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- PDB-5whk: Crystal structure of Fab fragment of antibody DX-2507 bound to Fc... -

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Basic information

Entry
Database: PDB / ID: 5whk
TitleCrystal structure of Fab fragment of antibody DX-2507 bound to FcRn-B2M
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • DX-2507 Fab heavy chain
  • DX-2507 Fab light chain
  • IgG receptor FcRn large subunit p51
KeywordsIMMUNE SYSTEM / neonatal receptor / Fc / antibody recycling
Function / homology
Function and homology information


IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / endosome membrane / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IgG receptor FcRn large subunit p51 / Beta-2-microglobulin / IGL@ protein / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsEdwards, T.E. / Clifton, M.C. / Nixon, A.E. / Kenniston, J.A.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural basis for pH-insensitive inhibition of immunoglobulin G recycling by an anti-neonatal Fc receptor antibody.
Authors: Kenniston, J.A. / Taylor, B.M. / Conley, G.P. / Cosic, J. / Kopacz, K.J. / Lindberg, A.P. / Comeau, S.R. / Atkins, K. / Bullen, J. / TenHoor, C. / Adelman, B.A. / Sexton, D.J. / Edwards, T.E. / Nixon, A.E.
History
DepositionJul 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: 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
H: DX-2507 Fab heavy chain
L: DX-2507 Fab light chain
A: IgG receptor FcRn large subunit p51
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7378
Polymers92,1984
Non-polymers5394
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-23 kcal/mol
Surface area34870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.560, 70.450, 256.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#3: Protein IgG receptor FcRn large subunit p51 / FcRn / IgG Fc fragment receptor transporter alpha chain / Neonatal Fc receptor


Mass: 32824.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGRT, FCRN / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P55899
#4: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 13732.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P61769

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Antibody , 2 types, 2 molecules HL

#1: Antibody DX-2507 Fab heavy chain


Mass: 22981.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: S6BAN1
#2: Antibody DX-2507 Fab light chain


Mass: 22659.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q6NS95

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Non-polymers , 3 types, 258 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.92 Å3/Da / Density % sol: 57.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: DX-2507 Fab FcRn B2M complex at 6.6 mg/mL at 70 uM against an optimization screen against JCSG+ A7 18% PEG 8000, 0.1 M CHES pH 9.8 with seeding from an earlier crystal obtained under similar ...Details: DX-2507 Fab FcRn B2M complex at 6.6 mg/mL at 70 uM against an optimization screen against JCSG+ A7 18% PEG 8000, 0.1 M CHES pH 9.8 with seeding from an earlier crystal obtained under similar conditions, supplemented with 20% ethylene glycol as cro-protectant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→47.429 Å / Num. obs: 38312 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.888 % / Biso Wilson estimate: 44.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.081 / Χ2: 0.991 / Net I/σ(I): 16.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.564.980.6292.4227720.8150.703100
2.56-2.644.9990.5033.0527270.8970.561100
2.64-2.714.9810.3963.8226730.9320.443100
2.71-2.84.9830.2995.0425410.950.334100
2.8-2.894.9840.2516.1825070.9660.2899.9
2.89-2.994.980.1898.0124170.9760.211100
2.99-3.14.9530.159.9423390.9860.167100
3.1-3.234.9360.11912.2122390.990.133100
3.23-3.374.9360.09115.5821850.9940.102100
3.37-3.544.9060.07119.1320860.9960.07999.9
3.54-3.734.8770.06222.3619900.9960.0799.8
3.73-3.954.8860.05425.1218430.9970.06199.6
3.95-4.234.8260.04529.2217680.9970.0599.8
4.23-4.564.7940.03933.1716480.9980.04499.9
4.56-54.7460.03733.9415370.9980.04299.7
5-5.594.7770.03833.3413780.9980.04399.6
5.59-6.454.7140.0431.612610.9970.04699.8
6.45-7.914.6630.03234.4510580.9990.03799.5
7.91-11.184.4920.02740.048510.9980.03199.8
11.18-47.4293.9670.02440.34920.9990.02795

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX(1.10_2155)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M17, 5WHJ

3m17

5whj


Resolution: 2.5→47.429 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.37
RfactorNum. reflection% reflection
Rfree0.2246 1922 5.02 %
Rwork0.1693 --
obs0.1722 38303 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.05 Å2 / Biso mean: 49.4345 Å2 / Biso min: 20.32 Å2
Refinement stepCycle: final / Resolution: 2.5→47.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5830 0 34 254 6118
Biso mean--51.59 47.23 -
Num. residues----776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076029
X-RAY DIFFRACTIONf_angle_d0.9138223
X-RAY DIFFRACTIONf_chiral_restr0.048897
X-RAY DIFFRACTIONf_plane_restr0.0051060
X-RAY DIFFRACTIONf_dihedral_angle_d13.733536
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4999-2.56240.30791160.229425702686100
2.5624-2.63170.28131090.214325552664100
2.6317-2.70910.28331320.215926062738100
2.7091-2.79660.29211440.208425232667100
2.7966-2.89650.31531470.210925462693100
2.8965-3.01250.26141320.191125692701100
3.0125-3.14950.24231210.196926092730100
3.1495-3.31550.26711350.193325862721100
3.3155-3.52320.25691480.189325872735100
3.5232-3.79510.21971530.169325592712100
3.7951-4.17690.1751260.146526332759100
4.1769-4.78080.17391430.117126202763100
4.7808-6.02130.17111390.140226662805100
6.0213-47.43760.22171770.17022752292999
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)
11.4183-0.91640.24721.5608-0.07252.2051-0.1142-0.3990.79430.61390.17910.3504-1.1561-0.12650.01950.53480.26360.13060.46180.01090.398-15.22764.479846.5246
21.79260.3481-0.92792.2167-0.23243.93580.2905-0.58930.98760.43720.1607-0.109-1.22680.3638-0.31750.5385-0.01030.04870.3807-0.11240.3106-4.98717.652938.8704
32.681-0.8918-1.43332.4471-0.56253.93620.0781-0.00510.19780.15120.13820.1382-0.7652-0.3757-0.18650.32180.10080.04830.3385-0.04070.292-13.98762.421935.4154
42.4829-0.2959-2.75181.638-0.06143.097-0.31980.0664-0.07440.14520.26270.1933-0.2717-0.43990.04430.39640.15160.04680.4312-0.01790.4465-18.8894-1.192941.2958
51.7518-0.10510.1042.18930.55740.6227-0.0757-0.8041-0.61180.62330.1349-0.24990.31270.30960.01610.34220.08680.01760.4088-0.02150.3863-2.0835-3.091439.74
60.31390.4084-0.32220.60920.2352.40120.0925-0.03160.74980.3297-0.04320.6468-0.0506-0.7284-0.02820.44190.18710.21080.6405-0.04090.7119-25.82460.613853.5682
75.8904-0.45260.25152.60851.40245.02920.4551-0.5011-0.27580.3470.0584-0.1301-0.3059-0.4067-0.54210.4336-0.14820.20020.4282-0.04770.6046-18.3843-5.574574.1861
82.16440.45680.41862.240.4714.0620.3972-0.00320.51870.1892-0.1251-0.2719-0.23560.11-0.23810.4567-0.10640.26960.4764-0.09980.6472-14.3832-3.744268.4609
96.4169-0.89393.7385.5393-3.45874.10240.4443-0.70441.43880.6975-0.75560.0781-1.0420.1940.27120.6271-0.16140.23410.4865-0.16290.7926-16.82743.246174.7665
104.28221.57850.49712.107-0.51246.0099-0.2070.0165-0.631-0.25750.28120.25260.67810.37840.13460.47620.11430.09690.31310.060.5453-7.9904-24.611439.8407
111.66080.8149-0.94813.2662-1.41443.8529-0.251-0.1061-0.3144-0.116-0.0236-0.0670.47480.48150.11840.29660.11050.04830.3780.00940.3766-1.2305-15.988535.3965
120.40620.5523-0.99350.4704-0.51754.44540.0357-0.24860.00670.1664-0.30350.14840.50.31940.2560.4077-0.03390.14490.4204-0.03370.4292-13.7602-17.076358.945
132.14440.6199-0.45213.373-0.69843.97970.0339-0.18440.2093-0.1912-0.0013-0.03490.5416-0.2656-0.02250.5687-0.20170.21910.5-0.09920.4968-23.2-19.623373.0012
142.90260.17590.06083.1363-0.15473.0002-0.09930.2138-0.0376-0.76720.2082-0.29170.18750.1662-0.13270.3682-0.03660.06150.2959-0.01590.25418.382-1.76043.3293
151.99780.4479-1.3423.1117-0.80932.1535-0.0888-0.02690.1257-0.1315-0.0502-0.1804-0.04010.16550.09490.257-0.0032-0.00460.2874-0.02540.25539.73822.913613.359
163.39010.47745.0130.62931.59198.9956-0.00210.6160.3759-0.07540.4523-0.1867-0.41220.9159-0.08710.4611-0.14770.13960.43240.07220.439210.323913.8794-3.3803
174.001-1.06560.12852.7359-0.19953.5105-0.01980.1703-0.088-0.4798-0.06840.36020.4107-0.33470.14040.4866-0.0369-0.07830.2993-0.03150.3436-16.4685.4832-17.0141
181.3565-0.5452-0.30261.7088-0.67572.7921-0.05740.11260.1582-0.1265-0.20570.0577-0.7864-0.95760.19780.25850.00980.00430.2901-0.07040.3277-9.755-7.1212-1.8674
191.3067-0.3176-0.44681.50950.02264.3740.11840.330.1656-0.7361-0.080.0825-0.40230.56050.00430.65860.0356-0.00110.39390.0050.3105-4.5809-7.0133-15.7224
200.47190.97921.1052.86942.99293.3560.1367-0.1026-0.16050.4501-0.15940.01991.16390.00340.17180.48610.0479-0.01520.3504-0.07810.3916-4.6283-17.6123-6.0413
210.95781.37681.33131.64441.30478.5611-0.0215-0.049-0.1112-0.4819-0.1713-0.0697-0.43310.33160.08490.34680.0349-0.03620.3311-0.02540.327-1.383-9.0406-8.2294
222.27041.1162-0.48662.6590.99477.19640.01260.0490.0779-0.1292-0.0440.19650.6118-0.50480.0130.35070.0357-0.0830.3122-0.06270.3508-12.0654-14.488-7.897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 17 )H1 - 17
2X-RAY DIFFRACTION2chain 'H' and (resid 18 through 33 )H18 - 33
3X-RAY DIFFRACTION3chain 'H' and (resid 34 through 83 )H34 - 83
4X-RAY DIFFRACTION4chain 'H' and (resid 84 through 98 )H84 - 98
5X-RAY DIFFRACTION5chain 'H' and (resid 99 through 109 )H99 - 109
6X-RAY DIFFRACTION6chain 'H' and (resid 110 through 122 )H110 - 122
7X-RAY DIFFRACTION7chain 'H' and (resid 123 through 148 )H123 - 148
8X-RAY DIFFRACTION8chain 'H' and (resid 149 through 206 )H149 - 206
9X-RAY DIFFRACTION9chain 'H' and (resid 207 through 217 )H207 - 217
10X-RAY DIFFRACTION10chain 'L' and (resid 1 through 23 )L1 - 23
11X-RAY DIFFRACTION11chain 'L' and (resid 24 through 77 )L24 - 77
12X-RAY DIFFRACTION12chain 'L' and (resid 78 through 154 )L78 - 154
13X-RAY DIFFRACTION13chain 'L' and (resid 155 through 212 )L155 - 212
14X-RAY DIFFRACTION14chain 'A' and (resid 4 through 39 )A4 - 39
15X-RAY DIFFRACTION15chain 'A' and (resid 40 through 156 )A40 - 156
16X-RAY DIFFRACTION16chain 'A' and (resid 157 through 180 )A157 - 180
17X-RAY DIFFRACTION17chain 'A' and (resid 181 through 270 )A181 - 270
18X-RAY DIFFRACTION18chain 'B' and (resid 1 through 11 )B1 - 11
19X-RAY DIFFRACTION19chain 'B' and (resid 12 through 30 )B12 - 30
20X-RAY DIFFRACTION20chain 'B' and (resid 31 through 46 )B31 - 46
21X-RAY DIFFRACTION21chain 'B' and (resid 47 through 77 )B47 - 77
22X-RAY DIFFRACTION22chain 'B' and (resid 78 through 99 )B78 - 99

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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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