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- PDB-7ndt: UL40:01 TCR in complex with HLA-E with a non-natural amino acid -

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Basic information

Entry
Database: PDB / ID: 7ndt
TitleUL40:01 TCR in complex with HLA-E with a non-natural amino acid
Components
  • (T cell receptor ...) x 2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, alpha chain E
  • UL40(15-23 H4C)
KeywordsIMMUNE SYSTEM / TCR-pHLA complex / non-natural amino acid
Function / homology
Function and homology information


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 natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation ...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 natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / alpha-beta T cell receptor complex / positive regulation of natural killer cell proliferation / positive regulation of immunoglobulin production / T cell receptor complex / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of interleukin-4 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / MHC class I protein binding / alpha-beta T cell activation / Generation of second messenger molecules / protection from natural killer cell mediated cytotoxicity / PD-1 signaling / beta-2-microglobulin binding / T cell receptor binding / negative regulation of T cell proliferation / immunoglobulin complex, circulating / immunoglobulin receptor 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 / DAP12 interactions / negative regulation of receptor binding / complement activation, classical pathway / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen binding / response to bacterium / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of tumor necrosis factor production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / Downstream TCR signaling / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding
Similarity search - Function
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain ...T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
T cell receptor alpha variable 26-1 / T cell receptor alpha joining 37 / T cell receptor beta joining 2-3 / T cell receptor beta variable 14 / T cell receptor beta constant 2 / T cell receptor alpha chain constant / HLA class I histocompatibility antigen, alpha chain E / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.999 Å
AuthorsPengelly, R.J. / Robinson, R.A.
CitationJournal: Eur.J.Immunol. / Year: 2022
Title: Structure-guided stabilization of pathogen-derived peptide-HLA-E complexes using non-natural amino acids conserves native TCR recognition.
Authors: Barber, C. / De Souza, V.A. / Paterson, R.L. / Martin-Urdiroz, M. / Mulakkal, N.C. / Srikannathasan, V. / Connolly, M. / Phillips, G. / Foong-Leong, T. / Pengelly, R. / Karuppiah, V. / ...Authors: Barber, C. / De Souza, V.A. / Paterson, R.L. / Martin-Urdiroz, M. / Mulakkal, N.C. / Srikannathasan, V. / Connolly, M. / Phillips, G. / Foong-Leong, T. / Pengelly, R. / Karuppiah, V. / Grant, T. / Dembek, M. / Verma, A. / Gibbs-Howe, D. / Blicher, T.H. / Knox, A. / Robinson, R.A. / Cole, D.K. / Leonard, S.
History
DepositionFeb 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_CSD / _citation.pdbx_database_id_DOI
Revision 2.0Feb 16, 2022Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / entity_src_gen / struct_conn
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_atom_id / _atom_site.label_atom_id / _atom_site.pdbx_formal_charge / _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_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.pdbx_synonyms / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.gene_src_common_name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Apr 20, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2Jul 27, 2022Group: Derived calculations / Category: atom_type / Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 2.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: HLA class I histocompatibility antigen, alpha chain E
BBB: Beta-2-microglobulin
CCC: UL40(15-23 H4C)
DDD: T cell receptor alpha variable 26-1,T cell receptor alpha joining 37,T cell receptor alpha chain constant
EEE: T cell receptor beta variable 14,T cell receptor beta joining 2-3,T cell receptor beta constant 2
FFF: HLA class I histocompatibility antigen, alpha chain E
GGG: Beta-2-microglobulin
HHH: UL40(15-23 H4C)
III: T cell receptor alpha variable 26-1,T cell receptor alpha joining 37,T cell receptor alpha chain constant
JJJ: T cell receptor beta variable 14,T cell receptor beta joining 2-3,T cell receptor beta constant 2


Theoretical massNumber of molelcules
Total (without water)188,92610
Polymers188,92610
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23000 Å2
ΔGint-85 kcal/mol
Surface area73460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.614, 76.577, 130.341
Angle α, β, γ (deg.)90.000, 107.639, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21FFF
32BBB
42GGG
53DDD
63III
74EEE
84JJJ

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERPROPROAAAA2 - 2803 - 277
221SERSERPROPROFFFF2 - 2813 - 277
332ILEILEMETMETBBBB1 - 992 - 100
442ILEILEMETMETGGGG1 - 992 - 100
553LYSLYSASNASNDDDD3 - 2064 - 190
663LYSLYSASNASNIIII3 - 2064 - 190
774GLYGLYALAALAEEEE3 - 2574 - 242
884GLYGLYALAALAJJJJ3 - 2574 - 242

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8

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Components

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Protein , 2 types, 4 molecules AAAFFFBBBGGG

#1: Protein HLA class I histocompatibility antigen, alpha chain E / MHC class I antigen E


Mass: 31911.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-E, HLA-6.2, HLAE / Production host: Escherichia coli (E. coli) / References: UniProt: P13747
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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T cell receptor ... , 2 types, 4 molecules DDDIIIEEEJJJ

#4: Protein T cell receptor alpha variable 26-1,T cell receptor alpha joining 37,T cell receptor alpha chain constant


Mass: 22012.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV26-1, TRAJ37, TRAC, TCRA / Production host: Escherichia coli (E. coli)
References: UniProt: A0A087WT03, UniProt: A0A087X096, UniProt: P01848
#5: Protein T cell receptor beta variable 14,T cell receptor beta joining 2-3,T cell receptor beta constant 2


Mass: 27613.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: TRBV14, TCRBV14S1, TCRBV16S1A1N1, TRBJ2-3, hCG_2039521, TRBC2, TCRBC2
Production host: Escherichia coli (E. coli)
References: UniProt: A0A5B0, UniProt: A0A0B4J200, UniProt: A0A5B9

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Protein/peptide / Non-polymers , 2 types, 5 molecules CCCHHH

#3: Protein/peptide UL40(15-23 H4C)


Mass: 1046.370 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 12% (w/v) PEG 8000, 55 mM MOPS pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.999→65.27 Å / Num. obs: 44666 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.064 / Net I/σ(I): 13.4
Reflection shellResolution: 2.999→3.05 Å / Rmerge(I) obs: 2.198 / Num. unique obs: 2218 / CC1/2: 0.134 / Rpim(I) all: 1.425

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ESV

2esv


Resolution: 2.999→65.27 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.186 / SU B: 69.637 / SU ML: 0.489 / Average fsc free: 0.7953 / Average fsc work: 0.8117 / Cross valid method: FREE R-VALUE / ESU R: 1.326 / ESU R Free: 0.455
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2694 2205 4.938 %
Rwork0.2212 42447 -
all0.224 --
obs-44652 99.904 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 68.634 Å2
Baniso -1Baniso -2Baniso -3
1--1.311 Å20 Å2-0.27 Å2
2--1.668 Å20 Å2
3----0.154 Å2
Refinement stepCycle: LAST / Resolution: 2.999→65.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13021 0 0 3 13024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01313375
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712004
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.65218178
X-RAY DIFFRACTIONr_angle_other_deg1.0641.58227698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.63851605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.36822.288778
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.177152179
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg0.051152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.181594
X-RAY DIFFRACTIONr_chiral_restr0.0450.21701
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215299
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023209
X-RAY DIFFRACTIONr_nbd_refined0.1940.22630
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.211888
X-RAY DIFFRACTIONr_nbtor_refined0.1620.26066
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.26995
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2315
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1360.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1420.223
X-RAY DIFFRACTIONr_nbd_other0.1570.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1530.27
X-RAY DIFFRACTIONr_ncsr_local_group_10.1190.058300
X-RAY DIFFRACTIONr_ncsr_local_group_20.1350.052892
X-RAY DIFFRACTIONr_ncsr_local_group_30.1430.055121
X-RAY DIFFRACTIONr_ncsr_local_group_40.1370.057064
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.119070.05009
12FFFX-RAY DIFFRACTIONLocal ncs0.119070.05009
23BBBX-RAY DIFFRACTIONLocal ncs0.13460.0501
24GGGX-RAY DIFFRACTIONLocal ncs0.13460.0501
35DDDX-RAY DIFFRACTIONLocal ncs0.143030.05009
36IIIX-RAY DIFFRACTIONLocal ncs0.143030.05009
47EEEX-RAY DIFFRACTIONLocal ncs0.137030.05009
48JJJX-RAY DIFFRACTIONLocal ncs0.137030.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.999-3.0770.3541690.3723087X-RAY DIFFRACTION99.4502
3.077-3.1620.3551620.3663035X-RAY DIFFRACTION100
3.162-3.2530.3831640.3542951X-RAY DIFFRACTION99.9679
3.253-3.3530.331460.3312890X-RAY DIFFRACTION100
3.353-3.4630.3321450.3112759X-RAY DIFFRACTION99.691
3.463-3.5850.3461430.2932710X-RAY DIFFRACTION100
3.585-3.720.2861440.2712552X-RAY DIFFRACTION100
3.72-3.8720.31380.2522530X-RAY DIFFRACTION100
3.872-4.0440.2651190.2312406X-RAY DIFFRACTION100
4.044-4.2410.2621180.2142313X-RAY DIFFRACTION99.9589
4.241-4.470.2371120.1982185X-RAY DIFFRACTION100
4.47-4.7410.2371000.1722073X-RAY DIFFRACTION99.9081
4.741-5.0670.278970.1721969X-RAY DIFFRACTION99.9516
5.067-5.4730.268880.1921837X-RAY DIFFRACTION100
5.473-5.9940.322780.2121669X-RAY DIFFRACTION100
5.994-6.6990.312780.2131536X-RAY DIFFRACTION100
6.699-7.7320.266700.2121375X-RAY DIFFRACTION99.9308
7.732-9.460.212660.1631131X-RAY DIFFRACTION99.8332
9.46-13.340.179380.149918X-RAY DIFFRACTION99.7912
13.34-65.270.183300.227521X-RAY DIFFRACTION98.9228
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)
12.23580.10210.79461.3306-0.53163.3949-0.1206-0.11990.06730.1128-0.02290.0264-0.08840.02530.14350.1388-0.0148-0.05240.02890.0710.2589-0.82527.657586.5431
22.92230.33180.14564.0589-2.24534.8106-0.0809-0.2524-0.36410.5403-0.1022-0.29790.37920.48020.1830.29540.1189-0.07510.36850.19220.21839.7684-3.604497.8214
312.8621-0.9394-1.660.8158-1.20592.57770.4626-0.54610.95770.0098-0.09320.0656-0.11220.284-0.36940.34640.012-0.04860.25590.02460.30571.87549.528368.0485
42.5627-0.52091.47220.5811-0.45045.1035-0.20830.5161-0.0205-0.4130.04230.1262-0.1035-0.78950.1660.5273-0.2328-0.18960.49680.06220.4883-9.001813.734831.8989
51.7408-0.32590.27221.25860.00723.2498-0.40210.9343-0.1813-0.57330.05020.06870.62631.0490.35190.6644-0.21470.00350.89320.15210.318210.06848.33229.7134
61.418-0.3494-1.2171.3276-0.28833.64820.08470.7481-0.0956-0.4860.1729-0.04150.0866-0.6145-0.25760.5485-0.2454-0.01180.5875-0.0170.460940.959635.8777-2.7107
75.52150.0442-2.07411.4087-1.09213.4-0.51290.5612-0.5436-0.45830.197-0.44910.356-0.01810.31590.5649-0.1930.13550.3613-0.17340.447460.084735.1607-3.4217
86.0249-1.99953.12223.6441-5.10547.18150.61150.17240.1152-0.667-0.11050.36220.90890.1597-0.5010.4179-0.1335-0.01250.3804-0.06630.362830.902837.170513.2454
93.7599-0.484-3.21941.2183-0.01283.25180.10750.22660.23190.0037-0.09610.0595-0.412-0.1343-0.01140.2922-0.0001-0.16210.19030.10930.32282.935147.951635.7381
102.881-0.2227-1.86380.68060.54671.7628-0.1848-0.77570.01760.11220.1846-0.0784-0.13360.61330.00020.32530.0099-0.12520.39930.19840.312416.355241.486649.2383
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA2 - 280
2X-RAY DIFFRACTION2ALLBBB1 - 99
3X-RAY DIFFRACTION3ALLCCC1 - 9
4X-RAY DIFFRACTION4ALLDDD3 - 209
5X-RAY DIFFRACTION5ALLEEE3 - 258
6X-RAY DIFFRACTION6ALLFFF2 - 281
7X-RAY DIFFRACTION7ALLGGG1 - 99
8X-RAY DIFFRACTION8ALLHHH1 - 9
9X-RAY DIFFRACTION9ALLIII2 - 207
10X-RAY DIFFRACTION10ALLJJJ2 - 258

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  • 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

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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

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