[English] 日本語
Yorodumi
- PDB-5c08: 1E6 TCR in Complex with HLA-A0e carrying RQWGPDPAAV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c08
Title1E6 TCR in Complex with HLA-A0e carrying RQWGPDPAAV
Components
  • 1E6 TCR Alpha Chain
  • 1E6 TCR Beta Chain
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Marker peptide
KeywordsIMMUNE SYSTEM / IMMUNO / HLA-A02 / 1E6-TCR / Cross-reactivity
Function / homology
Function and homology information


T cell receptor complex / 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 / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / 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 ...T cell receptor complex / 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 / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / 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 / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / cell surface
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor alpha variable 12-3 / T cell receptor beta variable 12-4 / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.332 Å
AuthorsRizkallah, P.J. / Bulek, A.M. / Cole, D.K. / Sewell, A.K.
CitationJournal: J.Clin.Invest. / Year: 2016
Title: Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity.
Authors: Cole, D.K. / Bulek, A.M. / Dolton, G. / Schauenberg, A.J. / Szomolay, B. / Rittase, W. / Trimby, A. / Jothikumar, P. / Fuller, A. / Skowera, A. / Rossjohn, J. / Zhu, C. / Miles, J.J. / ...Authors: Cole, D.K. / Bulek, A.M. / Dolton, G. / Schauenberg, A.J. / Szomolay, B. / Rittase, W. / Trimby, A. / Jothikumar, P. / Fuller, A. / Skowera, A. / Rossjohn, J. / Zhu, C. / Miles, J.J. / Peakman, M. / Wooldridge, L. / Rizkallah, P.J. / Sewell, A.K.
History
DepositionJun 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Marker peptide
D: 1E6 TCR Alpha Chain
E: 1E6 TCR Beta Chain
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Marker peptide
I: 1E6 TCR Alpha Chain
J: 1E6 TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,02645
Polymers188,52610
Non-polymers2,50035
Water3,963220
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Marker peptide
D: 1E6 TCR Alpha Chain
E: 1E6 TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,66824
Polymers94,2635
Non-polymers1,40519
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Marker peptide
I: 1E6 TCR Alpha Chain
J: 1E6 TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,35821
Polymers94,2635
Non-polymers1,09516
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.800, 99.260, 122.150
Angle α, β, γ (deg.)96.330, 98.070, 96.420
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21F
12B
22G
13D
23I
14E
24J

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA1 - 2761 - 276
21GLYGLYPROPROFF1 - 2761 - 276
12METMETMETMETBB0 - 991 - 100
22METMETMETMETGG0 - 991 - 100
13GLUGLUASNASNDD3 - 1902 - 189
23GLUGLUASNASNII3 - 1902 - 189
14GLYGLYALAALAEE3 - 2452 - 244
24GLYGLYALAALAJJ3 - 2452 - 244

NCS ensembles :
ID
1
2
3
4

-
Components

-
Protein , 4 types, 8 molecules AFBGDIEJ

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2 / HLA-A02 Heavy Chain


Mass: 31951.316 Da / Num. of mol.: 2 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
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
#4: Protein 1E6 TCR Alpha Chain


Mass: 21423.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J271*PLUS
#5: Protein 1E6 TCR Beta Chain


Mass: 27911.346 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J2E0*PLUS

-
Protein/peptide , 1 types, 2 molecules CH

#3: Protein/peptide Marker peptide


Mass: 1097.203 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 4 types, 255 molecules

#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium cholride, 0.1M MES pH6, 20% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.332→48.913 Å / Num. all: 83315 / Num. obs: 83315 / % possible obs: 97.4 % / Redundancy: 2.2 % / Rpim(I) all: 0.05 / Rrim(I) all: 0.075 / Rsym value: 0.041 / Net I/av σ(I): 16.243 / Net I/σ(I): 12.7 / Num. measured all: 181534
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.33-2.392.20.2912.61335760970.4180.291296.5
2.39-2.462.20.2353.41311959930.3370.2352.596.7
2.46-2.532.20.19541265157740.2750.195396.6
2.53-2.612.20.1734.51240956670.2380.1733.596.9
2.61-2.692.20.1335.81203454930.1850.1334.497.2
2.69-2.792.20.17.81153252690.150.15.597.1
2.79-2.892.20.0898.71128951690.1210.0896.797.3
2.89-3.012.20.065121073849160.0920.0658.797.4
3.01-3.142.20.04915.91048948110.070.0491197.6
3.14-3.32.20.04317.9980744890.0580.04313.497.5
3.3-3.482.20.03620.6936143190.0490.03616.397.7
3.48-3.692.20.02826900641330.0370.02820.698
3.69-3.942.20.02626.3829138220.0330.02623.597.8
3.94-4.262.20.02428.7773635740.0310.0242698
4.26-4.662.10.02329.5706132910.030.02328.898.2
4.66-5.212.10.02229638629970.0290.02229.698.2
5.21-6.022.10.02129.8557226300.0270.02128.498.2
6.02-7.372.20.02428.2501022670.0260.02429.298.6
7.37-10.432.20.0232.2374317070.0220.0233.798
10.43-48.9132.20.0234.919438970.0230.0235.894.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 49.51 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.91 Å
Translation2.5 Å48.91 Å

-
Processing

Software
NameVersionClassification
SCALA3.3.15data scaling
PHASER2.1.4phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UTP and 3UTQ

3utp

3utq


Resolution: 2.332→48.91 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.901 / WRfactor Rfree: 0.2674 / WRfactor Rwork: 0.2002 / FOM work R set: 0.7782 / SU B: 19.389 / SU ML: 0.219 / SU R Cruickshank DPI: 0.3669 / SU Rfree: 0.2699 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.367 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2718 4159 5 %RANDOM
Rwork0.2061 ---
obs0.2095 79156 97.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 149.84 Å2 / Biso mean: 55.312 Å2 / Biso min: 19.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å20.19 Å2-0.19 Å2
2--0.24 Å21.68 Å2
3----2.56 Å2
Refinement stepCycle: final / Resolution: 2.332→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13254 0 153 220 13627
Biso mean--60.85 45.04 -
Num. residues----1641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01913746
X-RAY DIFFRACTIONr_angle_refined_deg1.9081.93618600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.03151631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39923.647702
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.659152212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.17315104
X-RAY DIFFRACTIONr_chiral_restr0.1460.21922
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110634
X-RAY DIFFRACTIONr_mcbond_it1.292.0756554
X-RAY DIFFRACTIONr_mcangle_it2.1193.1058175
X-RAY DIFFRACTIONr_scbond_it1.9812.2477192
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A3200.17
12F3200.17
21B1020.13
22G1020.13
31D2090.24
32I2090.24
41E2750.18
42J2750.18
LS refinement shellResolution: 2.332→2.393 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 301 -
Rwork0.315 5788 -
all-6089 -
obs--96.54 %
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)
13.5783-1.08430.03762.29320.05472.6001-0.0329-0.17370.2660.1970.00190.018-0.34740.22660.03110.1036-0.02710.02350.0818-0.09180.171513.06367.8168-8.7915
24.21630.55560.67561.9424-0.3787.06950.1316-0.61760.05350.6191-0.0788-0.2880.01620.5926-0.05270.5840.0120.03470.4975-0.15020.28047.64661.161126.3295
34.26712.2467-3.42563.0209-2.23944.9365-0.0225-0.2302-0.341-0.0847-0.0562-0.0030.2785-0.1010.07870.21660.0465-0.00250.2203-0.06420.15893.7354-11.85927.694
42.64252.1442-3.13436.5352-3.63375.2437-0.15430.0234-0.04870.0840.0524-0.0351-0.1910.13960.10190.25870.00770.04810.083-0.0710.244812.136530.9312-32.9813
51.66971.72660.12285.43761.75816.15970.19880.29360.1778-0.3607-0.02190.426-0.2971-0.1426-0.17691.0601-0.06810.06650.64420.05590.665510.512238.3498-65.3028
64.19740.31092.05471.2454-0.03356.36680.01160.24590.0313-0.10220.04490.2152-0.0767-0.1702-0.05650.0521-0.00310.05150.0429-0.03880.26547.19449.1487-38.3171
76.12963.5568-2.12454.1003-1.25823.76130.13590.25550.3748-0.27950.09540.0908-0.95180.2048-0.23130.6743-0.05680.0080.3658-0.06820.301111.726822.0701-65.9303
82.59681.34950.14463.3381-0.12443.4183-0.14890.1032-0.2805-0.48460.0206-0.15330.51690.34530.12820.17650.05660.07250.0943-0.06430.17875.9336-36.929265.3388
92.7627-0.228-1.6493.1005-1.18267.419-0.00710.235-0.0016-0.317-0.0495-0.38560.33250.7110.05660.42020.0360.06790.4774-0.10950.28510.1259-29.808730.1066
101.9968-0.94732.42181.5967-1.44026.7555-0.11130.24420.25460.06340.0070.0666-0.1802-0.12870.10430.1783-0.0310.07590.2363-0.03160.2039-1.7506-18.955446.2988
111.9497-1.98442.20924.9719-3.53496.9995-0.0421-0.1265-0.0273-0.1662-0.0046-0.05060.09040.12830.04670.20480.0220.00940.0577-0.08110.25232.8655-60.406388.9935
123.9972-3.9527-1.14835.93781.81285.4812-0.00980.0253-0.28050.2583-0.050.4220.6149-0.23220.05970.89740.03910.04910.49370.08340.5706-6.3862-68.9221119.8691
135.93940.4491-2.15771.6353-0.48424.77430.1113-0.1982-0.01320.0176-0.00910.19940.0874-0.2314-0.10220.0660.0125-0.02360.055-0.05440.2253-7.9458-40.313491.8777
144.9356-1.77762.07313.0656-1.11234.156-0.0181-0.3098-0.22030.1830.10680.07440.54380.0661-0.08870.32450.05320.14330.3298-0.05390.2433-9.1644-52.7987120.1412
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 10
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 113
6X-RAY DIFFRACTION5D114 - 210
7X-RAY DIFFRACTION6E1 - 114
8X-RAY DIFFRACTION7E115 - 247
9X-RAY DIFFRACTION8F1 - 180
10X-RAY DIFFRACTION8H1 - 10
11X-RAY DIFFRACTION9F181 - 276
12X-RAY DIFFRACTION10G0 - 99
13X-RAY DIFFRACTION11I1 - 113
14X-RAY DIFFRACTION12I114 - 210
15X-RAY DIFFRACTION13J1 - 114
16X-RAY DIFFRACTION14J115 - 247

+
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