[English] 日本語
Yorodumi
- PDB-2z65: Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2z65
TitleCrystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex
Components
  • Lymphocyte antigen 96
  • Toll-like receptor 4, Variable lymphocyte receptor B
KeywordsIMMUNE SYSTEM / TLR4 / toll-like receptor / MD-2 / LPS / E5564 / eritoran / Glycoprotein / Immune response / Inflammatory response / Innate immunity / Leucine-rich repeat / Membrane / Transmembrane / Secreted
Function / homology
Function and homology information


nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / detection of fungus / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / lipopolysaccharide immune receptor activity / Toll-like receptor 4 binding / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / lipopolysaccharide receptor complex / positive regulation of matrix metallopeptidase secretion / detection of lipopolysaccharide ...nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / detection of fungus / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / lipopolysaccharide immune receptor activity / Toll-like receptor 4 binding / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / lipopolysaccharide receptor complex / positive regulation of matrix metallopeptidase secretion / detection of lipopolysaccharide / regulation of dendritic cell cytokine production / intestinal epithelial structure maintenance / MyD88-independent TLR4 cascade / TRIF-mediated programmed cell death / negative regulation of interleukin-23 production / I-kappaB phosphorylation / cellular response to oxidised low-density lipoprotein particle stimulus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / Caspase activation via Death Receptors in the presence of ligand / wound healing involved in inflammatory response / B cell proliferation involved in immune response / Toll Like Receptor 4 (TLR4) Cascade / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of interleukin-1 production / positive regulation of lipopolysaccharide-mediated signaling pathway / macrophage activation / Regulation of TLR by endogenous ligand / microglia differentiation / TRIF-dependent toll-like receptor signaling pathway / astrocyte development / positive regulation of macrophage activation / NAD+ nucleotidase, cyclic ADP-ribose generating / negative regulation of interleukin-17 production / positive regulation of cytokine production involved in inflammatory response / NADP+ nucleosidase activity / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of MHC class II biosynthetic process / positive regulation of platelet activation / positive regulation of chemokine (C-X-C motif) ligand 2 production / MyD88 deficiency (TLR2/4) / positive regulation of extrinsic apoptotic signaling pathway / negative regulation of cold-induced thermogenesis / positive regulation of macrophage cytokine production / MyD88-dependent toll-like receptor signaling pathway / positive regulation of reactive oxygen species biosynthetic process / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / phagocytic cup / T-helper 1 type immune response / cellular response to platelet-derived growth factor stimulus / positive regulation of smooth muscle cell migration / negative regulation of osteoclast differentiation / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of interferon-alpha production / cellular response to lipoteichoic acid / negative regulation of interleukin-6 production / positive regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / cellular defense response / coreceptor activity / phagocytosis / positive regulation of B cell proliferation / positive regulation of chemokine production / JNK cascade / lipopolysaccharide-mediated signaling pathway / ERK1 and ERK2 cascade / ruffle / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / nitric oxide biosynthetic process / TRAF6-mediated induction of TAK1 complex within TLR4 complex / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / lipopolysaccharide binding / positive regulation of JNK cascade / positive regulation of smooth muscle cell proliferation / Heme signaling / positive regulation of MAP kinase activity / negative regulation of ERK1 and ERK2 cascade / positive regulation of inflammatory response / cellular response to type II interferon / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / cellular response to amyloid-beta / positive regulation of nitric oxide biosynthetic process / transmembrane signaling receptor activity / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / signaling receptor activity / gene expression / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding
Similarity search - Function
Lymphocyte antigen 96 / Immunoglobulin-like - #770 / ML domain / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / 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 4 ...Lymphocyte antigen 96 / Immunoglobulin-like - #770 / ML domain / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / 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 4 / Leucine-rich repeat N-terminal domain / Leucine Rich repeats (2 copies) / Leucine rich repeat N-terminal domain / Leucine Rich repeat / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Alpha-Beta Horseshoe / 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
Chem-E55 / Toll-like receptor 4 / Variable lymphocyte receptor B / Lymphocyte antigen 96
Similarity search - Component
Biological speciesHomo sapiens (human)
Eptatretus burgeri (inshore hagfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLee, J.-O. / Kim, H.M. / Park, B.S.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Crystal Structure of the TLR4-MD-2 Complex with Bound Endotoxin Antagonist Eritoran
Authors: Kim, H.M. / Park, B.S. / Kim, J.-I. / Kim, S.E. / Lee, J. / Oh, S.C. / Enkhbayar, P. / Matsushima, N. / Lee, H. / Yoo, O.J. / Lee, J.-O.
History
DepositionJul 22, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 9, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Toll-like receptor 4, Variable lymphocyte receptor B
B: Toll-like receptor 4, Variable lymphocyte receptor B
C: Lymphocyte antigen 96
D: Lymphocyte antigen 96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,97312
Polymers94,6534
Non-polymers4,3208
Water2,936163
1
A: Toll-like receptor 4, Variable lymphocyte receptor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1714
Polymers31,1421
Non-polymers1,0293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Toll-like receptor 4, Variable lymphocyte receptor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8054
Polymers31,1421
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Lymphocyte antigen 96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4982
Polymers16,1851
Non-polymers1,3141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Lymphocyte antigen 96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4982
Polymers16,1851
Non-polymers1,3141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.192, 80.987, 107.762
Angle α, β, γ (deg.)90.00, 93.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13C
23D
14C
24D

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUPROPROAA27 - 3021 - 276
21GLUGLUPROPROBB27 - 3021 - 276
12GLNGLNGLYGLYCC19 - 1231 - 105
22GLNGLNGLYGLYDD19 - 1231 - 105
13LYSLYSASNASNCC128 - 158110 - 140
23LYSLYSASNASNDD128 - 158110 - 140
14E55E55E55E55CK1
24E55E55E55E55DL1

NCS ensembles :
ID
1
2
3
4
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein Toll-like receptor 4, Variable lymphocyte receptor B / / E5564, commercial name eritoran / hToll / CD284 antigen(human)


Mass: 31141.719 Da / Num. of mol.: 2
Fragment: TV3, UNP residues 27-228(human), E5564, UNP residues 19-158(Inshore hagfish)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Eptatretus burgeri (inshore hagfish)
Gene: TLR4, VLRB.61 / Plasmid: pVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi-5 / References: UniProt: O00206, UniProt: Q4G1L2
#2: Protein Lymphocyte antigen 96 / / MD-2 protein / ESOP-1


Mass: 16184.761 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MD-2 / Plasmid: pVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi-5 / References: UniProt: Q9Y6Y9

-
Sugars , 2 types, 6 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}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 / N-Acetylglucosamine


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 , 2 types, 165 molecules

#5: Chemical ChemComp-E55 / 3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)-3-METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC-11-ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}-2-[(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE / E5564 / ERITORAN / Eritoran


Mass: 1313.656 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C66H126N2O19P2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsPOLYSACCHARIDES WERE ORIGINALLY ASSIGNED TO CHAINS M1401, M(1301-1304), M1201, N1401, N1301, AND ...POLYSACCHARIDES WERE ORIGINALLY ASSIGNED TO CHAINS M1401, M(1301-1304), M1201, N1401, N1301, AND N1201, RESPECTIVELY.
Sequence detailsTHIS CONSTRUCT INCLUDES A LINKER THAT CONSIST OF 229TH LYS AND 230TH GLU.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 4.5
Details: 0.2M Ammonium Sulfate, 0.1M Sodium Acetate, 20% PEG 4000, 5% Ethanol, pH 4.5, VAPOR DIFFUSION, temperature 296K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2007 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 30860 / Num. obs: 27898 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.089

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z62, 2Z64
Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.864 / SU B: 33.68 / SU ML: 0.35 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.414 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28874 1462 5 %RANDOM
Rwork0.23763 ---
obs0.2403 27898 92.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.542 Å2
Baniso -1Baniso -2Baniso -3
1-2.91 Å20 Å2-1.93 Å2
2---2.26 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6646 0 287 163 7096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227101
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3932.0239614
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5845828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.44224.899298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.508151222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7371526
X-RAY DIFFRACTIONr_chiral_restr0.0870.21100
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025132
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.23101
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.24715
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2242
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.2110
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6581.54282
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.22826788
X-RAY DIFFRACTIONr_scbond_it6.76933129
X-RAY DIFFRACTIONr_scangle_it9.9054.52826
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2189tight positional0.050.05
21C855tight positional0.030.05
31C245tight positional0.040.05
42A89tight positional0.040.05
11A2189tight thermal0.830.5
21C855tight thermal0.750.5
31C245tight thermal0.750.5
42A89tight thermal1.360.5
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 81 -
Rwork0.331 1582 -
obs--74.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.649-0.0828-0.29611.2047-1.30796.05210.0597-0.102-0.16460.18470.06870.01390.3559-0.2484-0.1284-0.09930.05510.0214-0.12950.0065-0.104822.63325.14132.1018
24.52340.97920.60256.68850.10963.47970.1359-0.066-0.11060.3325-0.0328-0.8884-0.06410.432-0.10310.08340.0835-0.08580.0066-0.0398-0.101546.627323.901839.4335
35.0762-1.32562.53331.6285-0.73812.4088-0.13-0.23850.29970.22730.02920.2098-0.2603-0.12780.1008-0.18870.03740.1019-0.16850.0053-0.106414.0299-32.191818.2252
42.96850.1268-0.60076.73941.256.4958-0.10250.1087-0.1935-0.79510.1712-0.2592-0.03250.225-0.0687-0.2172-0.02820.0236-0.17260.0367-0.049620.0682-50.623-6.462
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA27 - 3021 - 276
2X-RAY DIFFRACTION2CC19 - 1581 - 140
3X-RAY DIFFRACTION3BB27 - 3021 - 276
4X-RAY DIFFRACTION4DD19 - 1581 - 140

+
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