[English] 日本語
Yorodumi
- PDB-5naf: Co-crystal structure of an MeCP2 peptide with TBLR1 WD40 domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5naf
TitleCo-crystal structure of an MeCP2 peptide with TBLR1 WD40 domain
Components
  • F-box-like/WD repeat-containing protein TBL1XR1
  • Methyl-CpG-binding protein 2
KeywordsTRANSCRIPTION / WD40 domain / protein-peptide complex / transcriptional repressor / Rett syndrome
Function / homology
Function and homology information


cellular response to isoquinoline alkaloid / positive regulation of retrograde dense core granule transport / negative regulation of respiratory gaseous exchange / positive regulation of branching morphogenesis of a nerve / positive regulation of anterograde dense core granule transport / trans-synaptic signaling by BDNF / Regulation of MECP2 expression and activity / catecholamine secretion / proprioception / principal sensory nucleus of trigeminal nerve development ...cellular response to isoquinoline alkaloid / positive regulation of retrograde dense core granule transport / negative regulation of respiratory gaseous exchange / positive regulation of branching morphogenesis of a nerve / positive regulation of anterograde dense core granule transport / trans-synaptic signaling by BDNF / Regulation of MECP2 expression and activity / catecholamine secretion / proprioception / principal sensory nucleus of trigeminal nerve development / biogenic amine metabolic process / negative regulation of locomotion involved in locomotory behavior / cardiolipin metabolic process / regulation of triglyceride metabolic process / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of dendrite extension / negative regulation of smooth muscle cell differentiation / regulation of action potential firing threshold / nervous system process involved in regulation of systemic arterial blood pressure / negative regulation of primary miRNA processing / HDACs deacetylate histones / ventricular system development / glucocorticoid metabolic process / Notch-HLH transcription pathway / neuromuscular process controlling posture / regulation of respiratory gaseous exchange by nervous system process / negative regulation of dendritic spine development / ventricular cardiac muscle tissue development / inositol metabolic process / genomic imprinting / double-stranded methylated DNA binding / Regulation of lipid metabolism by PPARalpha / phosphatidylcholine metabolic process / Cytoprotection by HMOX1 / respiratory gaseous exchange by respiratory system / olfactory bulb development / blastocyst hatching / positive regulation of dendrite extension / neuron maturation / unmethylated CpG binding / striatum development / positive regulation of microtubule nucleation / thalamus development / positive regulation of synaptic plasticity / L-glutamine metabolic process / lung alveolus development / response to other organism / oligodendrocyte development / siRNA binding / methyl-CpG binding / cellular response to potassium ion / neuromuscular process / fat pad development / response to dietary excess / white fat cell differentiation / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of astrocyte differentiation / positive regulation of dendritic spine development / response to ionizing radiation / startle response / spinal cord development / adipose tissue development / dendrite development / histone deacetylase complex / regulation of synapse organization / negative regulation of blood vessel endothelial cell migration / associative learning / social behavior / behavioral fear response / multicellular organismal response to stress / positive regulation of glial cell proliferation / post-embryonic development / Notch signaling pathway / histone reader activity / lipid catabolic process / glial cell proliferation / long-term memory / adult locomotory behavior / transcription repressor complex / four-way junction DNA binding / heterochromatin / cerebellum development / multicellular organism growth / synapse assembly / sensory perception of pain / negative regulation of angiogenesis / learning / epigenetic regulation of gene expression / excitatory postsynaptic potential / hippocampus development / response to cocaine / brain development / molecular condensate scaffold activity / promoter-specific chromatin binding / visual learning / cerebral cortex development / chromatin DNA binding / regulation of synaptic plasticity / memory / cell population proliferation
Similarity search - Function
F-box-like/WD repeat-containing protein Ebi-like / Methyl-CpG binding protein MeCP2 / Methyl-CpG binding protein MeCP2/MBD4 / LisH / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain ...F-box-like/WD repeat-containing protein Ebi-like / Methyl-CpG binding protein MeCP2 / Methyl-CpG binding protein MeCP2/MBD4 / LisH / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
F-box-like/WD repeat-containing protein TBL1XR1 / Methyl-CpG-binding protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.493 Å
AuthorsKruusvee, V. / Cook, A.G.
Funding support United Kingdom, 7items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1000520/1 United Kingdom
Wellcome Trust091580 United Kingdom
Wellcome Trust107930 United Kingdom
Wellcome Trust092076 United Kingdom
Wellcome Trust095822 United Kingdom
Wellcome Trust108504 United Kingdom
Rett Syndrome TrustGrant to APB United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure of the MeCP2-TBLR1 complex reveals a molecular basis for Rett syndrome and related disorders.
Authors: Kruusvee, V. / Lyst, M.J. / Taylor, C. / Tarnauskaite, Z. / Bird, A.P. / Cook, A.G.
History
DepositionFeb 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: F-box-like/WD repeat-containing protein TBL1XR1
B: F-box-like/WD repeat-containing protein TBL1XR1
C: F-box-like/WD repeat-containing protein TBL1XR1
D: F-box-like/WD repeat-containing protein TBL1XR1
E: Methyl-CpG-binding protein 2
F: Methyl-CpG-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,22825
Polymers181,4786
Non-polymers1,75019
Water9,260514
1
A: F-box-like/WD repeat-containing protein TBL1XR1
E: Methyl-CpG-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4799
Polymers46,8342
Non-polymers6457
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-6 kcal/mol
Surface area14740 Å2
MethodPISA
2
B: F-box-like/WD repeat-containing protein TBL1XR1
F: Methyl-CpG-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2957
Polymers46,8342
Non-polymers4605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-10 kcal/mol
Surface area14270 Å2
MethodPISA
3
C: F-box-like/WD repeat-containing protein TBL1XR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9972
Polymers43,9051
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint0 kcal/mol
Surface area13780 Å2
MethodPISA
4
D: F-box-like/WD repeat-containing protein TBL1XR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4577
Polymers43,9051
Non-polymers5536
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-1 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.628, 58.643, 155.101
Angle α, β, γ (deg.)97.63, 91.17, 90.24
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
F-box-like/WD repeat-containing protein TBL1XR1 / Nuclear receptor corepressor/HDAC3 complex subunit TBLR1 / TBL1-related protein 1 / Transducin beta- ...Nuclear receptor corepressor/HDAC3 complex subunit TBLR1 / TBL1-related protein 1 / Transducin beta-like 1X-related protein 1


Mass: 43904.734 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tbl1xr1, Ira1, Tblr1 / Plasmid: pFL / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8BHJ5
#2: Protein/peptide Methyl-CpG-binding protein 2 / MeCp2


Mass: 2929.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9Z2D6
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM MOPS pH 7.5 PEG 3350 18%

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.493→49.64 Å / Num. obs: 50648 / % possible obs: 98 % / Redundancy: 2.4 % / Biso Wilson estimate: 33.53 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.08474 / Rsym value: 0.1099 / Net I/σ(I): 9.91
Reflection shellResolution: 2.493→2.582 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.4429 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 4583 / CC1/2: 0.686 / Rsym value: 0.5735 / % possible all: 88

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
SCALAdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LG9

4lg9


Resolution: 2.493→49.639 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.67
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2511 4.96 %randomly and uniformly distributed
Rwork0.203 ---
obs0.2053 50632 97.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.493→49.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9772 0 114 514 10400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410095
X-RAY DIFFRACTIONf_angle_d0.70713771
X-RAY DIFFRACTIONf_dihedral_angle_d11.7685757
X-RAY DIFFRACTIONf_chiral_restr0.0531560
X-RAY DIFFRACTIONf_plane_restr0.0061779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4927-2.54060.36171250.28422147X-RAY DIFFRACTION79
2.5406-2.59250.28851400.25212717X-RAY DIFFRACTION98
2.5925-2.64880.33341310.25052686X-RAY DIFFRACTION97
2.6488-2.71050.27691270.24892700X-RAY DIFFRACTION99
2.7105-2.77820.2811700.23812669X-RAY DIFFRACTION98
2.7782-2.85330.33011380.23482676X-RAY DIFFRACTION98
2.8533-2.93730.27761300.23442704X-RAY DIFFRACTION98
2.9373-3.03210.26881210.21932767X-RAY DIFFRACTION98
3.0321-3.14040.27971040.20832710X-RAY DIFFRACTION99
3.1404-3.26620.24541640.19252690X-RAY DIFFRACTION98
3.2662-3.41480.23471300.19352672X-RAY DIFFRACTION99
3.4148-3.59480.221490.19062713X-RAY DIFFRACTION98
3.5948-3.81990.1961260.17772738X-RAY DIFFRACTION99
3.8199-4.11470.23371300.17942695X-RAY DIFFRACTION99
4.1147-4.52850.20951530.16582749X-RAY DIFFRACTION99
4.5285-5.18320.20831680.16912698X-RAY DIFFRACTION99
5.1832-6.5280.25331580.22292694X-RAY DIFFRACTION99
6.528-49.64880.28371470.22652696X-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)
11.14640.0442-0.49322.10470.14551.4862-0.0034-0.2368-0.01340.0481-0.10490.0141-0.0061-0.16380.07290.1859-0.0363-0.03220.23850.00960.2218-4.872737.03752.2946
23.93010.4971-1.13422.17742.91094.7490.2527-0.2310.56330.1468-0.02660.4624-0.244-0.4532-0.26770.17860.01960.04540.4157-0.03190.3606-6.87647.679355.5389
30.73910.4833-0.47271.2215-0.00531.2452-0.0027-0.0740.00470.0170.0293-0.03910.040.0121-0.02710.11640.0082-0.05540.1662-0.00340.27218.8437.921339.9042
41.1826-0.3026-0.31971.60750.48111.2423-0.1562-0.0863-0.02420.13630.09890.03130.12580.31370.02740.18960.0385-0.01310.2807-0.0210.270737.501162.9632-0.6534
53.91810.64410.28893.5630.38953.2265-0.02390.31520.027-0.2990.1458-0.1832-0.05080.3017-0.16990.17930.0057-0.00880.30870.00250.237232.343770.0234-6.917
60.1877-0.6301-0.23842.43010.483.8257-0.07270.30680.1032-0.04450.2651-0.3259-0.33120.4373-0.0740.1988-0.01010.00130.25580.02480.300828.198579.3634-0.3726
71.1716-0.4009-0.60380.526-0.29011.2708-0.00220.3912-0.122-0.15140.1283-0.2057-0.13850.0195-0.05830.2046-0.0227-0.0780.2757-0.00960.342520.959179.92221.2372
82.8968-0.6517-0.61132.5395-0.7690.6766-0.14630.02480.0161-0.12120.2081-0.1774-0.1751-0.17830.0660.274-0.0032-0.01260.12060.00460.356916.088285.10046.6306
90.70060.11890.23960.8742-0.06852.10270.01610.06950.08950.0660.10110.0435-0.1716-0.0066-0.04610.1932-0.0012-0.01520.18070.00790.27513.326173.727815.931
102.1318-0.4226-0.00791.80340.33832.2086-0.07590.0349-0.13670.02840.01850.07590.13570.04720.04050.1893-0.003-0.04980.1644-0.0030.308117.011459.427416.5194
111.3497-0.3088-0.68281.9845-0.61763.1718-0.11320.0495-0.18870.20180.01350.03750.298-0.0496-0.01730.22070.022-0.03590.1654-0.00740.362824.912254.001511.3477
121.78781.1375-0.21583.1648-0.14431.60520.0699-0.16140.01720.0492-0.1379-0.02290.16320.150.04740.14830.0438-0.01680.2121-0.01570.279932.428854.71376.6733
136.72091.67442.34322.20160.42774.07380.07850.4711-0.0123-0.00630.1190.26730.50150.0779-0.12430.20110.0386-0.01780.2107-0.05060.262332.584758.9126-2.3612
142.2384-0.49050.20162.27070.59333.44980.13920.02990.26370.1051-0.07210.0367-0.3783-0.5349-0.13170.42820.0970.0870.40530.00040.266432.221957.393866.8722
150.2336-0.3645-0.25380.6899-0.04711.78750.18430.1350.3439-0.1145-0.00640.1959-1.3843-1.0753-0.33161.08540.39850.24520.74050.0860.422525.637771.418568.1776
164.6612-2.1092-0.68083.0855-1.99732.59420.06220.1570.3340.4632-0.03450.16-0.9739-0.75760.08441.17180.56350.16930.84040.16310.461622.926676.215865.158
174.1222-0.0419-0.00133.50920.49432.56-0.11410.04340.38390.0038-0.08850.6726-1.8409-0.85230.05431.4060.53210.2240.88080.06440.56522.791179.505676.354
180.9466-0.026-0.20671.24751.2082.46220.122-0.03060.21360.49280.02460.0769-0.7091-0.5029-0.08371.02260.20510.17790.63820.0360.334829.674663.511389.063
192.66520.4129-0.56051.7268-0.58322.64210.0242-0.03650.2803-0.23740.175-0.2596-0.84420.8042-0.20560.5594-0.21210.08780.5135-0.04470.3016-2.045228.9437-17.8403
201.00020.3589-0.25620.1355-0.17140.83630.2919-0.19450.29140.3357-0.1304-0.1535-1.34850.7805-0.22581.5641-0.74270.30191.0437-0.13550.64187.269845.1182-21.4269
212.24430.4271-1.07680.39240.00930.66090.3260.32670.7096-0.2949-0.1053-0.1266-1.3020.378-0.27132.0021-0.45670.23410.97070.0190.6345.769948.9264-36.0637
222.5047-0.00350.76092.3501-1.75251.53760.46190.6750.5649-0.1198-0.09730.0471-1.26590.315-0.36571.2971-0.22420.14570.78160.0420.32351.048637.8474-43.0673
232.54770.0855-1.4220.9983-0.65343.68340.06340.46830.2321-0.54690.2348-0.1147-0.49420.0233-0.26590.7554-0.14470.08320.6832-0.06650.2953-2.990726.0926-39.2322
243.56713.2249-3.23176.72862.2389.9091-0.25781.21070.8508-1.45410.5131.4322-0.9429-1.3268-0.17720.4351-0.0323-0.12760.38060.06990.353-7.821441.083232.1365
252.49962.6187-2.75294.3172-0.20227.594-0.09730.28180.41110.0155-0.1330.4116-0.2328-0.52830.05410.1447-0.0753-0.02760.40590.00730.5496-2.444945.132633.414
267.9533-3.7994-2.59644.2176-1.73974.54420.1175-0.53680.48330.4838-0.2441-1.2951-0.6371.15580.09070.33960.0822-0.15720.6405-0.12380.545237.243870.57416.2563
277.78521.370.7010.5855-0.55544.0089-0.1018-0.20640.79650.1289-0.0704-0.4393-0.5070.89310.10370.1512-0.0593-0.0630.3508-0.00090.570232.132174.527116.3402
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 155 through 197 )
2X-RAY DIFFRACTION2chain 'A' and (resid 198 through 227 )
3X-RAY DIFFRACTION3chain 'A' and (resid 228 through 513 )
4X-RAY DIFFRACTION4chain 'B' and (resid 155 through 177 )
5X-RAY DIFFRACTION5chain 'B' and (resid 178 through 211 )
6X-RAY DIFFRACTION6chain 'B' and (resid 212 through 253 )
7X-RAY DIFFRACTION7chain 'B' and (resid 254 through 285 )
8X-RAY DIFFRACTION8chain 'B' and (resid 286 through 304 )
9X-RAY DIFFRACTION9chain 'B' and (resid 305 through 368 )
10X-RAY DIFFRACTION10chain 'B' and (resid 369 through 428 )
11X-RAY DIFFRACTION11chain 'B' and (resid 429 through 461 )
12X-RAY DIFFRACTION12chain 'B' and (resid 462 through 491 )
13X-RAY DIFFRACTION13chain 'B' and (resid 492 through 514 )
14X-RAY DIFFRACTION14chain 'C' and (resid 158 through 262 )
15X-RAY DIFFRACTION15chain 'C' and (resid 263 through 285 )
16X-RAY DIFFRACTION16chain 'C' and (resid 286 through 304 )
17X-RAY DIFFRACTION17chain 'C' and (resid 305 through 342 )
18X-RAY DIFFRACTION18chain 'C' and (resid 343 through 513 )
19X-RAY DIFFRACTION19chain 'D' and (resid 159 through 274 )
20X-RAY DIFFRACTION20chain 'D' and (resid 275 through 326 )
21X-RAY DIFFRACTION21chain 'D' and (resid 327 through 384 )
22X-RAY DIFFRACTION22chain 'D' and (resid 385 through 419 )
23X-RAY DIFFRACTION23chain 'D' and (resid 420 through 512 )
24X-RAY DIFFRACTION24chain 'E' and (resid 297 through 302 )
25X-RAY DIFFRACTION25chain 'E' and (resid 303 through 307 )
26X-RAY DIFFRACTION26chain 'F' and (resid 298 through 302 )
27X-RAY DIFFRACTION27chain 'F' and (resid 303 through 307 )

+
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