[English] 日本語
Yorodumi
- PDB-1xz0: Crystal structure of CD1a in complex with a synthetic mycobactin ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xz0
TitleCrystal structure of CD1a in complex with a synthetic mycobactin lipopeptide
Components
  • Beta-2-microglobulin
  • T-cell surface glycoprotein CD1a
KeywordsIMMUNE SYSTEM / beta sheet platform / MHC-fold / Protein-lipopeptide complex
Function / homology
Function and homology information


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 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 ...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 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 / 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 / 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 / ER to Golgi transport vesicle membrane / 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 / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / endosome membrane / immune response / membrane raft / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma 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 / identical protein binding / membrane / 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-JH0 / T-cell surface glycoprotein CD1a / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZajonc, D.M. / Crispin, M.D. / Bowden, T.A. / Young, D.C. / Cheng, T.Y. / Hu, J. / Costello, C.E. / Miller, M.J. / Moody, D.B. / Wilson, I.A.
CitationJournal: Immunity / Year: 2005
Title: Molecular Mechanism of Lipopeptide Presentation by CD1a.
Authors: Zajonc, D.M. / Crispin, M.D. / Bowden, T.A. / Young, D.C. / Cheng, T.Y. / Hu, J. / Costello, C.E. / Rudd, P.M. / Dwek, R.A. / Miller, M.J. / Brenner, M.B. / Moody, D.B. / Wilson, I.A.
History
DepositionNov 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_struct_assembly ...chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_biol / struct_conn / struct_ref_seq_dif
Item: _chem_comp.type / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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 2.1Aug 23, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T-cell surface glycoprotein CD1a
B: Beta-2-microglobulin
C: T-cell surface glycoprotein CD1a
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3078
Polymers87,2884
Non-polymers3,0194
Water34219
1
A: T-cell surface glycoprotein CD1a
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2554
Polymers43,6442
Non-polymers1,6112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-13 kcal/mol
Surface area19790 Å2
MethodPISA
2
C: T-cell surface glycoprotein CD1a
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0524
Polymers43,6442
Non-polymers1,4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-8 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.961, 43.235, 209.944
Angle α, β, γ (deg.)90.00, 91.04, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUTRPTRPAA8 - 2778 - 277
21LEULEUTRPTRPCC8 - 2778 - 277
12ILEILEASPASPBB1 - 981 - 98
22ILEILEASPASPDD1 - 981 - 98

NCS ensembles :
ID
1
2

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein T-cell surface glycoprotein CD1a / CD1a antigen / T-cell surface antigen T6/Leu-6 / hTa1 thymocyte antigen


Mass: 31895.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1A / Plasmid: pRMHa3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 cells / References: UniProt: P06126
#2: Protein Beta-2-microglobulin / HDCMA22P


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pRMHa3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 cells / References: UniProt: P61769

-
Sugars , 2 types, 2 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

-
Non-polymers , 2 types, 21 molecules

#5: Chemical ChemComp-JH0 / 6-(HYDROXY-HEXADECANOYL-AMINO)-2-{[(4S)-2-(2-HYDROXY-PHENYL)-4,5-DIHYDRO-OXAZOLE-4-CARBONYL]-AMINO}-HEXANOIC ACID 2-[(3S)-1-(TERT-BUTYL-DIPHENYL-SILANYLOXY)-2-OXO-AZEPAN-3-YLCARBAMOYL]-(1S)-1-METHYL-ETHYL ESTER


Mass: 1040.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C58H85N5O10Si
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 2000 MME, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 14, 2003
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 25373 / Num. obs: 23923 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.098 / Net I/σ(I): 14.6
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 2.2 / Num. unique all: 2205 / Rsym value: 0.444 / % possible all: 85.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1ONQ

1onq


Resolution: 2.8→38.63 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.878 / SU B: 37.508 / SU ML: 0.321 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.42 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27712 1157 4.8 %RANDOM
Rwork0.21699 ---
all0.21797 24273 --
obs0.21992 22766 94.29 %-
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 mean: 52.263 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0.04 Å2
2--0 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6029 0 161 19 6209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216394
X-RAY DIFFRACTIONr_bond_other_d0.0010.025481
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9328690
X-RAY DIFFRACTIONr_angle_other_deg0.857312769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3645733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57423.812320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.35915994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.91534
X-RAY DIFFRACTIONr_chiral_restr0.0840.2899
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027049
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021366
X-RAY DIFFRACTIONr_nbd_refined0.1910.2983
X-RAY DIFFRACTIONr_nbd_other0.1780.24800
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22860
X-RAY DIFFRACTIONr_nbtor_other0.0840.23542
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.254
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.180.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.22
X-RAY DIFFRACTIONr_mcbond_it0.31.53682
X-RAY DIFFRACTIONr_mcbond_other0.1091.51495
X-RAY DIFFRACTIONr_mcangle_it0.64525942
X-RAY DIFFRACTIONr_scbond_it1.10832976
X-RAY DIFFRACTIONr_scangle_it1.9234.52748
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1586tight positional0.040.05
2B579tight positional0.030.05
1A2538medium positional0.210.5
2B962medium positional0.190.5
1A1586tight thermal0.050.5
2B579tight thermal0.050.5
1A2538medium thermal0.282
2B962medium thermal0.342
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.562 71 -
Rwork0.409 1367 -
obs--78.02 %
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)
14.0312.68680.41766.86861.38420.33860.0030.2366-0.1337-0.2617-0.0026-0.45410.27290.1578-0.0004-0.3570.04440.0194-0.05460.0196-0.239823.3122-8.774971.7522
21.0922-0.2937-0.68321.33881.08643.8972-0.05130.17310.070.0471-0.01780.2336-0.2227-0.27440.0691-0.4748-0.0295-0.0115-0.23850.0396-0.13790.38147.036188.0063
33.6972-3.04650.30896.62260.83642.12560.0997-0.33560.14310.2090.0493-0.2585-0.04610.1833-0.1490.1049-0.03550.0248-0.0133-0.0107-0.238831.56039.909541.832
40.992-0.3186-0.70011.83710.94483.5946-0.1217-0.0213-0.1489-0.19360.01670.15210.294-0.360.1050.1981-0.0178-0.0334-0.1710.0353-0.188920.8904-5.985215.5774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 1817 - 181
2X-RAY DIFFRACTION1AE501 - 531
3X-RAY DIFFRACTION2AA182 - 277182 - 277
4X-RAY DIFFRACTION2BB1 - 981 - 98
5X-RAY DIFFRACTION3CC8 - 1818 - 181
6X-RAY DIFFRACTION3CF501 - 532
7X-RAY DIFFRACTION4CC182 - 277182 - 277
8X-RAY DIFFRACTION4DD1 - 981 - 98

+
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