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- PDB-5c09: HLA class I histocompatibility antigen -

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Basic information

Entry
Database: PDB / ID: 5c09
TitleHLA class I histocompatibility antigen
Components
  • 1E6 TCR Alpha Chain
  • 1E6 TCR Beta Chain
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Marker peptide
KeywordsIMMUNE SYSTEM / IMMUNO / HLA-A02 / 1E6-TCR / Cross-reactivity
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / T cell receptor complex / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / T cell receptor complex / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / 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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity
Similarity search - Function
: / : / Domain of unknown function (DUF1968) / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type ...: / : / Domain of unknown function (DUF1968) / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / 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 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor alpha variable 12-3 / T cell receptor beta variable 12-4 / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.475 Å
AuthorsRizkallah, P.J. / Bulek, A.M. / Cole, D.K. / Sewell, A.K.
CitationJournal: J.Clin.Invest. / Year: 2016
Title: Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity.
Authors: Cole, D.K. / Bulek, A.M. / Dolton, G. / Schauenberg, A.J. / Szomolay, B. / Rittase, W. / Trimby, A. / Jothikumar, P. / Fuller, A. / Skowera, A. / Rossjohn, J. / Zhu, C. / Miles, J.J. / ...Authors: Cole, D.K. / Bulek, A.M. / Dolton, G. / Schauenberg, A.J. / Szomolay, B. / Rittase, W. / Trimby, A. / Jothikumar, P. / Fuller, A. / Skowera, A. / Rossjohn, J. / Zhu, C. / Miles, J.J. / Peakman, M. / Wooldridge, L. / Rizkallah, P.J. / Sewell, A.K.
History
DepositionJun 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Marker peptide
D: 1E6 TCR Alpha Chain
E: 1E6 TCR Beta Chain
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Marker peptide
I: 1E6 TCR Alpha Chain
J: 1E6 TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,60918
Polymers190,84010
Non-polymers7698
Water1,51384
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Marker peptide
D: 1E6 TCR Alpha Chain
E: 1E6 TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8049
Polymers95,4205
Non-polymers3844
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Marker peptide
I: 1E6 TCR Alpha Chain
J: 1E6 TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8049
Polymers95,4205
Non-polymers3844
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.830, 100.070, 122.440
Angle α, β, γ (deg.)96.910, 98.310, 96.520
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21F
12B
22G
13D
23I
14E
24J

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA1 - 2761 - 276
21GLYGLYPROPROFF1 - 2761 - 276
12METMETMETMETBB0 - 991 - 100
22METMETMETMETGG0 - 991 - 100
13GLUGLUPHEPHEDD3 - 1981 - 196
23GLUGLUPHEPHEII3 - 1981 - 196
14GLYGLYALAALAEE3 - 2453 - 245
24GLYGLYALAALAJJ3 - 2453 - 245

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 4 types, 8 molecules AFBGDIEJ

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2 / HLA-A02 Heavy Chain


Mass: 31951.316 Da / Num. of mol.: 2 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / 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
#4: Protein 1E6 TCR Alpha Chain


Mass: 22483.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J271*PLUS
#5: Protein 1E6 TCR Beta Chain


Mass: 28026.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J2E0*PLUS

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Protein/peptide , 1 types, 2 molecules CH

#3: Protein/peptide Marker peptide


Mass: 1079.203 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 92 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium cacodylate pH6.5, 15% PEG 4000, 0.2M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.475→98.457 Å / Num. all: 70968 / Num. obs: 70968 / % possible obs: 98.2 % / Redundancy: 2 % / Rpim(I) all: 0.084 / Rrim(I) all: 0.127 / Rsym value: 0.105 / Net I/av σ(I): 4.667 / Net I/σ(I): 4.9 / Num. measured all: 140157
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.47-2.5420.5631.21037951830.4070.5632.197.5
2.54-2.611.90.5171.2994151540.4080.5172.397.9
2.61-2.681.90.3881.6949249460.3230.3882.798.1
2.68-2.772.10.3341.81007348690.2340.3343.298.1
2.77-2.862.10.2692.4961746900.2070.2693.698.3
2.86-2.9620.2143916945170.1710.2144.198.2
2.96-3.0720.1773.7877343350.1430.1774.697.5
3.07-3.1920.154.3830441920.1230.15598
3.19-3.341.90.1195.6779440650.1010.1195.598.1
3.34-3.51.80.1076.2680537920.0990.1075.797.7
3.5-3.6920.1055.9729337200.090.1056.498.7
3.69-3.911.90.0966644834810.0860.0966.498.9
3.91-4.1820.0986.5650632790.0730.0986.998.9
4.18-4.522.10.0798.1631530400.0640.0797.498.5
4.52-4.9520.0827.8569927890.0640.0827.498.2
4.95-5.5320.097.5509125550.0670.097.398.8
5.53-6.391.80.0867404622320.0720.0866.998.8
6.39-7.8320.0838.3377118830.0630.0837.499.4
7.83-11.0720.0729.2300814740.0550.0727.698.9
11.07-98.4572.10.074916337720.0430.0747.896.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 46.46 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å98.46 Å
Translation2.5 Å98.46 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASER2.1.4phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UTP and 3UTQ

3utp

3utq


Resolution: 2.475→98.457 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.2929 / WRfactor Rwork: 0.2325 / FOM work R set: 0.8063 / SU B: 22.995 / SU ML: 0.24 / SU R Cruickshank DPI: 0.5242 / SU Rfree: 0.2939 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.524 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 3581 5 %RANDOM
Rwork0.2047 ---
obs0.2074 67353 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 158.5 Å2 / Biso mean: 63.284 Å2 / Biso min: 23.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20.45 Å20.26 Å2
2---0.45 Å21.78 Å2
3----2.48 Å2
Refinement stepCycle: final / Resolution: 2.475→98.457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13405 0 40 84 13529
Biso mean--98.76 48.1 -
Num. residues----1659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01913818
X-RAY DIFFRACTIONr_bond_other_d0.0040.0212403
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.93518760
X-RAY DIFFRACTIONr_angle_other_deg1.208328589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0851649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07923.681709
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.756152232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.38915102
X-RAY DIFFRACTIONr_chiral_restr0.1120.21945
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115727
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023383
X-RAY DIFFRACTIONr_mcbond_it1.7732.8376626
X-RAY DIFFRACTIONr_mcbond_other1.7722.8366625
X-RAY DIFFRACTIONr_mcangle_it2.9074.2488265
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A134070.17
12F134070.17
21B53400.14
22G53400.14
31D84970.19
32I84970.19
41E119890.18
42J119890.18
LS refinement shellResolution: 2.475→2.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 234 -
Rwork0.271 4938 -
all-5172 -
obs--97.35 %
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)
12.9641-1.004-0.90962.9256-0.32053.38840.0799-0.07480.16010.33640.04850.0554-0.66560.2845-0.12850.1642-0.02470.00070.1019-0.09890.123813.06797.8261-8.8203
23.30380.57170.56133.5797-0.44197.56330.0768-0.60420.12110.6787-0.0189-0.3959-0.04180.3713-0.05790.4758-0.01180.01030.3974-0.16420.25177.70871.150526.3851
34.64662.5508-3.87652.8816-2.52136.1744-0.0273-0.2896-0.4015-0.0222-0.0053-0.03940.3202-0.02980.03270.0860.04-0.0720.1914-0.04860.17263.941-12.01977.5992
42.28641.9273-1.37856.649-3.15044.5007-0.0543-0.0203-0.1193-0.04490.0426-0.0686-0.43690.01260.01170.22530.04630.02540.0715-0.09970.216712.163731.7347-33.0599
52.361.90540.34243.70542.11664.9476-0.15940.54220.1238-0.61130.18160.5083-0.6207-0.0906-0.02221.1923-0.11890.01380.57660.08110.694510.183940.5287-65.5475
63.38920.04561.75961.7418-0.11966.55050.04770.2449-0.0129-0.08380.04220.158-0.101-0.1983-0.08990.0149-0.00630.03170.071-0.0770.22077.47749.959-38.4211
75.91163.5715-1.10075.5667-0.8591.9388-0.16140.56110.5454-0.5030.48110.2039-0.76820.0469-0.31980.7652-0.0860.02230.4764-0.17840.248811.459923.3752-65.8764
82.01491.0340.25534.4058-0.22124.3181-0.1399-0.0509-0.1949-0.65030.051-0.12580.83020.33390.08890.24610.070.02750.1611-0.09340.109923.2787-20.5216-54.8341
93.3088-0.1306-1.83623.5946-0.62638.4695-0.13830.2478-0.1347-0.3977-0.0038-0.60330.6710.66240.14210.35630.07830.00990.4101-0.1440.301327.7646-13.6024-90.2112
102.0627-0.71982.50731.6172-1.27287.6809-0.02130.22820.2446-0.09820.06190.0603-0.1695-0.0857-0.04060.0812-0.0070.02070.2079-0.04220.179816.0364-2.15-73.7944
111.936-1.82571.63926.2918-3.47475.6603-0.0887-0.0274-0.0321-0.0055-0.0221-0.06720.24240.03450.11080.20510.0334-0.030.0808-0.12040.195620.2095-44.7832-31.0579
127.2206-2.1493-0.37583.74480.61745.2187-0.1274-0.4022-0.58070.00780.12060.6860.597-0.2610.00680.80950.0083-0.01840.46930.08990.612411.1052-54.41810.2477
135.4770.624-2.54771.45540.0925.63810.0155-0.2079-0.04890.0349-0.03640.15790.1565-0.23440.0210.04950.0468-0.07870.114-0.1070.17149.6634-24.6013-28.2267
146.1103-2.58372.77442.9658-1.60784.2405-0.0216-0.4394-0.38040.19030.16060.23170.5962-0.1287-0.1390.29710.04660.08410.3282-0.10240.22197.8523-37.3351-0.2831
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 10
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D0 - 113
6X-RAY DIFFRACTION5D114 - 203
7X-RAY DIFFRACTION6E0 - 114
8X-RAY DIFFRACTION7E115 - 246
9X-RAY DIFFRACTION8F1 - 180
10X-RAY DIFFRACTION8H1 - 10
11X-RAY DIFFRACTION9F181 - 276
12X-RAY DIFFRACTION10G0 - 99
13X-RAY DIFFRACTION11I0 - 113
14X-RAY DIFFRACTION12I114 - 203
15X-RAY DIFFRACTION13J0 - 114
16X-RAY DIFFRACTION14J115 - 246

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Yorodumi

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  • 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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