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- PDB-5naf: Co-crystal structure of an MeCP2 peptide with TBLR1 WD40 domain -

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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 / principal sensory nucleus of trigeminal nerve development / biogenic amine metabolic process ...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 / principal sensory nucleus of trigeminal nerve development / biogenic amine metabolic process / cardiolipin metabolic process / negative regulation of locomotion involved in locomotory behavior / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / regulation of action potential firing threshold / nervous system process involved in regulation of systemic arterial blood pressure / regulation of triglyceride metabolic process / negative regulation of primary miRNA processing / proprioception / negative regulation of dendrite extension / negative regulation of smooth muscle cell differentiation / HDACs deacetylate histones / Notch-HLH transcription pathway / neuromuscular process controlling posture / negative regulation of dendritic spine development / ventricular cardiac muscle tissue development / double-stranded methylated DNA binding / Regulation of lipid metabolism by PPARalpha / inositol metabolic process / phosphatidylcholine metabolic process / Cytoprotection by HMOX1 / regulation of respiratory gaseous exchange by nervous system process / glucocorticoid metabolic process / positive regulation of dendrite extension / ventricular system development / olfactory bulb development / unmethylated CpG binding / respiratory gaseous exchange by respiratory system / positive regulation of microtubule nucleation / blastocyst hatching / striatum development / genomic imprinting / positive regulation of synaptic plasticity / neuron maturation / thalamus development / response to other organism / L-glutamine metabolic process / oligodendrocyte development / siRNA binding / methyl-CpG binding / cellular response to potassium ion / fat pad development / lung alveolus development / negative regulation of astrocyte differentiation / neuromuscular process / response to ionizing radiation / negative regulation of gene expression via chromosomal CpG island methylation / spinal cord development / response to dietary excess / histone deacetylase complex / regulation of synapse organization / positive regulation of dendritic spine development / startle response / dendrite development / negative regulation of blood vessel endothelial cell migration / white fat cell differentiation / associative learning / positive regulation of glial cell proliferation / adipose tissue development / histone reader activity / social behavior / multicellular organismal response to stress / long-term memory / glial cell proliferation / lipid catabolic process / behavioral fear response / four-way junction DNA binding / Notch signaling pathway / heterochromatin / transcription repressor complex / synapse assembly / epigenetic regulation of gene expression / sensory perception of pain / negative regulation of angiogenesis / cerebellum development / learning / post-embryonic development / hippocampus development / adult locomotory behavior / response to cocaine / promoter-specific chromatin binding / molecular condensate scaffold activity / excitatory postsynaptic potential / chromatin DNA binding / brain development / cerebral cortex development / visual learning / regulation of synaptic plasticity / beta-catenin binding / response to lead ion / multicellular organism growth
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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%

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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

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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 )

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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

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