[English] 日本語
Yorodumi
- PDB-6bnl: Crystal structure of TCR-MHC-like molecule -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bnl
TitleCrystal structure of TCR-MHC-like molecule
Components
  • Antigen-presenting glycoprotein CD1d1
  • Beta-2-microglobulin
  • NKT Valpha14 (MOUSE) - 2C12 TCR - Hybrid mouse variable and human constant domains
  • NKT Vbeta8.2 (MOUSE) - 2C12 TCR - hybrid mouse variable and human constant domains
KeywordsIMMUNE SYSTEM / Lipids Cancer
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 regulation of macrophage activation ...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 regulation of macrophage activation / positive thymic T cell selection / 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 / 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 / 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 / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / late endosome / 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 / amyloid fibril formation / lysosome / early endosome / learning or memory / endosome membrane / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol
Similarity search - Function
MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 ...MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-QWV / CD1d1 antigen / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLe Nours, J. / Rossjohn, J.
CitationJournal: Cell Chem Biol / Year: 2018
Title: Dual Modifications of alpha-Galactosylceramide Synergize to Promote Activation of Human Invariant Natural Killer T Cells and Stimulate Anti-tumor Immunity.
Authors: Chennamadhavuni, D. / Saavedra-Avila, N.A. / Carreno, L.J. / Guberman-Pfeffer, M.J. / Arora, P. / Yongqing, T. / Koay, H.F. / Godfrey, D.I. / Keshipeddy, S. / Richardson, S.K. / Sundararaj, ...Authors: Chennamadhavuni, D. / Saavedra-Avila, N.A. / Carreno, L.J. / Guberman-Pfeffer, M.J. / Arora, P. / Yongqing, T. / Koay, H.F. / Godfrey, D.I. / Keshipeddy, S. / Richardson, S.K. / Sundararaj, S. / Lo, J.H. / Wen, X. / Gascon, J.A. / Yuan, W. / Rossjohn, J. / Le Nours, J. / Porcelli, S.A. / Howell, A.R.
History
DepositionNov 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 30, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _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
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antigen-presenting glycoprotein CD1d1
B: Beta-2-microglobulin
C: NKT Valpha14 (MOUSE) - 2C12 TCR - Hybrid mouse variable and human constant domains
D: NKT Vbeta8.2 (MOUSE) - 2C12 TCR - hybrid mouse variable and human constant domains
E: Antigen-presenting glycoprotein CD1d1
F: Beta-2-microglobulin
G: NKT Valpha14 (MOUSE) - 2C12 TCR - Hybrid mouse variable and human constant domains
H: NKT Vbeta8.2 (MOUSE) - 2C12 TCR - hybrid mouse variable and human constant domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,11416
Polymers192,4318
Non-polymers3,6838
Water3,099172
1
A: Antigen-presenting glycoprotein CD1d1
B: Beta-2-microglobulin
C: NKT Valpha14 (MOUSE) - 2C12 TCR - Hybrid mouse variable and human constant domains
D: NKT Vbeta8.2 (MOUSE) - 2C12 TCR - hybrid mouse variable and human constant domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0578
Polymers96,2164
Non-polymers1,8414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Antigen-presenting glycoprotein CD1d1
F: Beta-2-microglobulin
G: NKT Valpha14 (MOUSE) - 2C12 TCR - Hybrid mouse variable and human constant domains
H: NKT Vbeta8.2 (MOUSE) - 2C12 TCR - hybrid mouse variable and human constant domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0578
Polymers96,2164
Non-polymers1,8414
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.666, 150.318, 100.144
Angle α, β, γ (deg.)90.00, 96.12, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Antigen-presenting glycoprotein CD1d1 / MCG3074 / isoform CRA_a


Mass: 34662.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, mCG_3074 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0R4J090, UniProt: P11609*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01887
#3: Protein NKT Valpha14 (MOUSE) - 2C12 TCR - Hybrid mouse variable and human constant domains / Human nkt tcr beta chain


Mass: 22779.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, HDCMA22P / Production host: Escherichia coli (E. coli)
#4: Protein NKT Vbeta8.2 (MOUSE) - 2C12 TCR - hybrid mouse variable and human constant domains


Mass: 27113.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

-
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.: 2
Source method: isolated from a genetically manipulated source
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 / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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

-
Non-polymers , 2 types, 174 molecules

#7: Chemical ChemComp-QWV / N-[(2S,3R)-3-hydroxy-1-{[6-O-(3-phenylpropanoyl)-alpha-D-galactopyranosyl]oxy}octadecan-2-yl]hexacosanamide


Mass: 974.482 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H107NO9
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 18-20% PEG3350 8% tacsimate pH 5.0 0.5% dioxane

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→83.01 Å / Num. obs: 71925 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 66.88 Å2 / Rpim(I) all: 0.049 / Net I/σ(I): 21.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 10545 / Rpim(I) all: 0.375 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QUZ

3quz


Resolution: 2.6→38.07 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.333 / SU Rfree Blow DPI: 0.224 / SU Rfree Cruickshank DPI: 0.233
RfactorNum. reflection% reflectionSelection details
Rfree0.214 3633 5.05 %RANDOM
Rwork0.181 ---
obs0.183 71877 99.8 %-
Displacement parametersBiso mean: 62.8 Å2
Baniso -1Baniso -2Baniso -3
1--8.3006 Å20 Å2-8.8768 Å2
2--7.9626 Å20 Å2
3---0.338 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: 1 / Resolution: 2.6→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12164 0 250 172 12586
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112788HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1217476HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5682SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2168HARMONIC5
X-RAY DIFFRACTIONt_it12788HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.34
X-RAY DIFFRACTIONt_other_torsion2.83
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1712SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13436SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2584 296 5.52 %
Rwork0.2174 5063 -
all0.2197 5359 -
obs--99.96 %
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)
11.8008-0.35790.3752.0587-0.54942.7847-0.1057-0.21370.08160.5177-0.0943-0.1981-0.08160.43920.2-0.0955-0.0390.0042-0.19510.0057-0.192323.1359-18.970733.4234
26.874-0.59870.09410.9841-1.32592.6278-0.27860.1777-0.01950.0368-0.2141-0.67320.011.08770.4927-0.29720.0242-0.09760.14340.1367-0.031343.8993-21.619927.9369
31.4008-0.19660.91611.0428-0.06651.69260.1064-0.1172-0.1971-0.34540.01930.22190.0235-0.1733-0.1258-0.0103-0.0133-0.0255-0.19180.02810.0759-22.9829-28.885-3.5566
41.6158-0.72861.39610.8465-0.2931.4390.13350.0779-0.1223-0.2948-0.08060.1668-0.11980.1129-0.05290.04560.03610.029-0.2040.0124-0.0894-14.2608-15.1571-14.0173
52.45340.1779-1.55751.4153-0.4172.40920.041-0.0213-0.02920.43790.06860.31110.0047-0.4336-0.1096-0.0555-0.03990.1371-0.16070.0678-0.166817.1198-59.192534.4325
68.08351.1381-1.20790.0022-0.3976-0.1152-0.09010.82650.55550.00170.38230.8712-0.1684-1.0061-0.2921-0.36170.15910.23010.31280.2749-0.0348-2.2639-55.734629.7721
71.5888-0.1985-1.26681.13920.36952.20540.0844-0.14950.1776-0.24890.0357-0.2147-0.14990.1796-0.1201-0.0486-0.03590.065-0.2244-0.02780.065363.6543-49.8519-4.0473
81.051-0.5901-1.10560.78230.2351.58340.12810.21170.1143-0.1915-0.1055-0.12730.0432-0.1628-0.02260.0033-0.02080.0306-0.1612-0.0278-0.037454.3022-63.242-14.2691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more