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- PDB-4x7e: Crystal structure of norovirus GII.10 P domain in complex with Nano-85 -

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Basic information

Entry
Database: PDB / ID: 4x7e
TitleCrystal structure of norovirus GII.10 P domain in complex with Nano-85
Components
  • Capsid protein
  • Nano-85 Nanobody
KeywordsVIRAL PROTEIN / Nanobody / VHH domain / Norovirus / Protruding domain
Function / homology
Function and homology information


Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Capsid protein
Similarity search - Component
Biological speciesNorovirus
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsHansman, G.H. / Koromyslova, A.D.
CitationJournal: J.Virol. / Year: 2015
Title: Nanobody binding to a conserved epitope promotes norovirus particle disassembly.
Authors: Koromyslova, A.D. / Hansman, G.S.
History
DepositionDec 9, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Feb 18, 2015Group: Database references
Revision 1.3Nov 21, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Jan 10, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
C: Nano-85 Nanobody
B: Capsid protein
D: Nano-85 Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,55913
Polymers96,0094
Non-polymers5509
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-20 kcal/mol
Surface area33240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.940, 133.100, 67.570
Angle α, β, γ (deg.)90.000, 112.540, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain C and segid D000
12chain B and segid
22chain D and segid D000

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain C and segid D000C0
112chain B and segidB0
212chain D and segid D000D0

NCS ensembles :
ID
1
2

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Components

#1: Protein Capsid protein


Mass: 34506.660 Da / Num. of mol.: 2 / Fragment: UNP residues 224-538
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus / Strain: Vietnam 026 / Plasmid: pMBP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5F4T5
#2: Antibody Nano-85 Nanobody


Mass: 13497.894 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pHEN6C / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: calcium acetate, PEG8000, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.973 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 8, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.11→47.97 Å / Num. obs: 46632 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 29.24 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.09 / Χ2: 0.984 / Net I/σ(I): 11.63 / Num. measured all: 134998
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.11-2.170.7950.4712.249401362032860.57590.8
2.17-2.220.80.4712.289958344234030.57698.9
2.22-2.290.8780.4162.978695339731020.51391.3
2.29-2.360.9040.3133.429330334032530.38497.4
2.36-2.440.9070.2723.878878319931370.33398.1
2.44-2.520.9190.2354.37995311330190.29297
2.52-2.620.940.2065.318667300329380.25197.8
2.62-2.720.9620.1696.78266289127930.20696.6
2.72-2.850.9690.147.968011273926670.17197.4
2.85-2.980.980.10210.377624263425700.12497.6
2.98-3.150.990.07913.057051251124250.09796.6
3.15-3.340.9940.0615.826321241023120.07495.9
3.34-3.570.9950.05219.986591226321700.06395.9
3.57-3.850.9970.04223.945850206519500.05194.4
3.85-4.220.9970.03527.975364193318130.04393.8
4.22-4.720.9980.02830.974575174716490.03494.4
4.72-5.450.9980.02931.834259152014330.03594.3
5.45-6.670.9980.02831.613885133512430.03493.1
6.67-9.440.9980.02534.35266210139420.03193
9.440.9990.02241.9216155775270.02691.3

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ONU was used for GII.10 P domain (molecule 1) and recently deposited PDB entry 4X7F for Nano-85 (molecule 2)
Resolution: 2.11→47.97 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2182 2327 5 %
Rwork0.1886 44237 -
obs0.1901 46564 95.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.82 Å2 / Biso mean: 35.8568 Å2 / Biso min: 18.38 Å2
Refinement stepCycle: final / Resolution: 2.11→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6413 0 36 290 6739
Biso mean--43.46 35.27 -
Num. residues----847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026664
X-RAY DIFFRACTIONf_angle_d0.7019088
X-RAY DIFFRACTIONf_chiral_restr0.0291005
X-RAY DIFFRACTIONf_plane_restr0.0041197
X-RAY DIFFRACTIONf_dihedral_angle_d13.652379
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2772X-RAY DIFFRACTION3.233TORSIONAL
12C2772X-RAY DIFFRACTION3.233TORSIONAL
21B1026X-RAY DIFFRACTION3.233TORSIONAL
22D1026X-RAY DIFFRACTION3.233TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1102-2.15330.30981250.26522382250789
2.1533-2.20010.29521400.26882672281299
2.2001-2.25130.30111330.31142567270093
2.2513-2.30760.32191320.28042503263594
2.3076-2.370.26731410.22832668280998
2.37-2.43970.27321390.23352643278298
2.4397-2.51850.25151380.22982629276797
2.5185-2.60850.26571420.2182685282798
2.6085-2.71290.26371390.22032636277597
2.7129-2.83640.2441380.20862615275398
2.8364-2.98590.23741390.19832646278598
2.9859-3.17290.24711380.19222621275997
3.1729-3.41780.21021380.18072632277097
3.4178-3.76170.18681370.16312601273895
3.7617-4.30570.1711360.14652576271295
4.3057-5.42350.14971350.13472567270294
5.4235-47.98480.18961370.1642594273193
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)
10.2869-0.3066-0.48790.42120.78341.4596-0.1089-0.0195-0.10320.0191-0.00150.07710.1741-0.0775-0.00070.2216-0.00650.04340.21990.01210.272757.807424.794929.7469
20.6972-0.1893-0.17450.9210.11760.4689-0.0936-0.09140.00770.0391-0.04950.21240.0713-0.2197-00.20810.02590.03970.28440.00440.224252.414428.511541.702
30.9994-0.16440.03660.77350.21990.7379-0.0778-0.1576-0.15190.16710.04760.07510.2192-0.0971-00.26250.01090.06570.2590.03690.253459.502919.060437.4263
40.9276-0.7782-0.11850.75240.13230.6286-0.0515-0.1345-0.12060.00460.01980.1331-0.13950.0448-00.2417-0.04180.03420.2131-0.02020.252566.477722.270115.5294
50.0743-0.0266-0.17640.4311-0.05260.9388-0.05460.36-0.1421-0.10180.0105-0.09370.10450.139400.24870.02280.00850.2258-0.01520.335372.480213.202717.8441
60.1292-0.0432-0.27730.14990.20760.6486-0.0171-0.0402-0.15710.02490.09830.04660.07780.0598-00.25450.0112-0.0030.2321-0.02530.25770.008412.98678.8576
71.18660.35940.17330.11660.06960.03120.30640.1779-0.3159-0.62080.0321-0.0579-0.1023-0.39220.01910.56240.1303-0.02870.58860.01730.262869.40242.2632-13.0094
80.0058-0.0048-0.02890.00330.01120.05490.22910.0696-0.0188-0.27730.14790.06180.17830.41120.00010.52910.0215-0.01630.393-0.09940.501576.1057-19.2509-7.6349
92.43820.9197-0.26150.3631-0.0820.07610.0125-0.0326-0.2622-0.1489-0.0389-0.3682-0.20880.0587-0.07330.45860.0335-0.00960.3892-0.05430.162575.2645-2.167-9.2971
100.0953-0.0477-0.06120.06980.11870.16240.2416-0.0261-0.095-0.3195-0.2580.6082-0.0712-0.1739-0.00360.32780.06240.00490.24790.00050.433569.13122.3579-3.5616
110.0583-0.07780.01620.0782-0.0290.15760.1422-0.0372-0.3540.4482-0.00030.31310.2553-0.1891-0.00030.2609-0.0472-0.02060.2812-0.02380.386264.3447-7.67710.1193
120.209-0.02850.1340.2530.14540.081-0.08020.0417-0.0794-0.0320.0834-0.23940.0810.129900.29770.02850.02780.30720.0410.31674.5737-5.08534.3309
132.1634-0.1960.42150.3817-0.03820.09140.34450.127-0.28110.179-0.2480.037-0.2770.52630.12180.4077-0.00650.06870.3626-0.00390.151978.3423-0.89-5.3817
140.4925-0.39820.07570.4169-0.00470.02310.3287-0.4801-0.830.86520.22630.66740.2005-0.5295-0.0030.4448-0.0302-0.0590.42220.0470.48371.9309-18.7348-0.6773
150.03350.0490.09020.06140.09060.01150.22870.1764-0.1169-0.5228-0.25960.5251-0.3274-0.02890.00040.3477-0.002-0.04520.2818-0.04640.343666.44010.0852-4.7414
160.0352-0.0848-0.00521.18610.0690.11060.2530.0464-0.02870.0027-0.2590.9712-0.1908-0.33360.01820.3247-0.0144-0.04470.2868-0.05660.233163.431410.1318-4.5713
170.0161-0.01640.02890.06060.03470.0654-0.15720.0011-0.28260.2651-0.1508-0.12220.34430.0112-0.00050.50180.0413-0.09380.3972-0.06270.507770.1365-19.3834-9.1061
180.22420.07280.69550.2279-0.25121.1222-0.0992-0.11370.0736-0.07620.0703-0.0382-0.13570.0305-0.00180.2416-0.0007-0.01770.234-0.01610.216869.106443.169126.9074
190.3785-0.2040.17651.3734-0.4890.381-0.0642-0.110.02440.1402-0.0163-0.0865-0.06240.1775-00.21940.0199-0.05120.31470.0030.267677.157537.526842.9303
200.2326-0.22540.11940.5895-0.16150.6311-0.0090.00310.27370.1330.0037-0.0715-0.21670.1202-00.30170.0043-0.05790.2611-0.02710.316669.400552.584632.1582
210.5476-0.82550.00910.9389-0.04930.2838-0.0178-0.04010.1773-0.06460.0195-0.10160.1626-0.104100.2568-0.0407-0.04620.24690.03620.287163.373544.200515.5573
220.0308-0.1438-0.18070.51730.25010.6584-0.17460.24820.1722-0.20760.260.1298-0.1692-0.29850.00010.2450.0281-0.00050.2690.02060.336257.934253.193717.6365
230.1705-0.00410.24080.1947-0.34220.6391-0.01270.15970.1896-0.02530.118-0.1355-0.0142-0.12100.30750.0234-0.00020.25110.01440.308259.815253.50038.8846
241.59970.2656-0.30620.58470.02260.07310.55120.68920.4945-0.03950.01480.190.34720.65540.0430.75440.18080.1190.63380.00360.414260.423764.2841-12.963
250.02220.0086-0.0096-0.0021-0.00720.07980.388-0.03330.4583-0.11920.0842-0.15580.0748-0.1909-0.00010.44860.05140.0660.31250.14150.612853.786285.7438-7.5868
260.00910.02250.03720.03270.02070.05730.28360.395-0.2317-0.1211-0.1999-0.08020.1541-0.046-0.00020.5130.09580.00070.45270.0220.295854.583268.6991-9.1369
270.1717-0.02690.09720.0521-0.08470.18170.15760.0141-0.0275-0.3619-0.0859-0.5011-0.02210.20960.00040.37380.04580.00210.2771-0.00230.420860.875563.5027-3.436
280.0529-0.00920.05170.03260.01550.069-0.0545-0.05270.4660.20750.1565-0.3035-0.19330.1378-0.00040.3089-0.02710.01480.3178-0.01760.483666.054174.331-0.1015
290.18150.0162-0.17740.2627-0.14960.0945-0.12470.0598-0.05710.06010.26370.1642-0.0639-0.0878-0.00010.2940.0039-0.02960.3005-0.04040.34955.288271.58014.352
300.39310.062-0.37140.0129-0.09830.45520.13950.30340.13830.30250.045-0.41790.16-0.03350.00010.3370.0171-0.04510.3524-0.03330.405754.140374.9864-3.4584
310.2197-0.0278-0.13890.03580.02570.07790.06420.18040.273-0.6076-0.0886-0.58660.41960.17150.00020.42280.0210.05540.35250.0210.358463.39866.4006-4.7354
320.165-0.1150.19030.1858-0.20110.2555-0.26950.47220.0256-0.1835-0.204-0.32760.090.0159-0.02410.3378-0.0021-0.0190.2585-0.08920.326866.223148.2597-0.5984
330.02370.02650.03160.05510.06460.10220.0586-0.31660.5910.43750.0802-0.4154-0.450.44940.01380.43080.02530.13260.4351-0.00210.448266.311364.9416-8.5705
340.019-0.0062-0.03320.0538-0.0250.05260.0925-0.0359-0.02540.38390.0313-0.1519-0.17390.03630.00020.37970.0260.08190.3650.18070.570459.970884.9413-8.8728
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 224 through 317 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 318 through 380 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 381 through 455 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 456 through 491 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 492 through 520 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 521 through 538 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 7 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 8 through 17 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 18 through 26 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 27 through 39 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 40 through 52 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 53 through 72 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 73 through 82 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 83 through 90 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 100 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 101 through 113 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 114 through 121 )B0
18X-RAY DIFFRACTION18chain 'C' and (resid 224 through 294 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 300 through 406 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 407 through 455 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 456 through 491 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 492 through 520 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 521 through 538 )C0
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 7 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 8 through 17 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 18 through 26 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 27 through 39 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 40 through 52 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 53 through 72 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 73 through 90 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 91 through 100 )D0
32X-RAY DIFFRACTION32chain 'D' and (resid 101 through 106 )D0
33X-RAY DIFFRACTION33chain 'D' and (resid 107 through 113 )D0
34X-RAY DIFFRACTION34chain 'D' and (resid 114 through 120 )D0

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  • 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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