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- PDB-3fht: Crystal structure of human Dbp5 in complex with AMPPNP and RNA -

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Basic information

Entry
Database: PDB / ID: 3fht
TitleCrystal structure of human Dbp5 in complex with AMPPNP and RNA
Components
  • ATP-dependent RNA helicase DDX19B
  • RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsHYDROLASE/RNA / Dbp5 / DEAD-box helicase / RNA dependent ATPase / mRNA export / nucleocytoplasmic transport / Nup214 / CAN / Nup159 / DDX19b / nuclear pore / gle1 / ATP-binding / Helicase / Hydrolase / Membrane / mRNA transport / Nuclear pore complex / Nucleotide-binding / Nucleus / Phosphoprotein / Protein transport / RNA-binding / Translocation / Transport / HYDROLASE-RNA COMPLEX
Function / homology
Function and homology information


poly(A)+ mRNA export from nucleus / mRNA export from nucleus / nuclear pore / helicase activity / cytoplasmic stress granule / nuclear envelope / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity ...poly(A)+ mRNA export from nucleus / mRNA export from nucleus / nuclear pore / helicase activity / cytoplasmic stress granule / nuclear envelope / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal ...RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / RNA / ATP-dependent RNA helicase DDX19B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
Authorsvon Moeller, H. / Conti, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: The mRNA export protein DBP5 binds RNA and the cytoplasmic nucleoporin NUP214 in a mutually exclusive manner
Authors: von Moeller, H. / Basquin, C. / Conti, E.
History
DepositionDec 10, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DDX19B
B: ATP-dependent RNA helicase DDX19B
C: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
D: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,70812
Polymers99,2794
Non-polymers1,4298
Water5,405300
1
A: ATP-dependent RNA helicase DDX19B
C: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2625
Polymers49,6392
Non-polymers6233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-28 kcal/mol
Surface area17930 Å2
MethodPISA
2
B: ATP-dependent RNA helicase DDX19B
D: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4467
Polymers49,6392
Non-polymers8075
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-35 kcal/mol
Surface area17300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.600, 79.660, 124.540
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / RNA chain , 2 types, 4 molecules ABCD

#1: Protein ATP-dependent RNA helicase DDX19B / DEAD-box helicase 5 / Dbp5 / DEAD box protein 19B / DEAD box RNA helicase DEAD5


Mass: 46622.645 Da / Num. of mol.: 2
Fragment: Helicase ATP-binding domain, C-terminal domain, residues 68-479
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX19B (Dbp5) / Plasmid: pETMC / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21
References: UniProt: Q9UMR2, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: RNA chain RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 3016.700 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 4 types, 308 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.08 Å3/Da / Density % sol: 40.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100mM Tris pH 7.0, 20% PEG 2000 mono-methyl-ether, 3% PEG 3350, 30mM NaF, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1tris11
2PEG 2000 mono-methyl-ether11
3PEG 335011
4NaF11
5HOH11
6tris12
7PEG 2000 mono-methyl-ether12
8PEG 335012
9NaF12
10HOH11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0068 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0068 Å / Relative weight: 1
ReflectionResolution: 2.2→41.52 Å / Num. all: 41194 / Num. obs: 41211 / % possible obs: 99.5 % / Redundancy: 4.11 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 10.89
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 4.11 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 4.54 / Num. unique all: 5113 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0063refinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J0S

2j0s


Resolution: 2.2→41.52 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 0 / SU B: 10.469 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.277 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22518 2061 5 %RANDOM
Rwork0.16846 ---
obs0.1713 39149 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.93 Å2 / Biso mean: 21.053 Å2 / Biso min: 3.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20.08 Å2
2--0.66 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6178 237 88 300 6803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226517
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8552.0298867
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3045777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66124.559272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.626151108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0711540
X-RAY DIFFRACTIONr_chiral_restr0.1160.21018
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214740
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9341.53882
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75526263
X-RAY DIFFRACTIONr_scbond_it3.20132635
X-RAY DIFFRACTIONr_scangle_it5.0664.52604
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 149 -
Rwork0.185 2821 -
all-2970 -
obs--100 %
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)
10.8467-0.9491-1.00472.94461.95184.13850.0057-0.0278-0.0757-0.0535-0.03340.2320.101-0.2030.02770.0518-0.0117-0.00330.05340.00920.1018-8.2304-2.448915.1426
20.88040.05380.04010.64310.19120.55280.0079-0.0709-0.0360.0689-0.02850.04030.0245-0.00750.02050.05960.0014-0.00250.07710.0080.0973-2.85297.424121.1273
30.73490.51410.44571.80.80180.5137-0.0107-0.11620.11630.118-0.05880.07670.0608-0.12550.06950.05860.0065-0.00230.0838-0.01230.08921.282422.39120.8591
44.49772.8021-1.21922.1717-1.58942.1374-0.0213-0.01270.2130.04740.05310.1971-0.1232-0.0917-0.03180.06280.0362-0.01220.0597-0.01140.1498-6.171823.468819.4233
56.4556-5.0054-2.37613.90241.82890.88630.41930.53080.8689-0.2506-0.1926-0.6233-0.1273-0.2896-0.22660.29730.0254-0.0420.82750.20550.40091.919935.533922.0828
60.7794-0.6218-0.69311.67140.13531.74120.029-0.09540.08020.1086-0.0553-0.0309-0.16960.06730.02630.071-0.0154-0.02670.08680.00020.088.454925.299522.5101
71.7774-0.1679-1.74061.66160.52565.55420.0407-0.07120.01310.1012-0.03-0.2254-0.03640.1574-0.01070.0291-0.0109-0.04220.10110.02240.110516.720720.043122.1796
82.3242-0.9557-2.35011.75531.84114.3920.02830.0335-0.00090.02190.0273-0.1543-0.01310.1452-0.05560.04310.005-0.01430.08950.02410.088411.58248.71417.3722
91.35120.3805-0.1080.4795-0.10291.66080.0741-0.149-0.11770.1102-0.0553-0.08160.14430.0328-0.01880.07020.0195-0.00170.05230.02340.110115.44333.743219.0984
101.4370.26870.39761.9271-0.68742.9003-0.04040.0946-0.1607-0.4285-0.1084-0.07670.2790.16950.14880.1350.05290.00380.0337-0.01430.04289.61426.6395-11.3086
1111.10822.3062-7.44131.9638-0.81765.62870.0270.0096-0.17850.1186-0.05980.09790.0833-0.22260.03290.1637-0.0194-0.03050.19240.04690.12650.148612.411-16.1476
120.660.10530.31311.4369-0.35151.16540.01890.05370.0615-0.2034-0.00020.00520.04720.0341-0.01870.1263-0.0079-0.0030.05230.00050.07086.387421.9583-10.3813
134.18041.62391.29163.54711.18911.3723-0.10420.02510.068-0.03210.07780.2307-0.2353-0.12320.02640.07590.0135-0.01510.09020.02470.0743-1.146527.0619-0.2815
140.1438-0.2553-0.26871.3326-0.36841.3785-0.0015-0.0160.0201-0.1359-0.0249-0.03590.11210.06480.02640.0883-0.00570.00190.07540.00110.08887.144611.3266-1.3969
150.98880.1486-0.81912.0198-1.464.4035-0.06160.0854-0.0408-0.3227-0.0685-0.27210.41470.21150.13010.10550.04630.06940.0603-0.00310.089416.35332.2865-7.6516
160.68081.18250.91733.0341.37882.1537-0.06930.04350.0521-0.01330.01460.2348-0.1193-0.01940.05470.02890.01350.00010.0817-0.0050.108111.1058-1.547345.0089
172.9629-0.6791-2.11350.7936-0.13962.13850.13770.26730.045-0.0962-0.1378-0.0147-0.0597-0.143300.0850.0281-0.02740.0911-0.00240.10318.2341-3.386339.8367
180.4156-0.2671-0.49241.02670.24080.6886-0.03270.1013-0.0142-0.1303-0.01710.09950.0042-0.06490.04980.0755-0.0238-0.01670.11140.00760.081121.833-13.057438.9735
191.0665-0.65860.65290.8345-0.12271.343-0.0306-0.0595-0.03730.0320.04560.0070.0583-0.0661-0.0150.0796-0.00770.00990.05760.00010.122.7602-21.476347.7638
207.8476-3.36561.91072.792-1.47251.27250.04340.2222-0.3164-0.18850.04880.28510.2226-0.1191-0.09220.0652-0.04160.00920.0929-0.03350.105914.5514-23.990242.1467
214.0663-1.36981.70641.94160.30192.99970.21990.1883-0.2541-0.0408-0.23120.10590.37590.08690.01130.12690.00070.02470.0443-0.00970.072427.2739-30.554340.2882
221.060.19770.18311.4750.34172.5816-0.00780.1161-0.0179-0.0627-0.0769-0.08180.06650.13490.08470.04780.01140.02510.09530.0180.088334.214-19.808139.6806
231.6624-0.53450.24221.0568-0.72360.51590.0323-0.02970.04210.0714-0.0381-0.0567-0.06270.02430.00580.0501-0.00550.01840.1042-0.01940.111634.7187-7.715444.9861
240.7051-0.5265-0.24340.8081-0.10451.59210.11240.08320.1694-0.1714-0.052-0.2107-0.19840.0935-0.06040.1003-0.02120.01410.10030.01790.122635.7395-4.14841.4055
250.83870.4532-1.68552.1539-1.90564.11430.0827-0.05430.02010.4664-0.2069-0.093-0.41630.3340.12410.1505-0.0619-0.04350.12750.04150.103530.6856-4.681470.7634
268.9272-1.39224.28071.8835-0.87682.89380.2212-0.05930.182-0.0535-0.06470.2432-0.0934-0.2434-0.15650.24880.0350.00360.21570.01240.156523.4353-13.165679.8575
271.14920.12260.33871.0488-0.79471.8344-0.0593-0.0838-0.01990.15380.03550.0046-0.07350.03630.02380.1279-0.0006-0.00110.0366-0.00030.064626.9463-21.646672.6499
285.0083-2.4111-1.04094.21681.11911.0661-0.0551-0.1063-0.10610.05190.08890.23750.136-0.0491-0.03380.0624-0.0130.01320.07750.02110.087419.5563-26.887862.6377
290.11170.05460.27361.1588-0.51241.3876-0.02120.0244-0.04270.1546-0.0156-0.0234-0.09210.07790.03680.09350.00170.0020.06210.00260.089828.1005-11.279963.6066
301.7404-0.131-0.00542.4747-1.7362.2383-0.1-0.1920.10540.5355-0.0743-0.42-0.59430.25120.17430.1803-0.0638-0.07990.0958-0.01790.10537.1862-2.302370.4526
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A75 - 99
2X-RAY DIFFRACTION2A100 - 154
3X-RAY DIFFRACTION3A155 - 179
4X-RAY DIFFRACTION4A180 - 200
5X-RAY DIFFRACTION5A201 - 211
6X-RAY DIFFRACTION6A212 - 246
7X-RAY DIFFRACTION7A247 - 268
8X-RAY DIFFRACTION8A269 - 279
9X-RAY DIFFRACTION9A280 - 301
10X-RAY DIFFRACTION10A302 - 323
11X-RAY DIFFRACTION11A324 - 333
12X-RAY DIFFRACTION12A334 - 365
13X-RAY DIFFRACTION13A366 - 384
14X-RAY DIFFRACTION14A385 - 441
15X-RAY DIFFRACTION15A442 - 466
16X-RAY DIFFRACTION16B75 - 111
17X-RAY DIFFRACTION17B112 - 130
18X-RAY DIFFRACTION18B131 - 163
19X-RAY DIFFRACTION19B164 - 182
20X-RAY DIFFRACTION20B183 - 200
21X-RAY DIFFRACTION21B201 - 230
22X-RAY DIFFRACTION22B231 - 268
23X-RAY DIFFRACTION23B269 - 283
24X-RAY DIFFRACTION24B284 - 299
25X-RAY DIFFRACTION25B300 - 320
26X-RAY DIFFRACTION26B321 - 332
27X-RAY DIFFRACTION27B333 - 365
28X-RAY DIFFRACTION28B366 - 384
29X-RAY DIFFRACTION29B385 - 441
30X-RAY DIFFRACTION30B442 - 467

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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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