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- PDB-7q43: Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2... -

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Basic information

Entry
Database: PDB / ID: 7q43
TitleCrystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of dedicator of cytokinesis protein 10
Components
  • Dedicator of cytokinesis protein 10 peptide
  • E3 ubiquitin-protein ligase HERC2
KeywordsPROTEIN BINDING / 7-bladed beta-propeller E3 ubiquitin-protein ligase HERC2 RCC1-like Domain 2 RLD2 ubiquitin ligase dedicator of cytokinesis protein 10 Dock 10 DXDKDED motif
Function / homology
Function and homology information


marginal zone B cell differentiation / SUMO binding / regulation of Rho protein signal transduction / HECT-type E3 ubiquitin transferase / dendritic spine morphogenesis / small GTPase-mediated signal transduction / B cell homeostasis / CDC42 GTPase cycle / regulation of postsynapse assembly / negative regulation of Notch signaling pathway ...marginal zone B cell differentiation / SUMO binding / regulation of Rho protein signal transduction / HECT-type E3 ubiquitin transferase / dendritic spine morphogenesis / small GTPase-mediated signal transduction / B cell homeostasis / CDC42 GTPase cycle / regulation of postsynapse assembly / negative regulation of Notch signaling pathway / RAC2 GTPase cycle / RAC3 GTPase cycle / SUMOylation of DNA damage response and repair proteins / RAC1 GTPase cycle / centriole / positive regulation of GTPase activity / regulation of cell migration / guanyl-nucleotide exchange factor activity / intracellular protein transport / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / neuron differentiation / small GTPase binding / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / dendritic spine / protein ubiquitination / DNA repair / ubiquitin protein ligase binding / DNA damage response / glutamatergic synapse / extracellular exosome / zinc ion binding / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Dedicator of cytokinesis D, C2 domain / HERC2, APC10 domain / HERC2, zinc finger, ZZ-type / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / : / Beta-propeller repeat TECPR / Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins. / Mib-herc2 / Mib/herc2 domain superfamily ...Dedicator of cytokinesis D, C2 domain / HERC2, APC10 domain / HERC2, zinc finger, ZZ-type / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / : / Beta-propeller repeat TECPR / Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins. / Mib-herc2 / Mib/herc2 domain superfamily / Mib_herc2 / MIB/HERC2 domain profile. / CPH domain / Mouse development and cellular proliferation protein Cullin-7 / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C / DOCKER, Lobe A / DOCKER, Lobe B / DOCKER, Lobe C / DHR-2, Lobe A / C2 domain in Dock180 and Zizimin proteins / DHR-2, Lobe C / DHR-2, Lobe B / C2 DOCK-type domain profile. / DOCKER domain profile. / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / PH domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Galactose-binding-like domain superfamily / PH-like domain superfamily / Ribosomal protein L2, domain 2
Similarity search - Domain/homology
CITRIC ACID / E3 ubiquitin-protein ligase HERC2 / Dedicator of cytokinesis protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4000234708 Å
AuthorsDemenge, A. / Howard, E. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / McEwen, A.G. / Trave, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of dedicator of cytokinesis protein 10
Authors: Demenge, A. / Howard, E. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / McEwen, A.G. / Trave, G.
History
DepositionOct 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: E3 ubiquitin-protein ligase HERC2
A: E3 ubiquitin-protein ligase HERC2
E: E3 ubiquitin-protein ligase HERC2
B: Dedicator of cytokinesis protein 10 peptide
D: Dedicator of cytokinesis protein 10 peptide
F: Dedicator of cytokinesis protein 10 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,0027
Polymers136,8106
Non-polymers1921
Water9,440524
1
C: E3 ubiquitin-protein ligase HERC2
D: Dedicator of cytokinesis protein 10 peptide


Theoretical massNumber of molelcules
Total (without water)45,6032
Polymers45,6032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: E3 ubiquitin-protein ligase HERC2
B: Dedicator of cytokinesis protein 10 peptide


Theoretical massNumber of molelcules
Total (without water)45,6032
Polymers45,6032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: E3 ubiquitin-protein ligase HERC2
F: Dedicator of cytokinesis protein 10 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7963
Polymers45,6032
Non-polymers1921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.820, 108.820, 243.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein E3 ubiquitin-protein ligase HERC2 / HECT domain and RCC1-like domain-containing protein 2 / HECT-type E3 ubiquitin transferase HERC2


Mass: 42770.566 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HERC2 / Production host: Escherichia coli (E. coli)
References: UniProt: O95714, HECT-type E3 ubiquitin transferase
#2: Protein/peptide Dedicator of cytokinesis protein 10 peptide / Zizimin-3 / Dedicator of cytokinesis protein 10


Mass: 2832.874 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: n-terminally biotinylated peptide via 1,13-diamino-4,7,10-trioxatridecan-succinamic acid
Source: (synth.) Homo sapiens (human) / References: UniProt: Q96BY6
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 59.15 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: hanging drop 20% PEG 3350 0.18M tris amonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999997 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999997 Å / Relative weight: 1
ReflectionResolution: 2.4→49.665 Å / Num. obs: 57945 / % possible obs: 99.7 % / Redundancy: 37.6713780309 % / Biso Wilson estimate: 33.6856059616 Å2 / CC1/2: 0.983 / Net I/σ(I): 5.77
Reflection shellResolution: 2.4→2.46 Å / Num. unique obs: 4230 / CC1/2: 0.41

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KCI

3kci


Resolution: 2.4000234708→49.6652591346 Å / SU ML: 0.336717390306 / Cross valid method: FREE R-VALUE / σ(F): 1.34350427896 / Phase error: 25.8287899636
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.264969422568 2916 5.04123230123 %
Rwork0.202444119505 54927 -
obs0.205598267093 57843 99.753388749 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.167441888 Å2
Refinement stepCycle: LAST / Resolution: 2.4000234708→49.6652591346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8386 0 13 524 8923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007774019179198557
X-RAY DIFFRACTIONf_angle_d0.91059276313311554
X-RAY DIFFRACTIONf_chiral_restr0.05487021457981289
X-RAY DIFFRACTIONf_plane_restr0.005512420657951492
X-RAY DIFFRACTIONf_dihedral_angle_d18.77938190463055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4000234708-2.43940.328064837691400.2709398619582585X-RAY DIFFRACTION100
2.4394-2.48140.3265495463751550.2709425392762575X-RAY DIFFRACTION99.8902305159
2.4814-2.52660.3225197572741460.2584287962862546X-RAY DIFFRACTION100
2.5266-2.57510.3319428159661250.2599725132592563X-RAY DIFFRACTION99.8885172798
2.5751-2.62770.3390697345261220.2607576373952590X-RAY DIFFRACTION99.9631404349
2.6277-2.68480.2948363469041410.2550318355622596X-RAY DIFFRACTION100
2.6848-2.74730.326910553881220.2412071035012616X-RAY DIFFRACTION99.9634903249
2.7473-2.8160.2966299218761400.230767093062557X-RAY DIFFRACTION100
2.816-2.89210.3281541380291480.2199813221692589X-RAY DIFFRACTION100
2.8921-2.97720.2658417283561260.2185004843632588X-RAY DIFFRACTION100
2.9772-3.07330.3167342663711540.2130960473092598X-RAY DIFFRACTION99.9636759898
3.0733-3.18310.2987052172771310.2143608742382613X-RAY DIFFRACTION99.9635701275
3.1831-3.31050.2559354804421460.2080081704472596X-RAY DIFFRACTION100
3.3105-3.46120.2712558643151510.2095507232422586X-RAY DIFFRACTION100
3.4612-3.64360.2814681684071390.197251165642571X-RAY DIFFRACTION97.7986286539
3.6436-3.87180.2457626781391350.2152481119692572X-RAY DIFFRACTION97.7609245215
3.8718-4.17060.225306777021350.1656036091172645X-RAY DIFFRACTION99.892202659
4.1706-4.590.2194756073541330.1507349255722661X-RAY DIFFRACTION100
4.59-5.25360.1900552729981270.1491780638522684X-RAY DIFFRACTION100
5.2536-6.61650.2360784026711650.1738159148172693X-RAY DIFFRACTION100
6.6165-49.66525913460.2376567635071350.2022364823362903X-RAY DIFFRACTION99.7701149425
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)
13.948820682231.54075589423-1.716127611741.88839795020.05944658705042.312056517-0.0266450406990.227874597242-0.264142254639-0.207171529120.08870525386040.02589078430920.150699396497-0.119870612644-0.06892778374130.2615434691250.0126133616853-0.06944569934280.1871235053180.007986334523210.24214223587732.7478649994-25.136695482516.6400097522
21.17942687525-0.0752125604132-0.3948023712526.479287784680.6470041091442.632960372710.209562955297-0.144640318442-0.183441073635-0.0382722189032-0.1121221078880.6742224554280.0990574092963-0.336461060587-0.09252867558640.186324771871-0.0516101954342-0.01972840981450.3488974404380.06170169107680.28047283900722.6600484545-19.222709543233.4631498506
34.657558779070.816039978250.1720973297084.26452722378-0.5389616432363.193921748760.0429696766429-0.1660572143640.2313446173710.1837149395810.01603036143840.294893771223-0.265433501061-0.141446750507-0.0544442050150.188708599978-0.01468473149960.007059135513170.1579224609820.003436064139670.18346955362533.757706956-3.4120359283732.5405342269
47.30384870148-1.414183146030.5753553266853.93897467495-0.3724750913484.709180695980.05713131322240.140974839690.0981575149354-0.150004862702-0.08390148245310.0359592919431-0.321019653515-0.009531967419020.01916265814180.240384684033-0.0344367207215-0.006262264015130.1962340703430.0234122590780.13266786063240.6985681278-6.818310630715.2420412722
51.50583320266-0.396765175121-0.0789172641523.36277065066-0.8775285872962.44927783711-0.04513731273040.229733346716-0.268695589906-0.248050685-0.034384621809-0.009259897283320.2813845414080.1219916467880.07809736972320.2232316016950.02166045484480.03652410022110.256302644634-0.0572069470960.20058866351860.3757295791-25.714315730754.1803256796
62.782969939581.117266833831.839655057895.276181278421.472679848696.57615442220.102591680487-0.00676143234181-0.5086467922780.305901565497-0.0175788450793-0.1964457971870.8336753586410.179809983446-0.08716520374140.311478920020.08399348997650.08898094685890.2768290832420.03581532301080.33968251492258.2676941698-35.330267713869.8183777186
71.73356619942-0.428628845348-0.09937615878542.82073307755-0.8794272123631.60773825403-0.078328882939-0.252388421764-0.06674427773180.313334904940.04440757614290.0895447223764-0.00228381483715-0.05515628163470.03781530886450.229120065103-0.000287104478630.01479649314090.219233712986-0.02911115539050.16180314687747.7323483331-19.994112907576.8437735608
86.50195628585-0.1328020312662.130043258824.58529342559-0.7082349198155.231666780590.0214411256839-0.1615030831380.0965757881204-0.00511557461902-0.02713482748290.102324462025-0.138191453403-0.2968483800980.009592401079260.162669603812-0.01394414390040.01635825490660.220222518691-0.008508897815740.14711991235449.0488403554-10.764363117956.9194136023
92.623383013621.504469842780.5648570146244.082948486790.3111077995964.44136913424-0.02169022592520.1246830021720.425721405817-0.4258901312020.07667555853980.23245218256-0.810227413719-0.00302876330797-0.04483543862630.4345116802910.0337131619770.01519054931190.2137428611410.003570342948910.31671432081856.271006810228.649855254434.0845802478
107.787598484780.7541816015731.464725981894.15310738503-0.2787142430743.81104623875-0.1410057702590.2460240595931.070285833-0.162769089495-0.01202055962470.156222631157-0.9044885480860.4436847744150.1696820594030.808058511785-0.1558551414430.007250731427030.367780021473-0.03996027596670.43092469202464.803275438437.645618284245.0946047304
112.18579193111.34576033042-0.2544409713674.490185472450.8804390240422.621354860770.182514595603-0.3279575531880.2535985612070.445082241002-0.0687914852779-0.361769964844-0.334587700060.414065518472-0.1237081569230.358786716324-0.071450678063-0.06583168226030.301540080147-0.03426137037920.30018871793764.831207701818.077401663853.8566855564
122.128807049580.5004537256411.223008700773.880009698961.085586958413.57930095435-0.113612028401-0.0453291010982-0.309785396878-0.01719366209470.0560286929945-0.1503283071780.3568093324790.1169746324810.02556641415630.273021704944-0.01300259592950.0416228495150.2169869110640.01123490584620.20165195622857.19962810156.4763668046437.8501439909
137.064933872-4.70316584925-2.559642731698.782794213178.782297960572.106521965920.0605393259857-0.07081136084020.276610394844-0.1111830288920.172485381174-0.1848404573350.0954398983570.234285016931-0.2227549462870.290226158385-0.02260811937660.04067702107420.3408372897360.06105021883850.22361827562559.911444131913.173454300529.8688852555
145.011056007242.32092307678-3.531244931057.1928447318-5.177947033257.967795183071.19248758128-1.561906966280.5283206656340.311137942349-0.4583008802880.213411502397-0.09589820552351.7364455882-0.675613702820.46121180608-0.112963239534-0.02807371264081.07988481541-0.1732939919790.69525069038167.6378032965-11.107622088164.3493963953
156.759962177145.480279935293.157525177542.00109048186-3.96205287617.37362935257-0.386999004547-2.1605846576-0.2746859142612.367452311140.77703251773-0.5006782968871.082102523210.750547450351-0.4034209820090.8851603145190.2763988961220.03903061009641.24490916391-0.3330829488630.82428531229448.235092242-18.775879213828.5814306954
161.997693108732.51449719461-8.171920694482.00125028987-0.3406702020051.998559634240.507869982288-0.6477593137380.5014336350010.2670201263621.040111264792.14893583813-0.898064188143-3.00355850128-1.501219504360.82307996220.1270662336690.1631544959421.174387232160.284198638151.0059342184344.12566723617.503792241345.1794966505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 2958 through 3082 )
2X-RAY DIFFRACTION2chain 'C' and (resid 3083 through 3169 )
3X-RAY DIFFRACTION3chain 'C' and (resid 3170 through 3250 )
4X-RAY DIFFRACTION4chain 'C' and (resid 3251 through 3326 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2959 through 3052 )
6X-RAY DIFFRACTION6chain 'A' and (resid 3053 through 3106 )
7X-RAY DIFFRACTION7chain 'A' and (resid 3107 through 3250 )
8X-RAY DIFFRACTION8chain 'A' and (resid 3251 through 3326 )
9X-RAY DIFFRACTION9chain 'E' and (resid 2959 through 3082 )
10X-RAY DIFFRACTION10chain 'E' and (resid 3083 through 3106 )
11X-RAY DIFFRACTION11chain 'E' and (resid 3107 through 3250 )
12X-RAY DIFFRACTION12chain 'E' and (resid 3251 through 3302 )
13X-RAY DIFFRACTION13chain 'E' and (resid 3303 through 3326 )
14X-RAY DIFFRACTION14chain 'B' and (resid 158 through 166 )
15X-RAY DIFFRACTION15chain 'D' and (resid 158 through 163 )
16X-RAY DIFFRACTION16chain 'F' and (resid 158 through 164 )

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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

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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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