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- PDB-7q9b: MHC Class I A02 Allele presenting EAAGIGILTV, in complex with Mel8 TCR -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7q9b
TitleMHC Class I A02 Allele presenting EAAGIGILTV, in complex with Mel8 TCR
Components
  • (Human T Cell Receptor Mel8, ...) x 2
  • Beta-2-microglobulinBeta-2 microglobulin
  • GLU-ALA-ALA-GLY-ILE-GLY-ILE-LEU-THR-VAL
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Melanoma epitope / Autoimmunity
Function / homology
Function and homology information


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 / 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 / Endosomal/Vacuolar 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 / 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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / 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 / negative regulation of epithelial cell proliferation / 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 / sensory perception of smell / 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 differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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 / 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 ...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 / 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
Similarity search - Domain/homology
Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsRizkallah, P.J. / Sewell, A.K. / Wall, A. / Fuller, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2023
Title: Targeting of multiple tumor-associated antigens by individual T cell receptors during successful cancer immunotherapy.
Authors: Dolton, G. / Rius, C. / Wall, A. / Szomolay, B. / Bianchi, V. / Galloway, S.A.E. / Hasan, M.S. / Morin, T. / Caillaud, M.E. / Thomas, H.L. / Theaker, S. / Tan, L.R. / Fuller, A. / Topley, K. ...Authors: Dolton, G. / Rius, C. / Wall, A. / Szomolay, B. / Bianchi, V. / Galloway, S.A.E. / Hasan, M.S. / Morin, T. / Caillaud, M.E. / Thomas, H.L. / Theaker, S. / Tan, L.R. / Fuller, A. / Topley, K. / Legut, M. / Attaf, M. / Hopkins, J.R. / Behiry, E. / Zabkiewicz, J. / Alvares, C. / Lloyd, A. / Rogers, A. / Henley, P. / Fegan, C. / Ottmann, O. / Man, S. / Crowther, M.D. / Donia, M. / Svane, I.M. / Cole, D.K. / Brown, P.E. / Rizkallah, P. / Sewell, A.K.
History
DepositionNov 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: MHC class I antigen
BBB: Beta-2-microglobulin
CCC: GLU-ALA-ALA-GLY-ILE-GLY-ILE-LEU-THR-VAL
DDD: Human T Cell Receptor Mel8, Alpha Chain
EEE: Human T Cell Receptor Mel8, Beta Chain
FFF: MHC class I antigen
GGG: Beta-2-microglobulin
HHH: GLU-ALA-ALA-GLY-ILE-GLY-ILE-LEU-THR-VAL
III: Human T Cell Receptor Mel8, Alpha Chain
JJJ: Human T Cell Receptor Mel8, Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,42612
Polymers187,30110
Non-polymers1242
Water95553
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.972, 53.645, 203.507
Angle α, β, γ (deg.)90.000, 94.333, 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
111GLYGLYGLUGLUAAAA1 - 2751 - 275
221GLYGLYGLUGLUFFFF1 - 2751 - 275
332METMETMETMETBBBB0 - 991 - 100
442METMETMETMETGGGG0 - 991 - 100
553GLNGLNPROPRODDDD1 - 1891 - 189
663GLNGLNPROPROIIII1 - 1891 - 189
774ASNASNASPASPEEEE1 - 2451 - 245
884ASNASNASPASPJJJJ1 - 2451 - 245

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 MHC class I antigen


Mass: 31854.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: U5YJM1
#2: Protein Beta-2-microglobulin / 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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Protein/peptide , 1 types, 2 molecules CCCHHH

#3: Protein/peptide GLU-ALA-ALA-GLY-ILE-GLY-ILE-LEU-THR-VAL


Mass: 943.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Human T Cell Receptor Mel8, ... , 2 types, 4 molecules DDDIIIEEEJJJ

#4: Protein Human T Cell Receptor Mel8, Alpha Chain


Mass: 21410.592 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)
#5: Protein Human T Cell Receptor Mel8, Beta Chain


Mass: 27563.498 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)

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Non-polymers , 2 types, 55 molecules

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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.91 Å3/Da / Density % sol: 57.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.24→99.7 Å / Num. obs: 34992 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 36.7 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.28 / Rpim(I) all: 0.22 / Rrim(I) all: 0.328 / Net I/σ(I): 2.7
Reflection shellResolution: 3.24→3.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.949 / Num. unique obs: 2579 / CC1/2: 0.686 / Rpim(I) all: 0.719 / Rrim(I) all: 1.102 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HG1

3hg1


Resolution: 3.24→99.686 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.856 / SU B: 89.445 / SU ML: 0.636 / Cross valid method: FREE R-VALUE / ESU R Free: 0.575
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2765 1742 4.98 %
Rwork0.2264 33241 -
all0.229 --
obs-34983 99.894 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 56.356 Å2
Baniso -1Baniso -2Baniso -3
1--0.525 Å20 Å2-0.611 Å2
2---1.764 Å20 Å2
3---2.355 Å2
Refinement stepCycle: LAST / Resolution: 3.24→99.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13160 0 8 53 13221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01313521
X-RAY DIFFRACTIONr_bond_other_d0.0020.01512057
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.65118371
X-RAY DIFFRACTIONr_angle_other_deg1.1261.58227796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.22651633
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51822.277786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.074152173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5311594
X-RAY DIFFRACTIONr_chiral_restr0.0540.21708
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215588
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023312
X-RAY DIFFRACTIONr_nbd_refined0.210.22627
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.212088
X-RAY DIFFRACTIONr_nbtor_refined0.1690.25975
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.27043
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2316
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0340.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2460.240
X-RAY DIFFRACTIONr_nbd_other0.2430.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2690.212
X-RAY DIFFRACTIONr_mcbond_it0.0430.4026562
X-RAY DIFFRACTIONr_mcbond_other0.0430.4016561
X-RAY DIFFRACTIONr_mcangle_it0.0810.6028185
X-RAY DIFFRACTIONr_mcangle_other0.0810.6028186
X-RAY DIFFRACTIONr_scbond_it0.0220.4026959
X-RAY DIFFRACTIONr_scbond_other0.0220.4026960
X-RAY DIFFRACTIONr_scangle_it0.0420.610186
X-RAY DIFFRACTIONr_scangle_other0.0420.60110187
X-RAY DIFFRACTIONr_lrange_it1.2664.43514405
X-RAY DIFFRACTIONr_lrange_other1.2664.43414403
X-RAY DIFFRACTIONr_ncsr_local_group_10.1040.058481
X-RAY DIFFRACTIONr_ncsr_local_group_20.1110.052959
X-RAY DIFFRACTIONr_ncsr_local_group_30.1660.054795
X-RAY DIFFRACTIONr_ncsr_local_group_40.1470.056958
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.103550.05009
12FFFX-RAY DIFFRACTIONLocal ncs0.103550.05009
23BBBX-RAY DIFFRACTIONLocal ncs0.110860.05008
24GGGX-RAY DIFFRACTIONLocal ncs0.110860.05008
35DDDX-RAY DIFFRACTIONLocal ncs0.165540.05008
36IIIX-RAY DIFFRACTIONLocal ncs0.165540.05008
47EEEX-RAY DIFFRACTIONLocal ncs0.147140.05009
48JJJX-RAY DIFFRACTIONLocal ncs0.147140.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.24-3.3240.3331030.33424590.33425750.7160.70599.49510.333
3.324-3.4150.3581160.30123300.30424490.7040.78299.87750.299
3.415-3.5140.3681350.30222900.30624250.7860.7841000.298
3.514-3.6220.3121140.28522370.28623510.7720.8051000.283
3.622-3.7410.3111000.2621760.26222770.8530.86899.95610.255
3.741-3.8720.32890.24221560.24522450.830.881000.239
3.872-4.0180.3121140.23420050.23821190.860.8811000.232
4.018-4.1810.219910.20819960.20820870.9150.911000.207
4.181-4.3670.253960.18818770.19119740.9010.9299.94930.189
4.367-4.580.226960.17617950.17918910.9260.931000.179
4.58-4.8270.199950.16516990.16617950.9340.94899.94430.168
4.827-5.1190.281080.19116040.19717130.8950.92399.94160.199
5.119-5.4710.316700.19615560.20116260.8970.9231000.201
5.471-5.9080.279720.20614570.2115290.910.9221000.208
5.908-6.470.272630.21512960.21813620.8970.91499.77970.213
6.47-7.230.273620.19812100.20212720.9160.9291000.198
7.23-8.3410.248750.17610470.18111250.9380.94699.73330.18
8.341-10.1970.235570.1869130.1899740.9380.95399.58930.194
10.197-14.3460.225440.1917210.1937650.9510.9551000.207
14.346-99.6860.235420.334160.3214580.9180.8751000.441
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)
13.10191.38340.49883.95881.33543.06160.12590.0050.2-0.104-0.1757-0.2432-0.05330.04740.04980.96060.0102-0.31960.01380.02240.176118.538429.337724.4178
27.0277-0.3031-4.32482.6492-1.3646.82890.14551.00070.2265-0.3604-0.0859-0.7717-0.0880.3582-0.05961.06740.0635-0.1790.4292-0.09430.401925.251336.6993-9.8145
35.3211-0.80724.56894.3256-0.73437.09140.11990.00860.07660.2226-0.08150.1198-0.1688-0.1019-0.03840.79010.0232-0.20260.0088-0.02270.186812.398447.94685.2698
40.80791.146-1.80992.7534-4.22618.46440.04310.0645-0.123-0.336-0.12340.03790.4035-0.17770.08040.85960.0315-0.28090.1135-0.06780.337613.91036.319945.1598
59.1599-1.6124-0.13793.10230.94993.9143-0.0478-0.2483-0.4850.3124-0.0770.72620.1405-0.67760.12481.0499-0.0559-0.16460.31160.10890.47191.3478-6.465171.7544
67.46420.6372-3.36263.5718-0.17193.9056-0.0688-0.10040.04880.16150.11520.4196-0.1985-0.3012-0.04650.92090.0699-0.29870.14030.0210.20322.486926.093548.65
75.3788-2.6561.43493.8675-2.3552.1897-0.0834-0.31470.26540.32840.09990.2161-0.0904-0.5289-0.01651.2721-0.0027-0.16550.3367-0.09430.324-0.00939.83874.2899
82.3973-0.4106-0.77974.5978-0.95913.18510.06310.10030.219-0.0357-0.19690.00580.0243-0.06190.13390.99780.0189-0.33780.0258-0.01840.17533.814419.299372.043
97.2331-0.738-2.82954.29090.94013.5708-0.3222-0.72390.03670.90370.08711.32020.3157-1.18170.23511.2739-0.1444-0.08761.00320.01770.555415.10326.51101.9421
101.5966-0.60481.76531.97811.08827.88210.0671-0.22110.2094-0.1212-0.1144-0.1676-0.12250.15670.04730.8193-0.0532-0.20380.14720.01510.327332.636437.803292.2072
113.1299-1.8214-4.8874.59333.34957.9184-0.22520.0917-0.5130.1432-0.2551-0.09960.3360.00780.48030.9427-0.1021-0.25530.2294-0.13410.567144.3692-4.079953.9103
126.75224.47372.4164.80230.44474.8346-0.3813-0.0002-0.72370.09330.0128-0.23550.59310.23650.36841.45760.05040.14790.6351-0.04921.049965.5554-17.571134.5922
138.7238-0.9912-1.73360.70190.25492.90170.0112-0.01940.5187-0.0492-0.01-0.2993-0.02260.2848-0.00120.792-0.0502-0.12360.3316-0.00090.52457.317115.019554.8869
143.24450.57731.18382.82783.61425.3687-0.22660.1607-0.2236-0.13360.1422-0.19680.34190.52390.08431.2041-0.0431-0.06640.47990.1710.739969.138-1.958932.2153
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA1 - 180
2X-RAY DIFFRACTION1ALLCCC1 - 10
3X-RAY DIFFRACTION2ALLAAA181 - 275
4X-RAY DIFFRACTION3ALLBBB1 - 99
5X-RAY DIFFRACTION4ALLDDD1 - 113
6X-RAY DIFFRACTION5ALLDDD114 - 193
7X-RAY DIFFRACTION6ALLEEE1 - 112
8X-RAY DIFFRACTION7ALLEEE113 - 245
9X-RAY DIFFRACTION8ALLFFF1 - 180
10X-RAY DIFFRACTION8ALLHHH1 - 10
11X-RAY DIFFRACTION9ALLFFF181 - 275
12X-RAY DIFFRACTION10ALLGGG1 - 99
13X-RAY DIFFRACTION11ALLIII1 - 113
14X-RAY DIFFRACTION12ALLIII114 - 190
15X-RAY DIFFRACTION13ALLJJJ1 - 112
16X-RAY DIFFRACTION14ALLJJJ113 - 245

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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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