[English] 日本語
Yorodumi
- PDB-5c0b: 1E6 TCR in complex with HLA-A02 carrying RQFGPDFPTI -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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 / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / 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 / 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 / T cell receptor binding / detection of bacterium / : / : / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / specific granule lumen / positive regulation of type II interferon production / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / late endosome membrane / sensory perception of smell / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / adaptive immune response / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / signaling receptor binding / innate immune response / 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 / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / : / 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 / Immunoglobulins / 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

-
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)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

-
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: 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

-
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)

-
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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

-
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.

3utq

4utq


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

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)
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

+
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