0643-0.5481-0.1690.09430.32890.01290.1229-0.0160.2612-0.0387-0.08330.16550.00120.3266-8.1542-15.806210.3664
113.6449-3.14431.43594.19871.6237.20250.39850.40540.4251-1.1012-0.26250.4406-0.03850.25460.160.39360.0613-0.12790.3826-0.13150.399-9.9075-5.9315-0.2104
125.45971.2447-3.80933.96860.3795.2451-0.3935-0.2751-0.2565-0.57170.01120.1544-0.16720.37840.37050.231-0.0589-0.08190.37160.0430.5288-7.9445-17.18962.2253
130.19270.6993-0.76815.4022-0.72924.544-0.1-0.0394-0.380.1641-0.17230.44870.1107-0.1250.24270.2566-0.07870.03320.49730.19370.5098-15.7392-19.783121.5721
142.25592.0276-1.42642.1709-0.51312.5937-0.13730.0147-0.72330.1107-0.1789-0.29230.476-0.20410.28130.4955-0.18110.22280.69690.17151.1553-17.269-23.472429.0479
150.314-0.25220.0251.77950.81830.44840.0878-0.1296-0.06340.4188-0.12230.59850.12-0.2418-0.17160.2713-0.09070.06380.6070.23450.4626-11.6608-14.922331.306
163.80841.64530.18961.88742.25654.0278-0.6994-0.42260.0559-0.0071-0.2081-0.2314-0.16330.3750.730.4716-0.0961-0.0890.72740.21880.3691-3.2234-7.96129.9944
176.91972.2530.16673.2355-2.40872.8824-0.0761-0.4495-0.060.40630.18740.1683-0.4603-0.0214-0.14610.2503-0.01080.02280.34360.00820.0965-2.7314-8.570121.7094
182.04691.6417-2.42541.4016-1.78043.1915-0.0075-0.3889-0.45590.4116-0.02030.38350.07510.21490.09890.3287-0.01750.08730.53710.19190.4219-5.3046-20.535425.9116
194.84120.17872.03840.50671.56225.27440.12710.0894-1.57750.15610.013-0.06530.7158-0.1751-0.51050.281-0.0571-0.11480.34040.06330.9105-10.5874-28.210218.9041
200.006-0.0588-0.09680.57230.88891.3943-0.17490.0823-0.2852-0.4399-0.01610.6524-0.2206-0.29280.29960.3162-0.0668-0.19470.3003-0.02380.5616-16.2368-13.6774.7846
212.7827-0.5025-0.96760.09140.17510.3356-0.09430.1001-0.0396-0.31880.038-0.2937-0.30820.4766-0.12850.5942-0.23680.28920.58710.3040.72422.39188.91634.0834
227.4954-5.4750.68767.4817-0.41133.11690.3674-0.10150.4792-0.3411-0.30650.1523-0.0762-0.0519-0.11090.1726-0.05040.01780.3301-0.02420.190719.7196-9.648813.307
233.43621.0401-0.32040.98440.80471.58390.19730.4105-0.1913-0.4241-0.3714-0.22260.32370.24450.10780.23750.08140.02670.24410.03590.102918.7294-13.341411.5296
242.17030.93690.43681.58390.05280.8537-0.153-0.06830.5439-0.0639-0.01340.0354-0.27520.07440.36030.4717-0.1478-0.38430.44170.06130.981312.40319.523514.1595
253.55091.26642.26260.4570.67494.0332-0.278-0.27960.4639-0.12460.05790.1964-0.321-0.66890.66170.43410.1092-0.22770.6481-0.25130.523514.00647.176431.6897
264.83042.0921.03453.3687-3.06255.22450.1209-0.79830.29180.47210.04650.0732-0.79350.1654-0.27470.30260.1003-0.01970.5514-0.05350.26235.52081.96419.9324
273.9945-2.08371.41212.935-1.84772.66290.1809-0.0908-0.6228-0.0064-0.187-0.06780.53330.2292-0.13240.286-0.0272-0.07510.22890.04360.225416.9503-21.657115.7439
283.3039-0.47961.37617.3523-1.43030.78110.46060.079-1.3375-0.459-0.04260.37840.3110.0066-0.18380.3970.0659-0.14430.256-0.02060.558911.2536-26.355910.515
291.97650.0428-0.14751.77770.76961.82640.21230.47440.1185-0.74860.16330.0787-0.04780.2033-0.05250.40520.11480.03410.40720.04920.153710.204-8.18951.738
305.51180.35381.57414.5678-1.70434.95010.34640.41730.28370.13510.0889-0.1263-0.41370.1164-0.18670.1761-0.03480.12780.35290.0370.324722.7001-3.06711.0907
311.7235-0.9645-3.70936.8659-0.29168.89360.24160.33930.1615-0.098-0.4746-0.1788-0.07220.95660.08260.33370.10280.05380.45380.07820.190725.2336-13.00777.0213
320.18290.0083-0.25241.9307-0.96680.81920.01890.2116-0.1375-0.6738-0.2415-0.24480.44560.12550.14160.57770.27020.10140.8282-0.07860.328418.9177-16.5261-3.6273
335.53071.10711.17172.8581-1.32812.25240.03180.6540.6541-0.4677-0.1159-0.45190.16780.4959-0.29310.18960.07340.08890.54620.1330.454523.2567-2.59796.9194
346.51761.23962.44460.25180.65453.1427-0.1318-0.08190.71870.0720.1372-0.1956-0.16040.21360.15550.3495-0.0296-0.2640.4880.05261.387930.48684.693924.1183
350.18740.00980.25460.00590.01680.3445-0.0206-0.0670.09780.06820.0272-0.0633-0.0320.09210.23750.16530.1019-0.37780.6136-0.23440.406324.5159-2.716928.1841
360.3221-0.74970.19823.59950.94421.19220.1584-0.35710.47290.2013-0.17940.0847-0.3815-0.0740.23150.61220.0147-0.0170.4125-0.21260.362118.9235-3.81434.2798
374.7553-2.191-0.36522.3367-0.55994.1666-0.012-0.54610.38340.40570.2311-0.24280.2845-0.0698-0.14810.2189-0.0571-0.06170.374-0.02540.154415.9297-7.961522.4308
381.32481.4685-0.60551.6477-0.57540.6907-0.2242-0.1040.68810.1354-0.0588-0.2011-0.31880.11240.32140.30040.0254-0.25360.2797-0.16590.854319.8068.033922.3534
390.12860.1397-0.20680.1517-0.22630.33570.0655-0.05840.42020.078-0.13820.1531-0.21030.1043-0.47540.3798-0.15560.12260.31030.17171.066425.15536.528411.0519
402.0124-0.0582-0.79450.6982-0.82971.35220.28290.68280.5602-0.2899-0.0884-0.1473-0.3242-0.37170.05520.36750.22870.17740.6880.21980.316428.6297-10.53872.8528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 6:21)
2X-RAY DIFFRACTION2(chain A and resid 22:41)
3X-RAY DIFFRACTION3(chain A and resid 42:52)
4X-RAY DIFFRACTION4(chain A and resid 53:59)
5X-RAY DIFFRACTION5(chain A and resid 60:66)
6X-RAY DIFFRACTION6(chain A and resid 67:83)
7X-RAY DIFFRACTION7(chain A and resid 84:90)
8X-RAY DIFFRACTION8(chain A and resid 91:99)
9X-RAY DIFFRACTION9(chain A and resid 100:112)
10X-RAY DIFFRACTION10(chain A and resid 113:134)
11X-RAY DIFFRACTION11(chain A and resid 135:142)
12X-RAY DIFFRACTION12(chain A and resid 143:153)
13X-RAY DIFFRACTION13(chain A and resid 154:161)
14X-RAY DIFFRACTION14(chain A and resid 162:174)
15X-RAY DIFFRACTION15(chain A and resid 175:188)
16X-RAY DIFFRACTION16(chain A and resid 189:194)
17X-RAY DIFFRACTION17(chain A and resid 195:204)
18X-RAY DIFFRACTION18(chain A and resid 205:210)
19X-RAY DIFFRACTION19(chain A and resid 211:222)
20X-RAY DIFFRACTION20(chain A and resid 223:234)
21X-RAY DIFFRACTION21(chain B and resid 6:11)
22X-RAY DIFFRACTION22(chain B and resid 12:25)
23X-RAY DIFFRACTION23(chain B and resid 26:40)
24X-RAY DIFFRACTION24(chain B and resid 41:45)
25X-RAY DIFFRACTION25(chain B and resid 46:58)
26X-RAY DIFFRACTION26(chain B and resid 59:64)
27X-RAY DIFFRACTION27(chain B and resid 65:90)
28X-RAY DIFFRACTION28(chain B and resid 91:100)
29X-RAY DIFFRACTION29(chain B and resid 101:117)
30X-RAY DIFFRACTION30(chain B and resid 118:127)
31X-RAY DIFFRACTION31(chain B and resid 128:139)
32X-RAY DIFFRACTION32(chain B and resid 140:145)
33X-RAY DIFFRACTION33(chain B and resid 146:157)
34X-RAY DIFFRACTION34(chain B and resid 158:175)
35X-RAY DIFFRACTION35(chain B and resid 176:187)
36X-RAY DIFFRACTION36(chain B and resid 188:191)
37X-RAY DIFFRACTION37(chain B and resid 192:208)
38X-RAY DIFFRACTION38(chain B and resid 209:214)
39X-RAY DIFFRACTION39(chain B and resid 215:224)
40X-RAY DIFFRACTION40(chain B and resid 225:234)

+
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