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- PDB-5y1z: Crystal structure of ZMYND8 PHD-BROMO-PWWP tandem in complex with... -

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Basic information

Entry
Database: PDB / ID: 5y1z
TitleCrystal structure of ZMYND8 PHD-BROMO-PWWP tandem in complex with Drebrin ADF-H domain
Components
  • Drebrin
  • Protein kinase C-binding protein 1
KeywordsTRANSCRIPTION / NUCLEAR PROTEIN / PROTEIN BINDING / ACTIN BINDING
Function / homology
Function and homology information


cell communication by chemical coupling / positive regulation of receptor localization to synapse / histone H3K4me1 reader activity / histone H3K14ac reader activity / cell communication by electrical coupling / regulation of postsynaptic density protein 95 clustering / regulation of dendrite development / positive regulation of synaptic plasticity / maintenance of protein location in cell / profilin binding ...cell communication by chemical coupling / positive regulation of receptor localization to synapse / histone H3K4me1 reader activity / histone H3K14ac reader activity / cell communication by electrical coupling / regulation of postsynaptic density protein 95 clustering / regulation of dendrite development / positive regulation of synaptic plasticity / maintenance of protein location in cell / profilin binding / positive regulation of dendritic spine morphogenesis / gap junction / actomyosin / RHOD GTPase cycle / neural precursor cell proliferation / RHOBTB1 GTPase cycle / positive regulation of filopodium assembly / generation of neurons / cortical cytoskeleton / positive regulation of dendritic spine development / modulation of excitatory postsynaptic potential / site of DNA damage / RHOH GTPase cycle / positive regulation of dendritic spine maintenance / regulation of neuronal synaptic plasticity / : / postsynaptic cytosol / RHOBTB2 GTPase cycle / protein localization to chromatin / actin filament organization / negative regulation of cell migration / dendritic shaft / double-strand break repair via homologous recombination / positive regulation of transcription elongation by RNA polymerase II / transcription corepressor activity / nervous system development / actin cytoskeleton / actin binding / growth cone / dendritic spine / DNA-binding transcription factor binding / in utero embryonic development / postsynaptic membrane / cytoskeleton / postsynaptic density / cadherin binding / protein domain specific binding / dendrite / chromatin / nucleolus / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Protein kinase C-binding protein 1 / RACK7, Bromo domain / : / Protein kinase C-binding protein 1 / ZMYND8 protein coiled-coil / PRKCBP1, PHD finger / : / ZMYND11/ZMYD8, MYND zinc finger / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein ...Protein kinase C-binding protein 1 / RACK7, Bromo domain / : / Protein kinase C-binding protein 1 / ZMYND8 protein coiled-coil / PRKCBP1, PHD finger / : / ZMYND11/ZMYD8, MYND zinc finger / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / Severin / Severin / ADF-H/Gelsolin-like domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Drebrin / MYND-type zinc finger-containing chromatin reader ZMYND8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.676 Å
AuthorsYao, N. / Li, J. / Liu, H. / Wan, J. / Liu, W. / Zhang, M.
CitationJournal: Structure / Year: 2017
Title: The Structure of the ZMYND8/Drebrin Complex Suggests a Cytoplasmic Sequestering Mechanism of ZMYND8 by Drebrin
Authors: Yao, N. / Li, J. / Liu, H. / Wan, J. / Liu, W. / Zhang, M.
History
DepositionJul 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Drebrin
B: Drebrin
C: Protein kinase C-binding protein 1
D: Protein kinase C-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,64617
Polymers104,5854
Non-polymers1,06113
Water86548
1
A: Drebrin
C: Protein kinase C-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8739
Polymers52,2932
Non-polymers5807
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-61 kcal/mol
Surface area21090 Å2
MethodPISA
2
B: Drebrin
D: Protein kinase C-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7738
Polymers52,2932
Non-polymers4806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-46 kcal/mol
Surface area20880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.183, 138.095, 161.164
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 16 or resid 18...
21(chain B and (resid 2 through 11 or (resid 12...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAALAALA(chain A and (resid 2 through 16 or resid 18...AA2 - 164 - 18
12GLUGLULEULEU(chain A and (resid 2 through 16 or resid 18...AA18 - 5120 - 53
13GLUGLUASNASN(chain A and (resid 2 through 16 or resid 18...AA53 - 6055 - 62
14GLNGLNGLNGLN(chain A and (resid 2 through 16 or resid 18...AA6163
15METMETLEULEU(chain A and (resid 2 through 16 or resid 18...AA1 - 1333 - 135
16METMETLEULEU(chain A and (resid 2 through 16 or resid 18...AA1 - 1333 - 135
17METMETLEULEU(chain A and (resid 2 through 16 or resid 18...AA1 - 1333 - 135
18METMETLEULEU(chain A and (resid 2 through 16 or resid 18...AA1 - 1333 - 135
21ALAALALEULEU(chain B and (resid 2 through 11 or (resid 12...BB2 - 114 - 13
22GLUGLUGLUGLU(chain B and (resid 2 through 11 or (resid 12...BB1214
23GLYGLYLEULEU(chain B and (resid 2 through 11 or (resid 12...BB-1 - 1331 - 135
24GLYGLYLEULEU(chain B and (resid 2 through 11 or (resid 12...BB-1 - 1331 - 135
25GLYGLYLEULEU(chain B and (resid 2 through 11 or (resid 12...BB-1 - 1331 - 135
26GLYGLYLEULEU(chain B and (resid 2 through 11 or (resid 12...BB-1 - 1331 - 135

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Drebrin / Developmentally-regulated brain protein


Mass: 14677.229 Da / Num. of mol.: 2 / Fragment: UNP residues 1-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DBN1, D0S117E / Production host: Escherichia coli (E. coli) / References: UniProt: Q16643
#2: Protein Protein kinase C-binding protein 1 / Cutaneous T-cell lymphoma-associated antigen se14-3 / CTCL-associated antigen se14-3 / Rack7 / Zinc ...Cutaneous T-cell lymphoma-associated antigen se14-3 / CTCL-associated antigen se14-3 / Rack7 / Zinc finger MYND domain-containing protein 8


Mass: 37615.461 Da / Num. of mol.: 2 / Fragment: UNP residues 83-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZMYND8, KIAA1125, PRKCBP1, RACK7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ULU4

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Non-polymers , 4 types, 61 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAuthors used fusion strategy to generate the crystallization construct. Chain A is fused to the C- ...Authors used fusion strategy to generate the crystallization construct. Chain A is fused to the C-terminus of Chain C; Chain B was fused to the C-terminus of Chain D with 22-aa flexible linkers. GS residues of the N-terminal of the chains A and B is the part of the linkers. Other parts of the linker are missing due to the disorder.

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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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.0 and 23% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2016
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 34299 / % possible obs: 98.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 53.36 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / Χ2: 1.768 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.76.30.95116380.7580.3921.0311.38994.5
2.7-2.746.20.8890.7770.3680.9641.497.8
2.74-2.86.10.7350.840.3050.7981.42797.1
2.8-2.856.20.5940.8730.2460.6441.41597.5
2.85-2.926.20.4870.9110.2020.5281.49198.4
2.92-2.986.10.4190.930.1760.4561.48798.4
2.98-3.066.20.3360.9440.140.3651.5498.9
3.06-3.146.10.2650.9630.1110.2881.55599.1
3.14-3.236.20.2060.9780.0860.2241.63999.4
3.23-3.346.20.1680.9840.0710.1831.68499.2
3.34-3.466.30.1270.9930.0530.1381.73699.8
3.46-3.66.40.1110.9920.0470.1211.98199.5
3.6-3.766.10.0940.9940.0410.1032.11499.4
3.76-3.966.90.0750.9970.030.0812.00199.8
3.96-4.217.20.0640.9970.0260.0692.024100
4.21-4.537.10.0550.9980.0220.062.201100
4.53-4.997.30.0490.9990.0190.0531.982100
4.99-5.717.20.0520.9990.0210.0561.956100
5.71-7.197.10.0480.9990.0190.0521.936100
7.19-506.60.0360.9990.0150.0391.96598.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
PDB_EXTRACT3.22data extraction
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4COS, 1X67

4cos

1x67


Resolution: 2.676→14.988 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.41
RfactorNum. reflection% reflection
Rfree0.2338 1648 4.85 %
Rwork0.1781 --
obs0.1808 34002 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 164.25 Å2 / Biso mean: 58.0754 Å2 / Biso min: 25.87 Å2
Refinement stepCycle: final / Resolution: 2.676→14.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6681 0 42 48 6771
Biso mean--115.66 45.87 -
Num. residues----874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096910
X-RAY DIFFRACTIONf_angle_d0.9419413
X-RAY DIFFRACTIONf_chiral_restr0.0531020
X-RAY DIFFRACTIONf_plane_restr0.0061219
X-RAY DIFFRACTIONf_dihedral_angle_d5.4974605
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A966X-RAY DIFFRACTION11.122TORSIONAL
12B966X-RAY DIFFRACTION11.122TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6757-2.75390.35421100.27992197230781
2.7539-2.84230.32271480.26762671281997
2.8423-2.94310.37311460.26022630277698
2.9431-3.060.29441180.2482692281099
3.06-3.1980.2551410.23682718285999
3.198-3.36480.25471390.21612721286099
3.3648-3.57290.25461380.190227102848100
3.5729-3.84450.2331530.16762725287899
3.8445-4.22350.22821440.147827542898100
4.2235-4.81680.16361390.125927712910100
4.8168-6.00310.19351280.156828442972100
6.0031-14.98810.21021440.15629213065100
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)
15.33472.05240.46963.46371.15623.81550.5835-1.3296-0.01790.693-0.4850.7105-0.2529-0.602-0.00110.2751-0.03380.0510.77940.13220.657-16.8891-3.372121.983
22.07082.25892.89983.91315.00876.40240.22480.5429-0.6711-0.20340.44950.33890.28330.0996-0.54210.313-0.0598-0.0660.636-0.05620.66-14.486-4.443914.5759
33.8911.413-0.69675.91661.41634.67650.1739-0.2236-0.10720.2239-0.24360.22310.059-0.0570.07870.30740.0229-0.01180.40770.07370.4806-11.16381.184412.6781
42.81472.0082-0.21721.72271.08745.6391-0.36820.1662-0.0399-0.78520.0976-0.1046-0.72380.89420.31560.5208-0.0145-0.01180.52960.10390.48-12.1766-3.2938.1434
56.45394.97793.29488.44133.03154.29-0.15660.02270.3499-1.44370.39950.8377-0.2762-1.0932-0.23680.50270.0059-0.10940.64950.26221.2614-23.81520.01039.4701
61.73120.31510.29453.8041-1.57343.55930.08720.1928-0.2096-0.6322-0.2251-0.45610.80410.19330.1090.61150.10970.11420.359-0.03190.409134.66964.601252.2252
75.0815-2.80975.13983.3457-2.46595.0024-0.19840.23750.4617-0.3806-0.2973-0.27210.26720.18350.47630.45280.00970.08380.49050.00340.434627.494221.314544.0006
83.143-1.17690.48381.8977-1.09945.7998-0.2548-0.55690.30210.18920.11930.1582-0.3415-0.17710.14620.3933-0.04-0.04110.5769-0.10640.433512.699333.507347.979
94.2286-0.187-0.7552.7602-0.07284.5719-0.24190.2850.0017-0.5160.09790.76660.4323-0.84470.16830.4993-0.1017-0.10610.551-0.00510.47167.080731.72935.7855
104.7387-0.5749-1.00975.33720.22146.20470.0322-0.03290.4387-0.2525-0.1779-0.5875-0.74190.49820.04370.5792-0.1268-0.07710.41090.08840.453716.171532.025713.1245
112.35190.5892-0.34784.32310.94833.0279-0.08770.08710.121-0.4360.056-0.1495-0.42880.18040.06310.4272-0.0597-0.04740.32910.09350.27058.142520.52185.031
121.0125-2.11771.03424.4061-2.3083.92540.1114-0.0041-0.07-0.3616-0.0080.0159-0.0769-0.1019-0.10210.2652-0.01560.01260.33650.00950.42128.9215-7.18835.7
134.1607-0.71460.41228.34881.07363.3964-0.1612-0.56390.0148-0.09120.29430.190.1931-0.2384-0.09480.2537-0.0186-0.00740.46990.09610.342212.7958-16.306213.024
145.6506-1.4066-2.29713.95521.22417.8250.25230.2429-0.9407-0.3925-0.1360.56930.0584-0.2896-0.13270.3204-0.0275-0.12860.32290.02520.53464.4661-17.16242.3659
152.9730.02150.81481.8174-0.53624.80260.01360.4349-0.1518-0.7348-0.0607-0.49660.48721.15680.11040.4640.11720.16550.58130.01740.577521.7429-18.12370.8076
166.73612.0278-2.10745.07270.68952.3981-0.03590.11370.43050.0551-0.04930.7588-0.1576-0.3020.14570.4546-0.0293-0.15670.5217-0.05110.46927.27543.645850.9278
173.8055-0.49810.82276.9771-0.23373.62540.11970.08220.1444-0.3107-0.1973-0.18640.0531-0.07140.07920.3493-0.0161-0.04450.379-0.04240.386239.414740.054751.6743
184.05750.3839-3.97911.6279-1.27584.3680.02190.02970.26840.8532-1.3292-1.1853-1.46980.77831.13370.6235-0.1008-0.13940.7430.19490.77962.51541.234318.482
197.8973.52792.73217.35810.63385.4978-0.4477-0.567-1.1461-0.05070.29591.0813-0.1773-0.31790.0830.36870.044-0.03540.50320.20610.6654-6.2004-12.928717.8665
205.36462.3974-0.1312.35352.27684.98570.2225-0.5772-0.86090.9741-0.0222-0.60140.460.0964-0.23480.4483-0.041-0.08660.61240.17450.6612-9.5153-5.604920.6575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 41 through 62 )B41 - 62
2X-RAY DIFFRACTION2chain 'B' and (resid 63 through 71 )B63 - 71
3X-RAY DIFFRACTION3chain 'B' and (resid 72 through 108 )B72 - 108
4X-RAY DIFFRACTION4chain 'B' and (resid 109 through 118 )B109 - 118
5X-RAY DIFFRACTION5chain 'B' and (resid 119 through 133 )B119 - 133
6X-RAY DIFFRACTION6chain 'C' and (resid 87 through 232 )C87 - 232
7X-RAY DIFFRACTION7chain 'C' and (resid 233 through 279 )C233 - 279
8X-RAY DIFFRACTION8chain 'C' and (resid 280 through 335 )C280 - 335
9X-RAY DIFFRACTION9chain 'C' and (resid 336 through 390 )C336 - 390
10X-RAY DIFFRACTION10chain 'D' and (resid 85 through 115 )D85 - 115
11X-RAY DIFFRACTION11chain 'D' and (resid 116 through 254 )D116 - 254
12X-RAY DIFFRACTION12chain 'D' and (resid 255 through 312 )D255 - 312
13X-RAY DIFFRACTION13chain 'D' and (resid 313 through 332 )D313 - 332
14X-RAY DIFFRACTION14chain 'D' and (resid 333 through 357 )D333 - 357
15X-RAY DIFFRACTION15chain 'D' and (resid 358 through 391 )D358 - 391
16X-RAY DIFFRACTION16chain 'A' and (resid 1 through 28 )A1 - 28
17X-RAY DIFFRACTION17chain 'A' and (resid 29 through 133 )A29 - 133
18X-RAY DIFFRACTION18chain 'B' and (resid -1 through 9 )B-1 - 9
19X-RAY DIFFRACTION19chain 'B' and (resid 10 through 21 )B10 - 21
20X-RAY DIFFRACTION20chain 'B' and (resid 22 through 40 )B22 - 40

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Yorodumi

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  • 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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