[English] 日本語
Yorodumi
- PDB-1lk2: 1.35A crystal structure of H-2Kb complexed with the GNYSFYAL peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lk2
Title1.35A crystal structure of H-2Kb complexed with the GNYSFYAL peptide
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN
  • INSULIN RECEPTOR, BETA-SUBUNIT
KeywordsIMMUNE SYSTEM / Class I MHC-peptide complex / high resolution / anisotropic and TLS refinement
Function / homology
Function and homology information


Signaling by Insulin receptor / Insulin receptor recycling / yolk / IRS activation / Insulin receptor signalling cascade / Signal attenuation / 3-phosphoinositide-dependent protein kinase binding / positive regulation of glycoprotein biosynthetic process / lipoic acid binding / regulation of hydrogen peroxide metabolic process ...Signaling by Insulin receptor / Insulin receptor recycling / yolk / IRS activation / Insulin receptor signalling cascade / Signal attenuation / 3-phosphoinositide-dependent protein kinase binding / positive regulation of glycoprotein biosynthetic process / lipoic acid binding / regulation of hydrogen peroxide metabolic process / regulation of female gonad development / positive regulation of meiotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of developmental growth / insulin-like growth factor II binding / male sex determination / exocrine pancreas development / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / TAP1 binding / TAP2 binding / nuclear lumen / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of protein-containing complex disassembly / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / cargo receptor activity / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / dendritic spine maintenance / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / insulin binding / PTB domain binding / neuronal cell body membrane / positive regulation of interleukin-13 production / adrenal gland development / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / negative regulation of feeding behavior / amyloid-beta clearance / inner ear development / positive regulation of respiratory burst / positive regulation of natural killer cell proliferation / regulation of embryonic development / positive regulation of receptor internalization / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / insulin receptor substrate binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / epidermis development / positive regulation of glycogen biosynthetic process / MHC class I protein binding / response to tumor necrosis factor / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / phosphatidylinositol 3-kinase binding / heart morphogenesis / TAP binding / positive regulation of phosphorylation / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / dendrite membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / insulin-like growth factor receptor binding / receptor-mediated endocytosis / neuron projection maintenance / detection of bacterium / Neutrophil degranulation / T cell receptor binding / positive regulation of glycolytic process / response to nutrient levels / positive regulation of mitotic nuclear division / 14-3-3 protein binding / negative regulation of protein phosphorylation / caveola
Similarity search - Function
Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain ...Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Growth factor receptor cysteine-rich domain superfamily / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Fibronectin type III domain / MHC class I alpha chain, alpha1 alpha2 domains / Fibronectin type 3 domain / Class I Histocompatibility antigen, domains alpha 1 and 2 / Fibronectin type-III domain profile. / Beta-2-Microglobulin / Fibronectin type III / MHC class I-like antigen recognition-like / Fibronectin type III superfamily / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Tyrosine-protein kinase, active site / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain / Insulin receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsLuz, J.G. / Rudolph, M.G. / Wilson, I.A. / Eisen, H.
CitationJournal: J.Immunol. / Year: 2004
Title: A peptide that antagonizes TCR-mediated reactions with both syngeneic and allogeneic agonists: functional and structural aspects.
Authors: Rudolph, M.G. / Shen, L.Q. / Lamontagne, S.A. / Luz, J.G. / Delaney, J.R. / Ge, Q. / Cho, B.K. / Palliser, D. / McKinley, C.A. / Chen, J. / Wilson, I.A. / Eisen, H.N.
History
DepositionApr 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / 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.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN
B: Beta-2-microglobulin
P: INSULIN RECEPTOR, BETA-SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3259
Polymers44,2873
Non-polymers1,0386
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-36 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.549, 87.650, 45.118
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN / MHC CLASS I H-2KB HEAVY CHAIN


Mass: 31648.322 Da / Num. of mol.: 1
Fragment: EXTRACELLULAR DOMAIN, SEQUENCE DATABASE RESIDUES 22-295, NUMBERED 1-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01901
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11704.359 Da / Num. of mol.: 1 / Fragment: SEQUENCE DATABASE RESIDUES 21-119, NUMBERED 1-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01887

-
Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide INSULIN RECEPTOR, BETA-SUBUNIT / / GNYSFYAL peptide


Mass: 934.005 Da / Num. of mol.: 1 / Fragment: sequence database residues 423-430, numbered 1-8 / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS FOUND NATURALLY IN MUS MUSCULUS.
References: UniProt: P15208

-
Sugars , 2 types, 2 molecules

#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
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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 , 4 types, 391 molecules

#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 3.02 Å3/Da / Density % sol: 59.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: K/Na-Phosphate, MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Details: Stura, E.A., (1992) J. Mol. Biol., 228, 975.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 13, 2000 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: single crystal Si(311) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 117515 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 16.5 Å2 / Rsym value: 0.053 / Net I/σ(I): 23.95
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.13 / Num. unique all: 5606 / Rsym value: 0.813 / % possible all: 95.3
Reflection
*PLUS
Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 95.3 % / Num. unique obs: 5606 / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 1.1

-
Processing

Software
NameVersionClassification
REFMAC5refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→18.35 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.001 / SU ML: 0.041 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.047 / ESU R Free: 0.043 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1639 5552 5 %RANDOM
Rwork0.14949 ---
obs0.15023 104434 93.64 %-
all-109986 --
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: 9.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.35→18.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3119 0 67 387 3573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213342
X-RAY DIFFRACTIONr_bond_other_d0.0010.022916
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9594548
X-RAY DIFFRACTIONr_angle_other_deg1.1936797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6383378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.93415606
X-RAY DIFFRACTIONr_chiral_restr0.1660.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023618
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02692
X-RAY DIFFRACTIONr_nbd_refined0.2180.3582
X-RAY DIFFRACTIONr_nbd_other0.2010.32755
X-RAY DIFFRACTIONr_nbtor_other0.5660.54
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.5370
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.352
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.522
X-RAY DIFFRACTIONr_symmetry_hbond_other0.1280.51
X-RAY DIFFRACTIONr_mcbond_it1.1241.51916
X-RAY DIFFRACTIONr_mcangle_it1.69123118
X-RAY DIFFRACTIONr_scbond_it2.75531426
X-RAY DIFFRACTIONr_scangle_it4.0434.51430
X-RAY DIFFRACTIONr_rigid_bond_restr1.16323342
X-RAY DIFFRACTIONr_sphericity_free20.989387
X-RAY DIFFRACTIONr_sphericity_bonded3.5873249
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 357
Rwork0.261 6364
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)
111.35920.96833.56831.29990.38972.0030.02670.191-0.3310.00110.0149-0.08010.07770.0987-0.04150.06550.0070.0110.04290.00780.015748.367147.6778-0.57
215.2112.32483.12923.65281.35492.79380.1625-0.2456-0.14020.2304-0.07180.5526-0.0233-0.3899-0.09070.0958-0.00860.01210.14050.00380.147725.609446.8227-3.3321
313.1154-3.9882.89421.5264-1.39831.6037-0.0185-0.1284-0.10690.04120.00070.066-0.0083-0.08290.01790.063-0.00280.01170.0314-0.01070.010942.95548.06032.7054
412.137-2.3825-5.8672.7053-0.89696.8109-0.238-0.1885-0.38-0.00760.0235-0.19330.32410.14140.21450.0756-0.00620.0030.0304-0.00330.02849.728946.14437.3466
519.45941.11316.53332.99153.03337.7910.1616-0.4183-0.590.34460.04730.20170.3621-0.3102-0.20890.08040.00420.00890.07820.00550.030837.316449.11536.6088
68.4306-0.48165.34462.0936-0.4067.10990.0094-0.62650.04180.13230.03320.30890.0692-0.816-0.04260.1088-0.0040.02940.13540.00180.065537.788450.625411.2805
72.5238-0.29982.01415.4545-0.50425.8905-0.0118-0.07560.11780.09520.0683-0.1948-0.2410.2202-0.05650.0828-0.00250.00160.0797-0.00980.048849.80553.915815.5799
82.34580.46133.68920.75071.754610.0158-0.1-0.09460.08-0.0316-0.03840.1133-0.226-0.32240.13840.08880.00820.00610.04180.00990.064535.899556.7535-2.7568
95.3931-0.09053.31284.1721-5.232616.65530.07820.1817-0.1463-0.27660.33040.7136-0.0095-1.2758-0.40860.12270.0031-0.05280.1891-0.00990.178126.765545.7639-15.134
1017.6744.40586.36961.88781.52162.594-0.05430.01570.2513-0.0268-0.0748-0.0289-0.07780.0510.12910.0699-0.00470.01240.06470.01370.012248.113849.3361-5.2211
1114.68130.499711.69732.90261.247323.15970.19020.6297-0.2621-0.16660.0394-0.4774-0.02390.4316-0.22970.07260.00060.02180.11280.02090.115663.666252.9449-2.347
1215.94858.10434.87044.34472.83153.42850.00960.0393-0.3056-0.12780.0043-0.1337-0.01820.181-0.01390.08620.00170.00370.06020.01940.006445.644549.1877-10.7195
135.89142.1962-2.65732.6364-2.64974.7154-0.00050.1639-0.329-0.2783-0.03450.00160.2708-0.0570.03490.09920.0036-0.01060.0806-0.01080.013641.220546.2189-15.7451
1424.763214.79635.584314.552512.909913.01210.0888-0.7249-0.2348-0.24580.0856-0.3725-0.3021-0.0536-0.17440.08470.00430.00420.11580.02380.012250.57452.8323-13.8448
1513.69353.448412.369910.63774.240121.0918-0.29050.03020.2273-0.42740.1842-0.382-0.41580.84780.10630.1096-0.03250.0290.1723-0.00380.061954.596255.851-15.6014
162.94663.85053.94928.592.0695.33410.01010.23-0.3828-0.02270.0711-0.01660.1490.1606-0.08120.1230.00990.01350.0721-0.00990.018245.266548.8651-21.2958
174.33451.88491.01069.30373.47576.2402-0.08410.14560.1697-0.30870.03320.0224-0.22410.07680.05090.08750.02210.00580.06420.01290.026442.243557.7668-20.906
187.0821-1.30391.37065.5865-3.556510.60770.00730.50090.0482-0.2504-0.2608-0.3111-0.01410.50470.25350.08570.00230.00790.09530.01860.070651.841161.0634-8.4763
194.3789-0.10780.29492.4681-2.92978.5-0.0234-0.03120.29340.0955-0.045-0.0048-0.29190.15630.06840.0548-0.0088-0.00760.0385-0.00860.071456.272156.54766.8126
205.9426-0.06031.326817.79155.227319.2064-0.1145-0.1265-0.17990.2764-0.02740.22290.166-0.17190.14190.06490.01120.00270.0775-0.0010.102757.665446.873113.9445
21-0.1701-4.02771.694934.08614.9199-0.167-0.0883-0.1293-0.03780.26850.0979-0.57460.01950.0233-0.00950.0941-0.0060.01930.1241-0.01130.146360.749136.281413.2303
2216.624122.11129.509337.016316.19126.60740.1386-0.1947-0.34190.4508-0.2748-0.21210.2916-0.19920.13620.1562-0.00040.01980.08980.04350.173855.182114.3188.3217
2361.2126-2.0544-10.921217.7263.1588.7901-0.09462.7663-1.9406-1.967-0.0145-0.41450.0212-0.94510.10920.4498-0.06470.09380.2913-0.09960.266551.56974.6139-2.5922
242.03241.7504-0.33518.62228.56734.7897-0.07480.0694-0.28760.17350.0363-0.17440.2417-0.00090.03850.09730.01230.00950.06720.02520.133854.915317.73995.8145
255.377-0.6584-2.40835.86853.66464.64180.23470.16120.2611-0.33430.0982-0.2597-0.3840.1076-0.33290.0674-0.00440.03790.06520.00670.123758.728633.96046.286
266.67872.93430.200617.47150.42271.3965-0.16960.1668-0.2586-0.79770.1625-0.77810.00630.29950.00710.1633-0.00780.06820.134-0.03260.200863.391418.8837-0.3456
274.45480.94690.58215.01551.31944.56650.08140.6448-0.5518-0.56720.1508-0.64480.34930.475-0.23220.16860.0530.04880.1744-0.05050.208356.08325.26640.3784
281.6443-0.4014-0.348611.40743.49392.1052-0.07020.1867-0.3557-0.378-0.0001-0.28610.1437-0.01820.07030.13380.01420.04780.0745-0.01290.154955.505417.93950.9912
2919.105111.83084.057938.43272.59838.0519-0.10470.0443-2.09010.44810.0179-1.04630.81110.19450.08680.27910.05780.08620.1205-0.00810.591660.72384.22191.8697
3024.7543-4.4749-7.93646.2389-35.946253.544-0.1929-0.2593-1.8828-1.0329-0.5464-1.92622.40621.29370.73930.28780.12430.02310.1457-0.04670.667267.10157.37082.7442
312.88685.0264-0.099722.17763.1182-0.5214-0.15840.028-0.6766-0.4410.0789-0.56280.070.19940.07950.11130.01730.04770.1071-0.01040.260465.155420.46412.9404
3213.7686-3.87351.502-0.2065-0.30884.4745-0.0129-0.4591-0.03810.20940.1809-0.2337-0.05720.2649-0.1680.0859-0.02330.02730.1488-0.03570.159267.620630.22298.8118
3365.126162.03919.622681.1282-0.45859.05871.0435-0.7136-2.52230.879-0.5073-2.24680.8089-0.5429-0.53620.2108-0.001-0.0410.19320.06490.34564.214.81728.1216
3421.5112-9.377119.992916.4632-11.310353.48790.22271.44140.5015-0.7348-0.7269-0.1437-0.59540.62090.50420.24890.0008-0.02720.1404-0.00120.128437.467730.9399-8.3001
355.09070.61634.57632.67460.78457.55470.06640.0208-0.2117-0.16050.05230.10740.12370.0367-0.11870.07410.0090.00470.03090.00680.070942.767225.9586.5452
364.21973.072-3.96185.5257-4.82715.07730.2514-0.7805-0.53830.5487-0.465-0.58050.04250.56070.21360.1642-0.0443-0.04340.20350.07220.132648.421724.442920.5049
372.5916-0.14963.11681.8127-3.525512.91210.079-0.0632-0.003-0.0302-0.02890.09450.2396-0.0325-0.05020.06350.00170.0070.0183-0.00390.062942.43230.30248.1633
384.55471.261-2.02744.7467-1.37718.62430.18980.20670.0578-0.12730.10460.4477-0.128-0.3463-0.29440.1184-0.0167-0.02510.04630.01580.098334.600735.3915-3.424
392.04042.9818-2.484514.828-16.670519.3622-0.0407-0.12260.1521-0.20750.16530.3460.0901-0.2776-0.12460.09560.00360.01720.0598-0.01210.113532.969928.183811.3986
409.459913.2048-6.135626.828-10.36474.32090.9392-0.43041.23411.554-0.40181.6965-0.62640.0039-0.53740.1874-0.02730.10340.1179-0.03920.200931.984730.89116.3435
4110.18124.4925-8.85822.4137-2.944712.16790.05710.11680.34810.10360.0620.777-0.3401-0.2762-0.11910.08910.00550.00130.0333-0.0060.090238.898538.46378.6205
421.29490.67921.1772.2939-2.022420.3214-0.05740.07310.017-0.1272-0.0847-0.0993-0.16360.60630.1420.0865-0.0098-0.00090.06030.00680.089544.072639.7013-4.9392
431.72130.38470.63524.1949-4.21839.74270.016-0.2333-0.01270.2605-0.06550.0688-0.32620.05160.04940.0461-0.00460.01390.0465-0.0020.081741.352933.150510.3892
447.56342.36785.62254.225-1.89638.76110.4184-0.5-0.53060.31-0.2419-0.29420.27920.0271-0.17650.1222-0.0299-0.00590.1350.03320.126338.799919.312719.8477
455.1884-6.95019.7716.4301-15.786823.93890.0047-0.4313-0.2101-0.36390.62080.86980.3089-1.1781-0.62540.0902-0.0198-0.00570.08980.02020.13331.015227.074.9477
46-0.19413.817-4.574418.3077-18.429425.0732-0.30360.2973-0.1314-1.02620.55540.54551.0661-0.4376-0.25180.2184-0.0718-0.07090.120.00730.17729.471726.7561-3.2265
477.4040.37.54482.1293-3.105513.95290.0943-0.0112-0.1413-0.5649-0.01720.13890.0530.007-0.07710.1525-0.006-0.00670.0314-0.01060.102935.121620.7356.3751
4815.4866-8.5976-5.97288.50056.0199-0.097-0.0878-0.2854-0.59110.0839-0.03690.08180.32570.4820.12470.1584-0.00210.01060.09050.03160.208444.610718.047211.8423
494.2572-0.44485.07730.3663-0.43288.04180.0499-0.00050.0216-0.0822-0.04120.0302-0.0026-0.1933-0.00870.08850.01260.0020.0691-0.00350.074941.870358.0917-6.9533
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 121 - 12
2X-RAY DIFFRACTION2AA13 - 2113 - 21
3X-RAY DIFFRACTION3AA22 - 2822 - 28
4X-RAY DIFFRACTION4AA28 - 3428 - 34
5X-RAY DIFFRACTION5AA34 - 3734 - 37
6X-RAY DIFFRACTION6AA37 - 5037 - 50
7X-RAY DIFFRACTION7AA50 - 5650 - 56
8X-RAY DIFFRACTION8AA57 - 8557 - 85
9X-RAY DIFFRACTION9AA85 - 9485 - 94
10X-RAY DIFFRACTION10AA94 - 10394 - 103
11X-RAY DIFFRACTION11AA103 - 111103 - 111
12X-RAY DIFFRACTION12AA111 - 118111 - 118
13X-RAY DIFFRACTION13AA118 - 124118 - 124
14X-RAY DIFFRACTION14AA124 - 126124 - 126
15X-RAY DIFFRACTION15AA126 - 133126 - 133
16X-RAY DIFFRACTION16AA133 - 137133 - 137
17X-RAY DIFFRACTION17AA138 - 151138 - 151
18X-RAY DIFFRACTION18AA152 - 162152 - 162
19X-RAY DIFFRACTION19AA163 - 175163 - 175
20X-RAY DIFFRACTION20AA176 - 179176 - 179
21X-RAY DIFFRACTION21AA179 - 186179 - 186
22X-RAY DIFFRACTION22AA186 - 193186 - 193
23X-RAY DIFFRACTION23AA193 - 198193 - 198
24X-RAY DIFFRACTION24AA198 - 206198 - 206
25X-RAY DIFFRACTION25AA206 - 214206 - 214
26X-RAY DIFFRACTION26AA214 - 219214 - 219
27X-RAY DIFFRACTION27AA219 - 241219 - 241
28X-RAY DIFFRACTION28AA241 - 250241 - 250
29X-RAY DIFFRACTION29AA250 - 254250 - 254
30X-RAY DIFFRACTION30AA254 - 256254 - 256
31X-RAY DIFFRACTION31AA257 - 262257 - 262
32X-RAY DIFFRACTION32AA262 - 270262 - 270
33X-RAY DIFFRACTION33AA270 - 274270 - 274
34X-RAY DIFFRACTION34BB1 - 61 - 6
35X-RAY DIFFRACTION35BB6 - 116 - 11
36X-RAY DIFFRACTION36BB11 - 2111 - 21
37X-RAY DIFFRACTION37BB21 - 2821 - 28
38X-RAY DIFFRACTION38BB28 - 3628 - 36
39X-RAY DIFFRACTION39BB36 - 4136 - 41
40X-RAY DIFFRACTION40BB41 - 5041 - 50
41X-RAY DIFFRACTION41BB50 - 5250 - 52
42X-RAY DIFFRACTION42BB52 - 6252 - 62
43X-RAY DIFFRACTION43BB62 - 7062 - 70
44X-RAY DIFFRACTION44BB70 - 7870 - 78
45X-RAY DIFFRACTION45BB78 - 8378 - 83
46X-RAY DIFFRACTION46BB83 - 9183 - 91
47X-RAY DIFFRACTION47BB91 - 9491 - 94
48X-RAY DIFFRACTION48BB94 - 9994 - 99
49X-RAY DIFFRACTION49PC1 - 81 - 8
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.164 / Rfactor Rwork: 0.149
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.19
LS refinement shell
*PLUS
Lowest resolution: 1.39 Å

+
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