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- PDB-4y4h: Crystal structure of the mCD1d/GCK152/iNKTCR ternary complex -

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Basic information

Entry
Database: PDB / ID: 4y4h
TitleCrystal structure of the mCD1d/GCK152/iNKTCR ternary complex
Components
  • (Chimeric TCR ...) x 2
  • Antigen-presenting glycoprotein CD1d1
  • Beta-2-microglobulin
KeywordsIMMUNE SYSTEM / MHC-fold / Ig-fold / glycolipid antigen presentation / T cell receptor
Function / homology
Function and homology information


regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive thymic T cell selection ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive thymic T cell selection / positive regulation of macrophage activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / positive regulation of interleukin-4 production / antigen processing and presentation / regulation of immune response / cellular defense response / T cell receptor binding / positive regulation of interleukin-2 production / Neutrophil degranulation / response to bacterium / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of type II interferon production / sensory perception of smell / late endosome / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / lysosome / early endosome / endosome membrane / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
MHC-I family domain / Domain of unknown function (DUF1968) / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 ...MHC-I family domain / Domain of unknown function (DUF1968) / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 subtype / 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
Chem-49X / T cell receptor alpha variable 11 / Beta-chain / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsZajonc, D.M. / Yu, E.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI074952 United States
CitationJournal: To Be Published
Title: Structural modifications of alphaGalCer in both lipid and carbohydrate moiety influence activation of murine and human iNKT cells
Authors: Birkholz, A. / Nemcovic, M. / Yu, E.D. / Girardi, E. / Wang, J. / Khurana, A. / Pauwels, N. / Franck, R.W. / Tsuji, M. / Howell, A. / Calenbergh, S. / Kronenberg, M. / Zajonc, D.M.
History
DepositionFeb 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antigen-presenting glycoprotein CD1d1
B: Beta-2-microglobulin
C: Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain/ human constant domain)
D: Chimeric TCR Vbeta8.2 chain (mouse variable domain/ human constant domain)
E: Antigen-presenting glycoprotein CD1d1
F: Beta-2-microglobulin
G: Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain/ human constant domain)
H: Chimeric TCR Vbeta8.2 chain (mouse variable domain/ human constant domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,04416
Polymers188,7518
Non-polymers3,2938
Water00
1
A: Antigen-presenting glycoprotein CD1d1
B: Beta-2-microglobulin
C: Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain/ human constant domain)
D: Chimeric TCR Vbeta8.2 chain (mouse variable domain/ human constant domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1248
Polymers94,3764
Non-polymers1,7484
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Antigen-presenting glycoprotein CD1d1
F: Beta-2-microglobulin
G: Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain/ human constant domain)
H: Chimeric TCR Vbeta8.2 chain (mouse variable domain/ human constant domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9208
Polymers94,3764
Non-polymers1,5454
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.417, 150.379, 102.490
Angle α, β, γ (deg.)90.000, 96.380, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12B
22F
13C
23G
14D
24H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 279
2111E1 - 279
1121B1 - 99
2121F1 - 99
1131C1 - 205
2131G1 - 205
1141D1 - 240
2141H1 - 240

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.997043, 0.041398, 0.064737), (-0.041125, -0.999139, 0.005554), (0.064912, 0.002876, 0.997887)40.811939, -36.778488, -2.33907
3given(1), (1), (1)
4given(-0.995314, 0.056389, 0.078557), (-0.057122, -0.998342, -0.007124), (0.078025, -0.011578, 0.996884)40.958801, -36.31078, -3.08952
5given(1), (1), (1)
6given(-0.999613, 0.002857, 0.027687), (-0.003041, -0.999974, -0.006609), (0.027667, -0.00669, 0.999595)40.280251, -37.932919, -1.69107
7given(1), (1), (1)
8given(-0.999839, 0.007597, 0.016282), (-0.007633, -0.999969, -0.002158), (0.016265, -0.002281, 0.999865)40.230671, -37.58942, -1.03432
9given(1), (1), (1)
10given(-0.997757, 0.049491, 0.045079), (-0.050664, -0.998396, -0.025261), (0.043757, -0.027488, 0.998664)41.594681, -35.80098, -3.00205

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Components

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Protein , 2 types, 4 molecules AEBF

#1: Protein Antigen-presenting glycoprotein CD1d1


Mass: 32632.668 Da / Num. of mol.: 2 / Fragment: Ectodomain, UNP residues 19-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, Cd1.1 / Plasmid: pBACpHp10 / Details (production host): dual promotor / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P11609
#2: Protein Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pBACp10pH / Details (production host): dual promotor / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P01887

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Chimeric TCR ... , 2 types, 4 molecules CGDH

#3: Protein Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain/ human constant domain) / Protein Trav11d / Human nkt tcr beta chain


Mass: 23055.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Gene: Trav11, Trav11d, HDCMA22P / Plasmid: pET22b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: A0A0B4J1J9*PLUS
#4: Protein Chimeric TCR Vbeta8.2 chain (mouse variable domain/ human constant domain) / Beta-chain / T-cell receptor beta-2 chain C region


Mass: 27026.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Gene: TRBC2, TCRBC2 / Plasmid: pET22b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: A2NTY6*PLUS

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Sugars , 2 types, 6 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 2 molecules

#7: Chemical ChemComp-49X / (1R)-1,5-anhydro-1-{(1E,3S,4S,5R)-4,5-dihydroxy-3-[(8-phenyloctanoyl)amino]nonadec-1-en-1-yl}-D-galactitol / GCK152


Mass: 677.951 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H67NO8

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Details

Sequence detailsTCR alpha chain (chain C): ...TCR alpha chain (chain C): MKTQVEQSPQSLVVRQGENCVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSNGRYSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGRLHFGAGTQLIVI (murine variable domain) PDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS (human constant domain) TCR beta chain (chain D): MEAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGDEGYTQYFGPGTRLLVLEDLRNVTPPKVSLFEPSK (murine variable domain) AEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA (human constant domain)

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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: 3.32 Å3/Da / Density % sol: 62.98 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop / Details: 16% PEG 4000, 0.2M di-ammonium hydrogen citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2011
RadiationMonochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. obs: 42694 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.113 / Χ2: 2.686 / Net I/av σ(I): 21.504 / Net I/σ(I): 9.3 / Num. measured all: 163518
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.1-3.1540.59921681.331100
3.15-3.2140.52221311.361100
3.21-3.2740.42721571.405100
3.27-3.3440.33721031.53100
3.34-3.4140.3121461.681100
3.41-3.4940.26421441.816100
3.49-3.584.10.23521361.971100
3.58-3.6840.21421152.08599.9
3.68-3.7840.18521642.2799.9
3.78-3.9140.17121212.46899.9
3.91-4.043.90.1521422.74899.7
4.04-4.213.90.12821473.01599.9
4.21-4.43.80.11321373.48899.8
4.4-4.633.70.09321153.58599.6
4.63-4.923.70.0921253.76399.1
4.92-5.33.70.09421583.98699.3
5.3-5.833.60.09921024.13299.1
5.83-6.673.60.09321494.05199.3
6.67-8.393.40.07121334.38298.4
8.39-4030.04921014.47495.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0104refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementResolution: 3.1→38.17 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.875 / SU B: 20.31 / SU ML: 0.361 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.496 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2868 1334 3.1 %RANDOM
Rwork0.2423 ---
obs0.2438 41334 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 219.11 Å2 / Biso mean: 71.077 Å2 / Biso min: 28.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0 Å20.12 Å2
2--0.13 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 3.1→38.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12247 0 222 0 12469
Biso mean--72.29 --
Num. residues----1608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02112824
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.94317546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.67351596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66424.311573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.498151765
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0741558
X-RAY DIFFRACTIONr_chiral_restr0.0770.21952
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219965
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1992TIGHT POSITIONAL0.040.05
1A1992TIGHT THERMAL11.150.5
2B719TIGHT POSITIONAL0.030.05
2B719TIGHT THERMAL10.410.5
3C1514TIGHT POSITIONAL0.040.05
3C1514TIGHT THERMAL4.240.5
4D1828TIGHT POSITIONAL0.040.05
4D1828TIGHT THERMAL4.360.5
LS refinement shellResolution: 3.104→3.184 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 85 -
Rwork0.312 2716 -
all-2801 -
obs--89.2 %

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