[English] 日本語
Yorodumi
- PDB-3u6f: Mouse TREX1 D200N mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3u6f
TitleMouse TREX1 D200N mutant
Components
  • 5'-D(*GP*AP*CP*G)-3'
  • Three prime repair exonuclease 1
KeywordsHYDROLASE/DNA / RNase H fold / 3' exonuclease / 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 type I interferon production / regulation of protein complex stability / cellular response to hydroxyurea / 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 / regulation of immunoglobulin production / DNA catabolic process / apoptotic cell clearance / regulation of T cell activation / DNA binding, bending / DNA duplex unwinding / regulation of glycolytic process / DNA metabolic process / negative regulation of type I interferon-mediated signaling pathway / cellular response to organic substance / regulation of innate immune response / 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 / kidney development / generation of precursor metabolites and energy / 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: 2.3 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 12, 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.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)70,0798
Polymers69,8504
Non-polymers2294
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-24 kcal/mol
Surface area17780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.886, 56.644, 68.143
Angle α, β, γ (deg.)90.00, 107.97, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 33709.406 Da / Num. of mol.: 2 / Mutation: D200N
Source method: isolated from a genetically manipulated source
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
#3: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL / 1,4-Butanediol


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.71 Å3/Da / Density % sol: 27.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: 0.1 M MES, 0.075M NaCl, 12% PEG 3350, 5% 1,4-butanediol, 2mM CaCl2, pH 5.5, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Oct 25, 2008
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→33 Å / Num. all: 21121 / Num. obs: 21073 / % possible obs: 99.77 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 2.3 Å / % possible all: 99.7

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→33.221 Å / SU ML: 0.72 / σ(F): 0 / Phase error: 32.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2885 1082 5.13 %random
Rwork0.2193 ---
obs0.2227 21073 99.77 %-
all-21121 --
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.148 Å2 / ksol: 0.397 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.1132 Å20 Å2-2.2616 Å2
2--5.6214 Å2-0 Å2
3---3.4918 Å2
Refinement stepCycle: LAST / Resolution: 2.3→33.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 162 14 176 3701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083625
X-RAY DIFFRACTIONf_angle_d1.2734966
X-RAY DIFFRACTIONf_dihedral_angle_d17.4981355
X-RAY DIFFRACTIONf_chiral_restr0.059564
X-RAY DIFFRACTIONf_plane_restr0.008616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40460.39011350.29792474X-RAY DIFFRACTION100
2.4046-2.53140.34871170.27652523X-RAY DIFFRACTION100
2.5314-2.68990.38241430.26862481X-RAY DIFFRACTION100
2.6899-2.89750.36811410.27242455X-RAY DIFFRACTION100
2.8975-3.18890.33261500.25132470X-RAY DIFFRACTION100
3.1889-3.64980.27761270.23142516X-RAY DIFFRACTION100
3.6498-4.59640.24771360.16752530X-RAY DIFFRACTION100
4.5964-33.22420.221330.18712542X-RAY DIFFRACTION99
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)
12.2293-0.9001-0.01741.8231-0.16120.61030.02230.7623-0.6130.0234-0.08020.15250.1616-0.07020.03950.3088-0.0444-0.03180.6506-0.250.3217-7.8729-16.629512.2956
22.2271-1.2412-1.30931.43991.12151.37270.28640.8702-0.0739-0.3008-0.41010.2167-0.1807-0.20070.03720.2608-0.0156-0.01620.6713-0.04450.1622-6.3526-7.642811.4149
33.98562.93721.05948.1399-4.48094.9139-0.5479-0.4414-0.93870.3730.0033-1.0480.6959-0.58640.54980.5026-0.0123-0.0710.5432-0.15970.71220.6544-29.547617.6644
44.86892.7347-2.09624.1358-3.00642.18860.72610.7288-0.21020.0004-0.3774-0.2957-0.2782-0.1188-0.3170.5471-0.0277-0.04480.45670.08830.374-2.9011-25.382634.8771
50.49251.64480.60657.49871.84990.7625-0.1842-1.1784-0.42040.99310.6129-0.32930.4481.5922-0.44540.40380.0736-0.0530.71060.15150.29063.148-20.42428.3803
60.9830.326-0.54670.38860.25770.9943-0.01020.46570.1462-0.0530.1063-0.0059-0.0363-0.1421-0.16120.25220.0148-0.08740.5234-0.00480.1598-0.8676-4.924912.5347
71.6154-0.5666-1.1493.6568-2.45893.8092-0.25591.24690.9562-0.0576-0.168-0.4054-0.52820.17380.38340.4187-0.0418-0.11910.590.19520.3786-2.33376.048213.8758
83.1493.901-0.82485.1988-1.74731.6490.34421.68910.4052-0.4131-0.09970.0265-0.1499-0.1891-0.18560.4660.2957-0.02781.26370.29590.3269-1.6762-1.24750.8036
92.0683-1.3713-0.183.0105-1.81424.04710.35391.1857-0.0999-0.6988-0.51220.08880.2066-0.23560.05560.32670.2228-0.0151.0136-0.17360.08682.1364-12.78411.7896
107.10480.5449-2.21490.0418-0.16950.6904-0.12451.888-0.9627-0.38320.05970.1033-0.0404-0.7563-0.02730.32690.0996-0.00480.843-0.45520.58642.1592-23.82915.8952
111.9374-0.21252.1712.39340.68093.06510.15950.647-0.1971-0.0334-0.49930.2128-0.0856-0.54520.2120.20920.0147-0.0460.6409-0.19930.3454-12.519-12.710811.164
120.6423-1.47220.65863.5705-2.40674.89940.4811.28120.2901-0.5575-0.36710.0566-0.408-1.0742-0.06820.3770.25010.06751.2630.10590.3484-9.4441-5.1357-0.466
132.94030.2267-2.23053.97762.37434.44750.33391.3736-0.2272-0.733-0.27570.1293-0.35830.0307-0.10410.36590.1302-0.01211.1217-0.35450.3808-7.1806-16.27260.3152
146.47542.9210.09616.8258-2.59564.22030.06290.1464-0.65180.5638-0.1459-0.17160.0439-0.1930.03770.3257-0.13470.13510.2936-0.12420.5475-15.2954-21.365522.6986
155.6407-0.5908-3.05910.40020.96542.8879-0.8382-0.0919-1.29540.56980.4930.45421.2285-0.43090.33540.6104-0.13260.39380.54760.05830.5945-18.2821-16.799729.2669
163.4655-3.32243.29523.8802-2.64943.5093-0.3048-0.7362-0.32360.82520.26290.4001-0.39290.11380.0580.4149-0.04550.07350.40560.04660.186-9.4512-15.13631.0457
177.30335.6082-5.44346.3207-5.72765.76260.2365-0.5099-0.17571.1659-0.1837-0.3111-0.60060.0572-0.04410.652-0.0479-0.0670.6769-0.04820.2226-4.1348-10.328432.1413
183.02121.4436-0.88894.774-5.21516.82860.08840.1421-0.00321.0809-0.1940.2948-0.5415-0.14680.10380.2818-0.00920.06720.3337-0.04960.1725-3.7523-13.947223.3382
191.51850.21641.2541.86192.32643.55530.16870.243-0.55110.372-0.44760.78350.5052-0.56910.18250.3596-0.12520.11130.5528-0.42640.8343-11.294-27.381916.8419
203.7816-1.79040.24563.68811.460.89240.50571.1291-0.8683-0.7748-0.85011.14940.0694-0.08740.4180.32380.1338-0.22530.8455-0.39780.4934-16.7787-11.23983.8125
212.72641.7045-0.43921.8876-0.05663.00950.37880.6751.404-0.88-0.2086-0.8206-0.59810.3069-0.11560.61660.01820.22840.75480.48390.831518.12873.70247.9368
224.7604-1.74671.98442.6361-1.55781.95530.57031.2539-0.1572-0.3631-0.6927-0.15410.10610.13140.05940.27740.0401-0.01360.5950.0480.132521.019-15.948712.8863
232.3739-0.66590.75511.75980.78634.175-0.4460.35891.71730.11850.2089-0.2516-0.3667-0.13410.25290.5878-0.0611-0.34620.65250.31331.240911.8198.975319.2807
244.74640.42671.71872.4771.94291.9324-0.2107-0.43190.7243-0.24950.25380.03-0.3843-0.56180.03610.3921-0.0549-0.20460.31870.08870.684612.07562.95130.0072
254.7915-0.08781.22650.0019-0.07632.4452-0.00351.22190.0815-0.04940.1306-0.33980.10330.3930.03950.1821-0.0421-0.00540.64860.06510.15211.3242-13.533412.417
262.9474-1.29452.44342.1446-0.75012.1509-0.3639-0.0674-0.3364-0.1116-0.06750.0294-1.25630.39860.44640.3513-0.0003-0.02780.3379-0.00450.233221.1357-24.06521.2164
275.5185-3.89792.30285.1062-0.50911.48990.55581.0949-1.618-0.30180.01360.37580.23860.6142-0.48830.39940.001-0.03670.6032-0.47380.974411.392-27.961412.3103
282.5721-1.91190.57281.60860.33773.19930.72471.27910.0751-0.5325-0.6449-0.06880.25890.01650.3770.33650.2345-0.10251.09590.1472-0.040811.2066-12.30891.7446
291.1219-0.0759-0.33760.52290.2370.19150.09361.38721.0264-0.3144-0.10910.0117-0.2253-0.34670.12850.17670.079-0.11440.80940.53630.631318.5925-1.48479.1067
305.4012-2.3527-2.79474.4585-3.07726.82330.34260.98560.93510.0319-0.4273-0.1968-0.37040.54780.12480.27480.0180.0430.92360.27680.437226.9403-10.647710.4055
314.1358-0.5824-1.01460.6939-0.6551.29120.07791.42680.0954-0.21960.00330.170.0711-0.12420.00280.39060.21310.06051.25440.16240.298822.644-16.85040.9121
322.33161.003-1.19421.6657-1.49752.3074-0.03481.3830.3989-0.58650.12260.13790.2216-0.7618-0.16180.45980.10370.12961.2090.48010.491720.6137-6.27711.3371
330.99471.09081.01451.55580.57381.8448-0.310.03431.18440.2061-0.236-0.7515-0.61120.67840.57170.3933-0.2284-0.16360.66280.27311.403428.93854.123422.2966
343.2523-2.1808-0.44813.12392.50965.3551-0.3906-0.39931.37940.69670.5392-0.90810.07910.7514-0.25850.5107-0.0665-0.37370.3151-0.06830.787824.4705-2.797729.8106
355.69760.33672.52244.22572.1562.24-0.081-0.12710.48540.9775-0.2536-0.53680.0939-0.13950.36680.6068-0.0154-0.15250.30980.06350.226715.6785-11.589827.9848
362.49-1.72441.79856.7366-1.8632.6504-0.1780.30670.81580.2067-0.2933-0.4189-0.34680.57670.43740.271-0.0725-0.08740.28120.16660.38616.0226-5.313721.3062
374.94014.8220.53714.70790.52410.0582-0.34340.4041.03270.2654-0.371-1.7341-0.53580.78310.76830.6585-0.0774-0.35920.41980.30251.479619.31017.811523.0556
386.13870.09-1.74892.0773-2.6383.78530.30260.98832.025-0.2466-0.3604-0.5739-0.30730.24050.01740.520.07380.2740.90250.76291.905824.49088.012613.2216
391.55061.53720.10712.6624-1.76953.09810.09441.59540.7537-0.8291-0.195-0.7050.05250.17310.05510.44520.10330.31311.15730.4880.750827.7026-4.24462.888
405.23632.7304-0.87488.3905-1.78441.6176-0.26241.5699-0.0185-0.85990.7277-0.04030.0322-0.9214-0.42210.44730.04860.02181.47740.24090.425229.9016-18.54392.5914
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 7:25)
2X-RAY DIFFRACTION2(chain A and resid 26:40)
3X-RAY DIFFRACTION3(chain A and resid 41:45)
4X-RAY DIFFRACTION4(chain A and resid 46:55)
5X-RAY DIFFRACTION5(chain A and resid 56:61)
6X-RAY DIFFRACTION6(chain A and resid 62:79)
7X-RAY DIFFRACTION7(chain A and resid 80:97)
8X-RAY DIFFRACTION8(chain A and resid 98:102)
9X-RAY DIFFRACTION9(chain A and resid 103:113)
10X-RAY DIFFRACTION10(chain A and resid 114:118)
11X-RAY DIFFRACTION11(chain A and resid 119:136)
12X-RAY DIFFRACTION12(chain A and resid 137:141)
13X-RAY DIFFRACTION13(chain A and resid 142:152)
14X-RAY DIFFRACTION14(chain A and resid 153:164)
15X-RAY DIFFRACTION15(chain A and resid 165:178)
16X-RAY DIFFRACTION16(chain A and resid 179:187)
17X-RAY DIFFRACTION17(chain A and resid 188:194)
18X-RAY DIFFRACTION18(chain A and resid 195:210)
19X-RAY DIFFRACTION19(chain A and resid 211:225)
20X-RAY DIFFRACTION20(chain A and resid 226:234)
21X-RAY DIFFRACTION21(chain B and resid 7:17)
22X-RAY DIFFRACTION22(chain B and resid 18:39)
23X-RAY DIFFRACTION23(chain B and resid 40:52)
24X-RAY DIFFRACTION24(chain B and resid 53:61)
25X-RAY DIFFRACTION25(chain B and resid 62:76)
26X-RAY DIFFRACTION26(chain B and resid 77:87)
27X-RAY DIFFRACTION27(chain B and resid 88:98)
28X-RAY DIFFRACTION28(chain B and resid 99:114)
29X-RAY DIFFRACTION29(chain B and resid 115:126)
30X-RAY DIFFRACTION30(chain B and resid 127:134)
31X-RAY DIFFRACTION31(chain B and resid 135:141)
32X-RAY DIFFRACTION32(chain B and resid 142:154)
33X-RAY DIFFRACTION33(chain B and resid 155:166)
34X-RAY DIFFRACTION34(chain B and resid 175:188)
35X-RAY DIFFRACTION35(chain B and resid 189:196)
36X-RAY DIFFRACTION36(chain B and resid 197:208)
37X-RAY DIFFRACTION37(chain B and resid 209:214)
38X-RAY DIFFRACTION38(chain B and resid 215:222)
39X-RAY DIFFRACTION39(chain B and resid 223:230)
40X-RAY DIFFRACTION40(chain B and resid 231:236)

+
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