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- PDB-8rjh: HLA A*2402-NF9_6F pMHC complex -

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Basic information

Entry
Database: PDB / ID: 8rjh
TitleHLA A*2402-NF9_6F pMHC complex
Components
  • ASN-TYR-ASN-TYR-LEU-PHE-ARG-LEU-PHE
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Peptide:HLA / NF9 / Covid-19 HLA A*2402
Function / homology
Function and homology information


: / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...: / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWall, A. / Sewell, A.K. / Motozono, C. / Rizkallah, P.J. / Fuller, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: HLA A*2402-NF9_6F pMHC complex
Authors: Motozono, C. / Wall, A. / Sewell, A.K. / Rizkallah, P.J. / Fuller, A.
History
DepositionDec 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: ASN-TYR-ASN-TYR-LEU-PHE-ARG-LEU-PHE
D: MHC class I antigen
E: Beta-2-microglobulin
F: ASN-TYR-ASN-TYR-LEU-PHE-ARG-LEU-PHE
G: MHC class I antigen
H: Beta-2-microglobulin
I: ASN-TYR-ASN-TYR-LEU-PHE-ARG-LEU-PHE
J: MHC class I antigen
K: Beta-2-microglobulin
L: ASN-TYR-ASN-TYR-LEU-PHE-ARG-LEU-PHE
M: MHC class I antigen
N: Beta-2-microglobulin
O: ASN-TYR-ASN-TYR-LEU-PHE-ARG-LEU-PHE
P: MHC class I antigen
Q: Beta-2-microglobulin
R: ASN-TYR-ASN-TYR-LEU-PHE-ARG-LEU-PHE


Theoretical massNumber of molelcules
Total (without water)269,44718
Polymers269,44718
Non-polymers00
Water3,045169
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: ASN-TYR-ASN-TYR-LEU-PHE-ARG-LEU-PHE


Theoretical massNumber of molelcules
Total (without water)44,9083
Polymers44,9083
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-20 kcal/mol
Surface area19200 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: ASN-TYR-ASN-TYR-LEU-PHE-ARG-LEU-PHE


Theoretical massNumber of molelcules
Total (without water)44,9083
Polymers44,9083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-19 kcal/mol
Surface area19160 Å2
MethodPISA
3
G: MHC class I antigen
H: Beta-2-microglobulin
I: ASN-TYR-ASN-TYR-LEU-PHE-ARG-LEU-PHE


Theoretical massNumber of molelcules
Total (without water)44,9083
Polymers44,9083
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-19 kcal/mol
Surface area19140 Å2
MethodPISA
4
J: MHC class I antigen
K: Beta-2-microglobulin
L: ASN-TYR-ASN-TYR-LEU-PHE-ARG-LEU-PHE


Theoretical massNumber of molelcules
Total (without water)44,9083
Polymers44,9083
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-18 kcal/mol
Surface area19080 Å2
MethodPISA
5
M: MHC class I antigen
N: Beta-2-microglobulin
O: ASN-TYR-ASN-TYR-LEU-PHE-ARG-LEU-PHE


Theoretical massNumber of molelcules
Total (without water)44,9083
Polymers44,9083
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-20 kcal/mol
Surface area19040 Å2
MethodPISA
6
P: MHC class I antigen
Q: Beta-2-microglobulin
R: ASN-TYR-ASN-TYR-LEU-PHE-ARG-LEU-PHE


Theoretical massNumber of molelcules
Total (without water)44,9083
Polymers44,9083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-21 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)344.797, 84.336, 91.453
Angle α, β, γ (deg.)90.00, 102.14, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
1515
1616
1717
1818
1919
2020
2121
2222
2323
2424
2525
2626
2727
2828
2929
3030

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30

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Components

#1: Protein
MHC class I antigen


Mass: 31778.117 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A411J078
#2: Protein
Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 6 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide
ASN-TYR-ASN-TYR-LEU-PHE-ARG-LEU-PHE


Mass: 1250.425 Da / Num. of mol.: 6 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 49.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Glycerol 15% v/v Polyethylene Glycol 4,000, 20% w/v MES, 0.1 M, pH7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→87 Å / Num. obs: 79258 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.072 / Rrim(I) all: 0.193 / Χ2: 0.98 / Net I/σ(I): 7.7
Reflection shellResolution: 2.6→2.65 Å / % possible obs: 99.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 1.738 / Num. measured all: 29665 / Num. unique obs: 4490 / CC1/2: 0.465 / Rpim(I) all: 0.73 / Rrim(I) all: 1.887 / Χ2: 0.97 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→87 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 38.822 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26431 3966 5 %RANDOM
Rwork0.22417 ---
obs0.2262 75257 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.237 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å2-0 Å2-2.38 Å2
2---0.05 Å2-0 Å2
3---2.26 Å2
Refinement stepCycle: 1 / Resolution: 2.6→87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18990 0 0 169 19159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01319530
X-RAY DIFFRACTIONr_bond_other_d0.0010.01517388
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.65926478
X-RAY DIFFRACTIONr_angle_other_deg1.1561.58540062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77452292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.77721.4491242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.385153210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.27715174
X-RAY DIFFRACTIONr_chiral_restr0.0570.22394
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0222422
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024902
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_it1.3072.7099222
X-RAY DIFFRACTIONr_mcbond_other1.3072.7099221
X-RAY DIFFRACTIONr_mcangle_it2.2044.0611496
X-RAY DIFFRACTIONr_mcangle_other2.2044.0611497
X-RAY DIFFRACTIONr_scbond_it1.4622.85610308
X-RAY DIFFRACTIONr_scbond_other1.4622.85610308
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4244.22314982
X-RAY DIFFRACTIONr_long_range_B_refined4.14829.39820496
X-RAY DIFFRACTIONr_long_range_B_other4.14629.38820490
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A88320.07
12D88320.07
21A88240.06
22G88240.06
31A88130.07
32J88130.07
41A88420.06
42M88420.06
51A88700.06
52P88700.06
61B31100.05
62E31100.05
71B30900.06
72H30900.06
81B30960.08
82K30960.08
91B31020.06
92N31020.06
101B31060.04
102Q31060.04
111D88140.06
112G88140.06
121D88080.07
122J88080.07
131D87900.06
132M87900.06
141D88530.06
142P88530.06
151E31180.05
152H31180.05
161E31110.08
162K31110.08
171E31340.05
172N31340.05
181E31110.06
182Q31110.06
191G87720.06
192J87720.06
201G88500.05
202M88500.05
211G88040.06
212P88040.06
221H30890.08
222K30890.08
231H31250.04
232N31250.04
241H30950.06
242Q30950.06
251J88700.05
252M88700.05
261J88560.06
262P88560.06
271K31050.08
272N31050.08
281K30920.08
282Q30920.08
291M88320.06
292P88320.06
301N31150.06
302Q31150.06
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 271 -
Rwork0.355 5519 -
obs--99.62 %
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)
13.82811.6208-2.93874.7374-3.44545.56370.0855-0.03530.07530.2770.30070.7953-0.1016-0.456-0.38620.04340.00240.00630.07250.05340.248464.33714.557215.7283
28.3598-1.9192.90223.5014-0.04894.2398-0.2988-0.9187-0.02450.62350.5588-0.6870.05641.0206-0.260.58460.1299-0.11630.705-0.05040.37483.5136-16.207637.7006
32.3679-0.2963-0.83657.0494-3.415.606-0.0245-0.0658-0.7822-0.3361-0.0656-0.19221.43690.14790.09010.4830.0707-0.09570.07730.03010.319675.8718-20.344916.8694
43.64771.0565-1.99564.9952-0.89995.2046-0.0917-0.2699-0.15180.16640.07550.6928-0.032-0.61630.01630.09810.0862-0.00760.23270.07810.326.801746.366416.5735
57.2286-0.21671.17273.2630.73193.72640.0679-0.9593-0.5510.58850.337-0.25320.44350.4376-0.40490.72570.0908-0.1350.50180.21440.422327.279323.492136.7236
63.0159-0.2158-0.49815.0407-0.75213.7147-0.0664-0.1425-1.16960.18550.19290.13180.8661-0.2028-0.12650.31780.0205-0.10230.17620.13960.603817.904121.251515.875
72.78831.3583-2.4796.0189-3.02255.0414-0.06130.0161-0.10680.15290.75271.57740.0184-0.6618-0.69140.06120.05080.01360.26640.36030.7368122.238244.98314.1067
88.0264-0.66971.80984.9498-0.40474.5856-0.1439-0.9772-0.40790.8120.3045-0.28190.01750.6277-0.16060.41890.03950.02090.40070.14070.2492140.553521.116235.0848
92.4520.566-1.44375.9895-3.07074.3304-0.17280.3673-0.6785-0.60770.32140.470.9232-0.2889-0.14860.2564-0.0647-0.14140.13380.00560.4186134.151520.240113.0034
103.357-1.07272.11324.6875-1.71224.3419-0.04270.0785-0.1361-0.05040.18220.63350.0385-0.5166-0.13950.0631-0.06290.02520.16480.02740.2208-12.3515-12.427173.1773
116.72570.3822-1.89514.89160.82614.6531-0.041.09070.6758-0.5620.1647-0.8058-0.61150.4326-0.12460.6597-0.2026-0.04890.59630.33920.49848.16510.450652.6433
124.29891.5452-0.04314.8816-1.153.6614-0.11730.24581.6546-0.0180.21230.3106-0.8816-0.1343-0.0950.2816-0.0019-0.02360.13030.1370.6844-1.091912.653573.9056
133.6006-1.86992.85276.3856-3.67614.9288-0.0702-0.1372-0.032-0.42490.80661.42230.114-0.6494-0.73640.0934-0.122-0.1520.24960.33470.602103.1667-11.233375.3867
147.53060.8985-0.97135.4288-0.86326.47370.00011.01790.2-0.82230.2904-0.3309-0.07240.5851-0.29050.4024-0.0571-0.04460.29610.05890.1797121.078112.95954.3852
151.8018-0.97031.49367.0806-2.74224.1347-0.1422-0.33550.42680.43180.36330.3021-0.7497-0.4012-0.2210.15450.03250.07040.15230.03030.3016115.006113.51876.5975
163.4453-0.98212.71214.6678-2.77784.72160.03520.01430.0655-0.32330.14410.69660.04-0.4206-0.17930.04710.0158-0.03260.09110.02350.259545.172229.16273.3631
175.53963.5817-5.25446.5304-1.81076.4962-0.34270.33270.0979-0.70180.2955-0.6508-0.34960.53960.04720.7884-0.2896-0.28510.81240.31370.43663.87751.526251.1209
182.41070.67640.43366.7477-1.64813.5346-0.0759-0.09440.8757-0.1803-0.08930.1591-1.0441-0.09110.16520.4133-0.0003-0.03440.07810.00080.361156.018754.396572.3446
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 180
6X-RAY DIFFRACTION4F1 - 9
7X-RAY DIFFRACTION5D181 - 276
8X-RAY DIFFRACTION6E0 - 99
9X-RAY DIFFRACTION7G1 - 180
10X-RAY DIFFRACTION7I1 - 9
11X-RAY DIFFRACTION8G181 - 276
12X-RAY DIFFRACTION9H0 - 99
13X-RAY DIFFRACTION10J1 - 180
14X-RAY DIFFRACTION10L1 - 9
15X-RAY DIFFRACTION11J181 - 276
16X-RAY DIFFRACTION12K0 - 99
17X-RAY DIFFRACTION13M1 - 180
18X-RAY DIFFRACTION13O1 - 9
19X-RAY DIFFRACTION14M181 - 276
20X-RAY DIFFRACTION15N0 - 99
21X-RAY DIFFRACTION16P1 - 180
22X-RAY DIFFRACTION16R1 - 9
23X-RAY DIFFRACTION17P181 - 276
24X-RAY DIFFRACTION18Q0 - 99

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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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