[English] 日本語
Yorodumi
- PDB-5ijd: The crystal structure of mouse TLR4/MD-2/lipid A complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ijd
TitleThe crystal structure of mouse TLR4/MD-2/lipid A complex
Components
  • Lymphocyte antigen 96
  • Toll-like receptor 4, Variable lymphocyte receptor B chimera
KeywordsIMMUNE SYSTEM / immune response / protein complex / natural agonist
Function / homology
Function and homology information


MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / Toll Like Receptor 4 (TLR4) Cascade / Heme signaling / nitric oxide production involved in inflammatory response / Regulation of TLR by endogenous ligand / growth plate cartilage morphogenesis / TRIF-mediated programmed cell death / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / NK T cell activation ...MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / Toll Like Receptor 4 (TLR4) Cascade / Heme signaling / nitric oxide production involved in inflammatory response / Regulation of TLR by endogenous ligand / growth plate cartilage morphogenesis / TRIF-mediated programmed cell death / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / NK T cell activation / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / lipopolysaccharide immune receptor activity / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Toll-like receptor 4 binding / positive regulation of matrix metallopeptidase secretion / mast cell activation / detection of lipopolysaccharide / regulation of dendritic cell cytokine production / innate immune response-activating signaling pathway / IKK complex recruitment mediated by RIP1 / lipopolysaccharide receptor complex / positive regulation of lymphocyte proliferation / negative regulation of interleukin-23 production / cellular response to oxidised low-density lipoprotein particle stimulus / wound healing involved in inflammatory response / regulation of toll-like receptor 4 signaling pathway / B cell proliferation involved in immune response / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of stress-activated MAPK cascade / leukotriene metabolic process / activation of NF-kappaB-inducing kinase activity / positive regulation of interleukin-1 production / TRIF-dependent toll-like receptor signaling pathway / positive regulation of interleukin-13 production / response to fatty acid / intestinal epithelial structure maintenance / macrophage activation / astrocyte development / microglia differentiation / regulation of tumor necrosis factor production / positive regulation of MHC class II biosynthetic process / positive regulation of platelet activation / signal transduction involved in regulation of gene expression / negative regulation of interleukin-17 production / positive regulation of macrophage activation / positive regulation of lipopolysaccharide-mediated signaling pathway / bone morphogenesis / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of cytokine production involved in inflammatory response / negative regulation of cold-induced thermogenesis / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of macrophage cytokine production / MyD88-dependent toll-like receptor signaling pathway / toll-like receptor 4 signaling pathway / positive regulation of smooth muscle cell migration / toll-like receptor signaling pathway / cellular response to lipoteichoic acid / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of type II interferon production / detection of temperature stimulus involved in sensory perception of pain / positive regulation of reactive oxygen species biosynthetic process / negative regulation of interleukin-6 production / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / phagocytosis / detection of mechanical stimulus involved in sensory perception of pain / phosphatidylinositol 3-kinase binding / phagocytic cup / positive regulation of B cell proliferation / ERK1 and ERK2 cascade / cellular response to platelet-derived growth factor stimulus / positive regulation of chemokine production / ruffle / positive regulation of interleukin-12 production / canonical NF-kappaB signal transduction / negative regulation of cytokine production involved in inflammatory response / activation of innate immune response / neurogenesis / positive regulation of interferon-beta production / positive regulation of smooth muscle cell proliferation / lipopolysaccharide-mediated signaling pathway / : / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / response to bacterium / lipopolysaccharide binding / cellular response to mechanical stimulus / microglial cell activation / negative regulation of ERK1 and ERK2 cascade / positive regulation of interleukin-6 production / positive regulation of JNK cascade / cellular response to type II interferon / positive regulation of type II interferon production / cellular response to amyloid-beta / positive regulation of nitric oxide biosynthetic process / positive regulation of tumor necrosis factor production
Similarity search - Function
Lymphocyte antigen 96 / Immunoglobulin-like - #770 / Variable lymphocyte receptor, C-terminal / : / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Toll-like receptor / : / Leucine rich repeat N-terminal domain ...Lymphocyte antigen 96 / Immunoglobulin-like - #770 / Variable lymphocyte receptor, C-terminal / : / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Toll-like receptor / : / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. / Alpha-Beta Horseshoe / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
LAURIC ACID / Chem-LP4 / Chem-LP5 / MYRISTIC ACID / Variable lymphocyte receptor B / Lymphocyte antigen 96 / Toll-like receptor 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Eptatretus burgeri (inshore hagfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWang, Y. / Su, L. / Morin, M.D. / Jones, B.T. / Whitby, L.R. / Surakattula, M. / Huang, H. / Shi, H. / Choi, J.H. / Wang, K. ...Wang, Y. / Su, L. / Morin, M.D. / Jones, B.T. / Whitby, L.R. / Surakattula, M. / Huang, H. / Shi, H. / Choi, J.H. / Wang, K. / Moresco, E.M. / Berger, M. / Zhan, X. / Zhang, H. / Boger, D.L. / Beutler, B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: TLR4/MD-2 activation by a synthetic agonist with no similarity to LPS.
Authors: Wang, Y. / Su, L. / Morin, M.D. / Jones, B.T. / Whitby, L.R. / Surakattula, M.M. / Huang, H. / Shi, H. / Choi, J.H. / Wang, K.W. / Moresco, E.M. / Berger, M. / Zhan, X. / Zhang, H. / Boger, D.L. / Beutler, B.
History
DepositionMar 1, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionApr 27, 2016ID: 5HG6
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / database_PDB_caveat / 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_struct_mod_residue / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / 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 / _citation.journal_id_CSD / _database_PDB_caveat.text / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _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 2.1Apr 3, 2024Group: 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
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: Toll-like receptor 4, Variable lymphocyte receptor B chimera
C: Lymphocyte antigen 96
D: Lymphocyte antigen 96
B: Toll-like receptor 4, Variable lymphocyte receptor B chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,12924
Polymers169,3474
Non-polymers7,78220
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20200 Å2
ΔGint48 kcal/mol
Surface area60170 Å2
MethodPISA
2
A: Toll-like receptor 4, Variable lymphocyte receptor B chimera
C: Lymphocyte antigen 96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,46312
Polymers84,6732
Non-polymers3,78910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint33 kcal/mol
Surface area31790 Å2
MethodPISA
3
D: Lymphocyte antigen 96
B: Toll-like receptor 4, Variable lymphocyte receptor B chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,66612
Polymers84,6732
Non-polymers3,99210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint33 kcal/mol
Surface area31800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.843, 145.737, 136.195
Angle α, β, γ (deg.)90.00, 100.67, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein Toll-like receptor 4, Variable lymphocyte receptor B chimera


Mass: 67280.703 Da / Num. of mol.: 2
Fragment: TLR4 ectodomain (UNP residues 26-544) + VLRB (UNP residues 126-200)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Eptatretus burgeri (inshore hagfish)
Gene: Tlr4, Lps, VLRB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9QUK6, UniProt: Q4G1L2
#2: Protein Lymphocyte antigen 96 / Ly-96 / ESOP-1 / Protein MD-2


Mass: 17392.793 Da / Num. of mol.: 2 / Fragment: UNP residues 19-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ly96, Esop1, Md2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9JHF9

-
Sugars , 2 types, 12 molecules

#3: 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.: 7
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)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 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.: 5
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 , 5 types, 240 molecules

#5: Chemical ChemComp-LP4 / 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose


Mass: 711.861 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H66NO12P
#6: Chemical ChemComp-LP5 / (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE


Mass: 711.861 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H66NO12P
#7: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
#8: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 3.93 Å3/Da / Density % sol: 68.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris, pH 8.0, 0.2 M lithium chloride, 14% PEG8000, 2.5% PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 54848 / % possible obs: 96.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.058 / Net I/av σ(I): 22.386 / Net I/σ(I): 8.3
Reflection shellResolution: 2.7→2.75 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5IJD

5ijd


Resolution: 2.7→39.34 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.842 / SU B: 14.782 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 1.232 / ESU R Free: 0.41 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28534 1978 3.6 %RANDOM
Rwork0.21476 ---
obs0.21727 52860 77.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.652 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20.82 Å2
2--0.21 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.7→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11903 0 242 232 12377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01912451
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211856
X-RAY DIFFRACTIONr_angle_refined_deg1.82.00116846
X-RAY DIFFRACTIONr_angle_other_deg2.739327316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.78251454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60624.716545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.137152110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.011545
X-RAY DIFFRACTIONr_chiral_restr0.0920.21944
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213565
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022822
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8144.1975822
X-RAY DIFFRACTIONr_mcbond_other2.8134.1975821
X-RAY DIFFRACTIONr_mcangle_it4.7036.2867271
X-RAY DIFFRACTIONr_mcangle_other4.7036.2877272
X-RAY DIFFRACTIONr_scbond_it2.7954.6396629
X-RAY DIFFRACTIONr_scbond_other2.7944.6396630
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8086.8619575
X-RAY DIFFRACTIONr_long_range_B_refined8.01634.58514190
X-RAY DIFFRACTIONr_long_range_B_other8.00934.61114161
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.691→2.761 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 53 -
Rwork0.328 1411 -
obs--27.92 %

+
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