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- PDB-5c0a: 1E6 TCR in complex with HLA-A02 carrying MVW peptide -

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Basic information

Entry
Database: PDB / ID: 5c0a
Title1E6 TCR in complex with HLA-A02 carrying MVW peptide
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 / Cross-reactivity
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 / 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 / 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 / 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 / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / 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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / 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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / antibacterial humoral response / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization 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 / 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: 2.46 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 16, 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)192,50836
Polymers190,47210
Non-polymers2,03626
Water3,063170
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)96,11916
Polymers95,2365
Non-polymers88311
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)96,38920
Polymers95,2365
Non-polymers1,15315
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.880, 100.020, 123.280
Angle α, β, γ (deg.)96.670, 98.580, 95.800
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
11GLYGLYPROPROAA1 - 2761 - 276
21GLYGLYPROPROFF1 - 2761 - 276
12METMETMETMETBB0 - 991 - 100
22METMETMETMETGG0 - 991 - 100
13GLUGLUPHEPHEDD3 - 1991 - 197
23GLUGLUPHEPHEII3 - 1991 - 197
14GLYGLYALAALAEE3 - 2453 - 245
24GLYGLYALAALAJJ3 - 2453 - 245

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: 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


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: 22202.574 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: 28026.434 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: 1176.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 196 molecules

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


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES pH7.5, 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: 2.46→31.236 Å / Num. all: 72534 / Num. obs: 72534 / % possible obs: 97.7 % / Redundancy: 1.9 % / Rpim(I) all: 0.067 / Rrim(I) all: 0.102 / Rsym value: 0.088 / Net I/av σ(I): 4.745 / Net I/σ(I): 4.7 / Num. measured all: 140414
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
2.46-2.521.80.2143.1934952490.3810.2142.696.2
2.52-2.591.90.223997952450.3260.222.996.9
2.59-2.671.90.1763.6959149470.2840.1763.396.4
2.67-2.751.90.1653.1965849870.2440.1653.696.6
2.75-2.841.90.1335.2910947100.1760.133497.1
2.84-2.941.90.1135.8898246560.1460.1134.497.4
2.94-3.051.80.0996807644370.1270.0994.598.3
3.05-3.1820.0996.6848542930.1070.099597.2
3.18-3.321.90.097.3786441490.0940.095.198.6
3.32-3.4820.0976.6792939670.0920.0975.598.8
3.48-3.6720.0875.2787138420.0660.0875.898.7
3.67-3.8920.0876.4713235360.0560.0875.998
3.89-4.1620.0837.7658833550.0580.0835.899
4.16-4.491.90.0768.7589631290.0530.0765.898.2
4.49-4.9220.079.5574129080.0470.07699.2
4.92-5.520.0788.6523926250.0490.078699.2
5.5-6.3520.0887.4466922810.0510.0886.198.6
6.35-7.781.90.097.7370619380.0530.095.999
7.78-111.90.0925.9293015160.060.0925.999.1
11-31.2362.10.088.216207640.0470.086.393.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.74 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å35.21 Å
Translation2.5 Å35.21 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: 3UTP and 3UTQ

3utp

3utq


Resolution: 2.46→31.236 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.2875 / WRfactor Rwork: 0.2369 / FOM work R set: 0.8228 / SU B: 19.662 / SU ML: 0.214 / SU R Cruickshank DPI: 0.4805 / SU Rfree: 0.2607 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.48 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 3655 5 %RANDOM
Rwork0.1928 ---
obs0.1948 68868 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 192.96 Å2 / Biso mean: 67.984 Å2 / Biso min: 24.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20.45 Å2-0.53 Å2
2--0.5 Å21.64 Å2
3----1.81 Å2
Refinement stepCycle: final / Resolution: 2.46→31.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13397 0 122 170 13689
Biso mean--78.62 51.57 -
Num. residues----1656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01913897
X-RAY DIFFRACTIONr_bond_other_d0.0040.0212512
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.93618834
X-RAY DIFFRACTIONr_angle_other_deg1.147328828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.78451650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15523.685711
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.663152238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.25315102
X-RAY DIFFRACTIONr_chiral_restr0.1060.21951
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115742
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023394
X-RAY DIFFRACTIONr_mcbond_it1.9683.0356624
X-RAY DIFFRACTIONr_mcbond_other1.9683.0356623
X-RAY DIFFRACTIONr_mcangle_it3.1334.5468266
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A141640.13
12F141640.13
21B52200.14
22G52200.14
31D86110.19
32I86110.19
41E124290.15
42J124290.15
LS refinement shellResolution: 2.46→2.523 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 260 -
Rwork0.293 4950 -
all-5210 -
obs--96.13 %
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)
12.65641.5480.04324.0292-0.23114.1175-0.19060.1302-0.3593-0.60880.0778-0.20.66430.25990.11280.19370.02820.0720.1407-0.03710.2304-8.0749-21.3494133.3525
24.2255-0.3589-2.45223.6747-0.89257.5712-0.05770.1868-0.047-0.3356-0.0747-0.58870.62750.65890.13250.4833-0.02840.03940.5232-0.09480.3529-3.4673-14.846397.8
32.2742-1.2262.6391.9873-1.03497.4291-0.06280.36570.4028-0.0681-0.07870.0164-0.3041-0.21140.14140.2395-0.08450.06190.3740.0390.2834-15.2318-3.1527113.9219
42.3622-1.48821.57095.6506-3.97266.2221-0.0704-0.0373-0.075-0.20720.0583-0.13310.416-0.08960.01210.24710.0049-0.00320.0311-0.08980.2868-11.5379-45.743157.3997
58.0286-1.5097-2.06544.6320.45724.9358-0.1364-0.3615-0.30490.1270.02640.25950.4799-0.10390.110.74610.0244-0.05390.38980.09270.5595-20.781-55.1829189.0149
65.39290.4516-2.21792.0444-0.26695.00230.0855-0.2409-0.0721-0.0589-0.04060.19980.2328-0.2606-0.0450.0282-0.0171-0.03890.0588-0.04730.2208-22.0429-25.6748160.5125
76.011-2.39162.50473.2523-1.82055.34030.0032-0.3308-0.36020.2110.12990.19030.6236-0.0175-0.13310.3142-0.01550.12080.227-0.07580.3077-23.9601-38.4082188.5001
83.687-1.0267-0.6122.3917-0.00032.3304-0.0332-0.18830.35030.24640.0579-0.0055-0.24180.1453-0.02470.0524-0.01610.02170.0383-0.07990.21990.368223.157158.6963
92.050.61590.30762.3343-0.06257.7063-0.0014-0.6508-0.03360.7442-0.0467-0.41730.02320.23140.04810.5483-0.00620.01470.4938-0.11060.4027-5.357416.864994.0166
105.22442.3588-3.53213.3081-1.574.6021-0.0227-0.3873-0.40580.0856-0.09790.01590.4103-0.10570.12060.18420.0004-0.01620.2563-0.0210.2115-9.40513.591475.4044
112.19991.78-1.42336.495-3.29764.9545-0.04910.0440.0039-0.07790.1215-0.1765-0.449-0.1327-0.07250.19430.0240.09590.0322-0.07420.3233-0.218747.090934.122
123.75620.49252.21596.47341.67575.4912-0.19950.71120.5363-0.88240.08720.733-0.61760.00030.11231.2194-0.07940.09820.66380.17220.842-1.235156.33760.9156
133.4210.30861.69651.24140.25836.77090.05320.21650.0679-0.14470.0430.1838-0.0646-0.3682-0.09630.0378-0.00740.0480.0644-0.03640.3001-5.29925.56528.4886
146.57454.2809-1.14615.9018-0.15573.3246-0.21030.3930.4018-0.51930.45140.1493-0.92540.0874-0.24110.6916-0.0445-0.00210.4318-0.04220.3303-0.75838.95961.0234
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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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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