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- PDB-5c0b: 1E6 TCR in complex with HLA-A02 carrying RQFGPDFPTI -

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Basic information

Entry
Database: PDB / ID: 5c0b
Title1E6 TCR in complex with HLA-A02 carrying RQFGPDFPTI
Components
  • 1E6 TCR Alpha Chain
  • 1E6 TCR Beta Chain
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Marker peptide
KeywordsIMMUNE SYSTEM / IMMUNO / HLA-A02 / 1E6-TCR
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / T cell receptor complex / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / T cell receptor complex / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / 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 / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of type II interferon production / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / antibacterial humoral response / MHC class II protein complex binding / E3 ubiquitin ligases ubiquitinate target proteins / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / innate immune response / signaling receptor binding / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity
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, 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: 2.03 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)195,84280
Polymers190,91310
Non-polymers4,92970
Water8,503472
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)98,07543
Polymers95,4565
Non-polymers2,61938
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)97,76737
Polymers95,4565
Non-polymers2,31032
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.940, 100.280, 122.440
Angle α, β, γ (deg.)96.980, 98.050, 96.530
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: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLUAA1 - 2751 - 275
21GLYGLYGLUGLUFF1 - 2751 - 275
12METMETMETMETBB0 - 991 - 100
22METMETMETMETGG0 - 991 - 100
13GLUGLUPHEPHEDD3 - 1981 - 196
23GLUGLUPHEPHEII3 - 1981 - 196
14GLYGLYALAALAEE3 - 2454 - 246
24GLYGLYALAALAJJ3 - 2454 - 246

NCS ensembles :
ID
1
2
3
4

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Components

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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: 31854.203 Da / Num. of mol.: 2 / Fragment: UNP residues 25-299
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


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: 22386.768 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: 28157.631 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

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Protein/peptide , 1 types, 2 molecules CH

#3: Protein/peptide Marker peptide


Mass: 1178.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 542 molecules

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


Mass: 62.068 Da / Num. of mol.: 55 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES, pH 7.5, 15% PEG 4000, 0.2M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.03→42.76 Å / Num. all: 128366 / Num. obs: 128366 / % possible obs: 97.6 % / Redundancy: 2 % / Rpim(I) all: 0.046 / Rrim(I) all: 0.069 / Rsym value: 0.05 / Net I/av σ(I): 8.876 / Net I/σ(I): 8 / Num. measured all: 253296
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.03-2.081.90.2682.81766694470.4280.268296.7
2.08-2.1420.2013.71812490960.3250.2012.696.1
2.14-2.21.90.1674.41707989570.2780.167396.7
2.2-2.2720.1395.31741886520.220.1393.797
2.27-2.3420.1186.31713484010.180.1184.297
2.34-2.4320.0997.41668082570.1530.099597.1
2.43-2.5220.089.21578077890.1210.08697.3
2.52-2.621.90.0739.61459376830.1070.0736.597.9
2.62-2.7420.06310.91442473120.090.0637.797.5
2.74-2.871.90.05811.81340969890.0760.0588.998.2
2.87-3.0320.051131359066830.0580.05110.698.5
3.03-3.212.10.0513.31299663390.0480.0511.998.5
3.21-3.4320.04713.81199059370.0430.04713.297.9
3.43-3.711.90.04115.71066255310.0380.0411498
3.71-4.061.90.0416.3979750950.0350.0414.798.5
4.06-4.541.90.03817.1883246140.0290.03815.399
4.54-5.242.10.03917.2836140600.0280.03916.198.4
5.24-6.4220.04113.8674934370.0270.04115.598.6
6.42-9.081.90.03815.6502126580.0280.03815.598.8
9.08-42.762.10.0416299114290.0240.0416.997.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 44.4 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å42.76 Å
Translation2.5 Å42.76 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASER2.1.4phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3UTQ for the MHC part and 4UTQ for the TCR part.
Resolution: 2.03→42.76 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2453 / WRfactor Rwork: 0.2038 / FOM work R set: 0.8187 / SU B: 10.357 / SU ML: 0.138 / SU R Cruickshank DPI: 0.1868 / SU Rfree: 0.1639 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 6446 5 %RANDOM
Rwork0.1921 ---
obs0.194 121919 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 135.32 Å2 / Biso mean: 52.559 Å2 / Biso min: 19.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20.29 Å2-0.77 Å2
2--0.95 Å20.6 Å2
3----2.68 Å2
Refinement stepCycle: final / Resolution: 2.03→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13402 0 306 472 14180
Biso mean--61.26 45.75 -
Num. residues----1657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01914036
X-RAY DIFFRACTIONr_bond_other_d0.0050.0212747
X-RAY DIFFRACTIONr_angle_refined_deg1.9231.9418918
X-RAY DIFFRACTIONr_angle_other_deg1.269329347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.52751651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02323.641714
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.315152245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9915105
X-RAY DIFFRACTIONr_chiral_restr0.1440.21951
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02115739
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023406
X-RAY DIFFRACTIONr_mcbond_it1.5031.9096628
X-RAY DIFFRACTIONr_mcbond_other1.5041.9096627
X-RAY DIFFRACTIONr_mcangle_it2.3062.8538271
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A145540.14
12F145540.14
21B55040.13
22G55040.13
31D92850.16
32I92850.16
41E131930.13
42J131930.13
LS refinement shellResolution: 2.03→2.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 467 -
Rwork0.3 8956 -
all-9423 -
obs--96.65 %
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)
11.70111.1338-0.30473.59280.14173.4186-0.1553-0.0488-0.241-0.43340.0552-0.18330.58150.30750.10010.18730.06230.06210.0915-0.00890.207310.7417-4.896812.2956
23.92470.4655-1.3723.1204-0.3545.8242-0.12920.2949-0.1708-0.36210.0923-0.41050.43750.58560.03690.46490.07330.10980.42-0.02170.284615.43532.5612-22.7595
32.0982-0.7672.10941.6689-1.26936.3868-0.0870.28060.2248-0.01430.0201-0.0475-0.1323-0.0270.0670.1791-0.02390.08160.22070.00050.19273.454413.4647-6.5797
41.8024-1.96481.39334.494-2.93366.2332-0.00850.026-0.0282-0.0269-0.006-0.10570.2283-0.060.01450.31820.008-0.01080.0181-0.06380.2527.5522-29.156236.1164
56.4884-2.4259-2.01964.32530.89844.2957-0.1128-0.6266-0.48070.16250.16020.58470.5345-0.1597-0.04740.79650.0214-0.00660.50710.18670.5428-1.5411-38.782267.1302
65.314-0.0183-1.99531.5849-0.01563.66290.1897-0.02180.1174-0.0086-0.08980.10490.0734-0.2681-0.09980.13130.02620.00210.0477-0.02170.2086-2.7523-8.775438.9716
75.0391-3.0372.24243.8864-1.00623.6524-0.1052-0.4963-0.34030.33280.34540.20960.44680.0071-0.24020.36970.03460.13770.3558-0.02890.2756-4.7637-21.821266.8181
82.7052-1.24150.09542.8693-0.11672.4845-0.0756-0.05670.17760.26250.0602-0.0396-0.29020.11290.01550.0821-0.00920.04550.0296-0.04340.167417.647840.7755-61.8064
93.24650.71091.43323.0449-0.78736.20580.0242-0.51860.09730.4466-0.0369-0.2585-0.05530.29580.01270.5233-0.0240.0360.4234-0.08750.265812.690134.0255-26.7401
104.27962.1164-3.13282.2097-1.58834.57520.0227-0.3321-0.34610.0418-0.1217-0.08590.29120.09250.0990.21250.01770.00590.17680.01710.18048.905520.8199-45.3397
111.88341.6793-1.5565.4177-2.95914.7009-0.02820.00450.0469-0.06790.0408-0.0881-0.3316-0.0677-0.01270.20440.03170.07650.0202-0.04580.261316.540364.5623-86.1408
125.10240.78881.16543.55582.6495.32790.01990.58770.1505-0.4474-0.01250.4698-0.66670.1141-0.00741.0859-0.14760.03720.43860.15280.502614.333573.8577-118.1276
133.39490.51792.48421.50840.53476.06870.11320.0769-0.0557-0.09090.01930.09240.0947-0.2205-0.13250.0653-0.00820.05980.0246-0.02660.242511.862842.6576-91.283
144.54042.9052-1.82634.491-1.97062.89830.00220.30120.3591-0.25540.20340.0943-0.75540.1893-0.20560.7416-0.09090.07140.3845-0.09870.274615.503956.2868-118.9312
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 DIFFRACTION4D0 - 113
6X-RAY DIFFRACTION5D114 - 203
7X-RAY DIFFRACTION6E0 - 114
8X-RAY DIFFRACTION7E115 - 246
9X-RAY DIFFRACTION8F1 - 180
10X-RAY DIFFRACTION8H1 - 10
11X-RAY DIFFRACTION9F181 - 276
12X-RAY DIFFRACTION10G0 - 99
13X-RAY DIFFRACTION11I0 - 113
14X-RAY DIFFRACTION12I114 - 203
15X-RAY DIFFRACTION13J0 - 114
16X-RAY DIFFRACTION14J115 - 246

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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

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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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