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- PDB-5zq5: SidE-Ubi -

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Basic information

Entry
Database: PDB / ID: 5zq5
TitleSidE-Ubi
Components
  • SidE
  • Ubiquitin
KeywordsCELL INVASION / ubiquitination
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase activity / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis ...NAD+-protein-arginine ADP-ribosyltransferase activity / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Termination of translesion DNA synthesis / Negative regulation of FGFR4 signaling / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Stabilization of p53 / EGFR downregulation / Negative regulation of NOTCH4 signaling / Negative regulation of FGFR1 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription
Similarity search - Function
SidE, DUB domain / SidE, mono-ADP-ribosyltransferase domain / SidE mono-ADP-ribosyltransferase domain / SidE DUB domain / SidE, PDE domain / SidE phosphodiesterase (PDE) domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family ...SidE, DUB domain / SidE, mono-ADP-ribosyltransferase domain / SidE mono-ADP-ribosyltransferase domain / SidE DUB domain / SidE, PDE domain / SidE phosphodiesterase (PDE) domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / Septation initiation protein / SidE
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.487 Å
AuthorsWang, Y. / Gao, A. / Gao, P.
Funding support China, 4items
OrganizationGrant numberCountry
91753133 China
31670903 China
31700687 China
XDB08020204 China
CitationJournal: Cell / Year: 2018
Title: Structural Insights into Non-canonical Ubiquitination Catalyzed by SidE.
Authors: Wang, Y. / Shi, M. / Feng, H. / Zhu, Y. / Liu, S. / Gao, A. / Gao, P.
History
DepositionApr 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SidE
B: Ubiquitin
D: Ubiquitin
C: SidE


Theoretical massNumber of molelcules
Total (without water)211,0104
Polymers211,0104
Non-polymers00
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-51 kcal/mol
Surface area79720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.672, 129.084, 191.507
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SidE


Mass: 96813.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6RCR1, UniProt: Q6BBR6*PLUS
#2: Protein Ubiquitin


Mass: 8691.896 Da / Num. of mol.: 2 / Mutation: R42A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Tacsimate

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. obs: 80934 / % possible obs: 100 % / Redundancy: 9 % / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.044 / Rrim(I) all: 0.134 / Net I/σ(I): 13.8
Reflection shellResolution: 2.49→2.56 Å / CC1/2: 0.769 / Rpim(I) all: 0.35

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Cootmodel building
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.487→48.688 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.2
RfactorNum. reflection% reflection
Rfree0.2329 4060 5.02 %
Rwork0.1895 --
obs0.1917 80934 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.487→48.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14374 0 0 250 14624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514646
X-RAY DIFFRACTIONf_angle_d0.71119783
X-RAY DIFFRACTIONf_dihedral_angle_d7.7368953
X-RAY DIFFRACTIONf_chiral_restr0.0442197
X-RAY DIFFRACTIONf_plane_restr0.0062592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4874-2.51670.32981240.28092284X-RAY DIFFRACTION87
2.5167-2.54730.31381590.27132562X-RAY DIFFRACTION100
2.5473-2.57960.34031420.26822655X-RAY DIFFRACTION100
2.5796-2.61350.31781390.26292622X-RAY DIFFRACTION100
2.6135-2.64930.31371410.25452657X-RAY DIFFRACTION100
2.6493-2.68720.31111360.24512629X-RAY DIFFRACTION100
2.6872-2.72730.32431540.24052627X-RAY DIFFRACTION100
2.7273-2.76990.28291310.22492624X-RAY DIFFRACTION100
2.7699-2.81530.31271220.23212665X-RAY DIFFRACTION100
2.8153-2.86380.24581370.23072626X-RAY DIFFRACTION100
2.8638-2.91590.27811220.22942644X-RAY DIFFRACTION100
2.9159-2.9720.32391390.23852634X-RAY DIFFRACTION100
2.972-3.03260.26491320.23522666X-RAY DIFFRACTION100
3.0326-3.09860.26311310.23622658X-RAY DIFFRACTION100
3.0986-3.17060.26971310.23062650X-RAY DIFFRACTION100
3.1706-3.24990.29571710.21972624X-RAY DIFFRACTION100
3.2499-3.33780.24321170.21612669X-RAY DIFFRACTION100
3.3378-3.4360.25721380.2032664X-RAY DIFFRACTION100
3.436-3.54680.25941230.20082684X-RAY DIFFRACTION100
3.5468-3.67360.22531620.1812628X-RAY DIFFRACTION100
3.6736-3.82060.22011450.18222652X-RAY DIFFRACTION100
3.8206-3.99440.21531450.16142658X-RAY DIFFRACTION100
3.9944-4.20490.19171500.14612679X-RAY DIFFRACTION100
4.2049-4.46820.19961450.14442685X-RAY DIFFRACTION100
4.4682-4.81290.17931470.14212694X-RAY DIFFRACTION100
4.8129-5.29670.18891390.15222702X-RAY DIFFRACTION100
5.2967-6.06190.21541500.17572710X-RAY DIFFRACTION100
6.0619-7.63260.2351290.18682775X-RAY DIFFRACTION100
7.6326-48.6970.16881590.16112847X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.07050.1367-0.21312.22010.87952.0764-0.0017-0.01810.1325-0.00470.1058-0.3503-0.14520.2573-0.07210.2607-0.00070.03360.2807-0.02140.365979.007298.5492125.8214
21.10120.79510.14072.194-0.26391.19430.1883-0.2283-0.08020.4276-0.1443-0.22320.0970.0188-0.02050.326-0.0514-0.01650.3392-0.01610.339174.511484.8543135.4508
30.7549-0.0106-0.22660.78070.50393.23460.05250.07920.0249-0.0916-0.1360.10410.0267-0.41410.07980.239-0.008-0.01460.281-0.010.308659.955675.51989.5987
41.96520.93050.92372.15491.17733.711-0.0499-0.1771-0.0840.1637-0.0146-0.10350.4455-0.07430.00710.6333-0.1175-0.01160.58530.04330.530246.545415.254557.0996
53.60310.314-0.07454.6516-1.44394.7334-0.2477-0.14691.1676-0.61390.0127-0.31-1.02360.2380.18820.81260.02580.01210.56460.08420.814471.8339106.879381.8386
68.2542-1.61022.34170.98820.81876.81110.02160.8781.2695-1.1001-0.2620.4356-1.64410.17750.3561.05330.0884-0.17210.42160.10381.053462.7571108.554670.6433
75.5385-1.2602-2.26697.9236-1.63273.6465-0.04530.68120.9185-0.82670.0446-0.4627-1.29310.78060.40870.8924-0.1522-0.0260.67080.17970.727372.3822102.34272.2484
83.90550.98251.2377.6179-0.77345.44280.07740.5145-0.1645-0.5653-0.2004-0.3064-0.10110.4762-0.2050.6966-0.01820.0450.63090.04460.668772.43495.380175.8831
91.0263-1.3472-0.6782.22041.02153.52320.04320.2259-0.29170.3519-0.15470.9292-0.1609-0.52650.1190.73090.18330.02940.62280.120.896860.13797.640682.9245
102.1311.82780.90211.57030.70013.58790.14250.0784-0.6912-0.2310.00210.5638-0.0487-0.0922-0.05520.87650.10040.03890.78-0.06860.85759.977496.798872.7596
111.6633-0.56740.38452.66591.26383.8672-0.24410.16830.66890.1341-0.60810.1545-0.3806-0.07220.82180.84420.06640.06660.6201-0.04010.97458.8627107.402677.9868
122.31310.12540.03253.34140.43183.84150.0592-0.23070.0520.30880.1086-0.2271-0.39290.1407-0.1970.5204-0.09280.15780.5137-0.04460.476770.966292.817580.6518
131.22910.49140.29332.1435-0.24612.3324-0.02460.1511-0.3041-0.07280.09220.63290.4087-0.70250.11570.3666-0.0981-0.03550.5388-0.0150.6993-15.9647-9.724819.0089
141.14390.19910.02752.50620.21192.7533-0.20240.6449-0.4386-0.62950.27680.30640.1492-0.14360.2850.4324-0.1123-0.09240.5563-0.09110.4502-4.6496-4.93227.5785
151.1240.00960.29051.53051.02432.9568-0.03650.5784-0.4369-0.36140.1795-0.02650.12260.28670.15810.4585-0.0592-0.00770.5484-0.12660.46994.7887-8.48649.6124
161.3038-0.16890.7770.9495-0.08762.7272-0.2238-0.26910.14460.26390.16090.0548-0.3607-0.12670.00270.37870.10710.00670.28980.00380.34068.715811.462553.8208
171.5301-0.66631.11390.6326-0.42992.0163-0.262-0.3720.05160.1439-0.0754-0.3924-0.4501-0.0956-0.37031.0263-0.2988-0.07310.78730.00290.840560.502744.398694.314
181.46320.5020.98381.50020.13934.2751-0.1470.44830.08740.28060.0312-0.0535-0.69080.4594-0.07790.9335-0.25380.01740.7652-0.01550.734261.868134.179184.374
191.524-0.6538-0.93951.11172.28645.796-0.1797-0.77750.19820.11730.03671.163-0.6136-1.4695-0.27570.83310.18720.19961.83680.04291.3472-23.09541.933963.1737
203.61522.0280.82144.7974-1.12883.03660.1925-0.1102-0.4890.1352-0.16320.1832-0.1494-1.4707-0.04450.87150.08620.14661.2915-0.14941.4445-20.3452-3.722462.8179
210.6938-0.6517-1.00470.66391.02221.57320.0683-0.3512-0.02530.45430.28120.143-0.2184-0.0486-0.52241.57730.26570.16063.22790.32331.4811-23.58579.51673.2631
226.02714.3871-0.21364.7257-1.53531.42970.023-0.391-0.59890.6437-0.13630.54890.1986-1.4653-0.41051.05370.22060.2712.07170.28151.0602-16.8773-0.692672.6864
239.87950.50860.06084.50031.62446.59860.0088-1.1454-0.59340.50640.07380.59450.1934-1.5962-1.26740.7470.04460.06541.34850.11310.8922-10.86580.887667.782
243.3491-2.2702-0.26691.66420.32460.80220.0445-0.4871-0.16440.1430.27770.0379-0.1494-0.5383-0.54130.66920.4026-0.10651.2553-0.1261.1718-11.507910.775661.9227
253.1999-1.1208-0.49921.01210.61370.42370.0212-0.61950.0250.33350.18240.6158-0.243-0.6485-0.31751.18720.47790.15692.3554-0.17241.3902-19.113212.247567.2635
262.26780.53050.2532.4132-1.59746.3596-0.1789-0.1881-0.18270.17160.28810.76550.1101-1.14040.04410.59930.05480.15651.00960.28520.6539-7.50750.369763.7742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 222 through 365 )
2X-RAY DIFFRACTION2chain 'A' and (resid 366 through 584 )
3X-RAY DIFFRACTION3chain 'A' and (resid 585 through 919 )
4X-RAY DIFFRACTION4chain 'A' and (resid 920 through 1058 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 16 )
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 22 )
7X-RAY DIFFRACTION7chain 'B' and (resid 23 through 34 )
8X-RAY DIFFRACTION8chain 'B' and (resid 35 through 44 )
9X-RAY DIFFRACTION9chain 'B' and (resid 45 through 49 )
10X-RAY DIFFRACTION10chain 'B' and (resid 50 through 54 )
11X-RAY DIFFRACTION11chain 'B' and (resid 55 through 65 )
12X-RAY DIFFRACTION12chain 'B' and (resid 66 through 76 )
13X-RAY DIFFRACTION13chain 'C' and (resid 223 through 372 )
14X-RAY DIFFRACTION14chain 'C' and (resid 373 through 480 )
15X-RAY DIFFRACTION15chain 'C' and (resid 481 through 584 )
16X-RAY DIFFRACTION16chain 'C' and (resid 585 through 919 )
17X-RAY DIFFRACTION17chain 'C' and (resid 920 through 978 )
18X-RAY DIFFRACTION18chain 'C' and (resid 979 through 1058 )
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 7 )
20X-RAY DIFFRACTION20chain 'D' and (resid 8 through 16 )
21X-RAY DIFFRACTION21chain 'D' and (resid 17 through 22 )
22X-RAY DIFFRACTION22chain 'D' and (resid 23 through 34 )
23X-RAY DIFFRACTION23chain 'D' and (resid 35 through 45 )
24X-RAY DIFFRACTION24chain 'D' and (resid 46 through 50 )
25X-RAY DIFFRACTION25chain 'D' and (resid 51 through 65 )
26X-RAY DIFFRACTION26chain 'D' and (resid 66 through 76 )

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