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- PDB-2ol3: crystal structure of BM3.3 ScFV TCR in complex with PBM8-H-2KBM8 ... -

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Basic information

Entry
Database: PDB / ID: 2ol3
Titlecrystal structure of BM3.3 ScFV TCR in complex with PBM8-H-2KBM8 MHC class I molecule
Components
  • (BM3.3 T-CELL RECEPTOR ...) x 2
  • ALLOGENEIC H-2KBM8 MHC CLASS I MOLECULE
  • Beta-2-microglobulin
  • NATURALLY PROCESSED OCTAPEPTIDE PBM8
KeywordsIMMUNE SYSTEM / T CELL RECEPTOR / CLASS I MHC / H-2KBm8 / TCR-PMHC COMPLEX
Function / homology
Function and homology information


mRNA Splicing - Major Pathway / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / spliceosomal complex assembly / regulation of alternative mRNA splicing, via spliceosome ...mRNA Splicing - Major Pathway / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / spliceosomal complex assembly / regulation of alternative mRNA splicing, via spliceosome / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / 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 / lumenal side of endoplasmic reticulum membrane / peptide binding / spliceosomal complex / 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 / 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 / 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 / mRNA splicing, via spliceosome / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / defense response to bacterium / immune response / positive regulation of apoptotic process / lysosomal membrane / external side of plasma membrane / signaling receptor binding / mRNA binding / apoptotic process / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular space / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
RNA-binding protein 5, RNA recognition motif 1 / RNA-binding protein 5, RNA recognition motif 2 / OCRE domain / OCRE domain / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / Zinc finger domain / Zn-finger in Ran binding protein and others ...RNA-binding protein 5, RNA recognition motif 1 / RNA-binding protein 5, RNA recognition motif 2 / OCRE domain / OCRE domain / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Zinc finger C2H2 type domain profile. / 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 / Zinc finger C2H2-type / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / RNA-binding domain superfamily / : / 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 subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Nucleotide-binding alpha-beta plait domain superfamily / 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
Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain / T-cell receptor beta chain V region E1 / TRADV16D / RNA-binding protein 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMazza, C. / Auphan-Anezin, N. / Gregoire, C. / Guimezanes, A. / Kellenberger, C. / Roussel, A. / Kearney, A. / Van der Merwe, P.A. / Schmitt-Verhulst, A.M. / Malissen, B.
CitationJournal: Embo J. / Year: 2007
Title: How much can a T-cell antigen receptor adapt to structurally distinct antigenic peptides?
Authors: Mazza, C. / Auphan-Anezin, N. / Gregoire, C. / Guimezanes, A. / Kellenberger, C. / Roussel, A. / Kearney, A. / van der Merwe, P.A. / Schmitt-Verhulst, A.M. / Malissen, B.
History
DepositionJan 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE FOR THE PROTEINS IN CHAINS A, B AND H

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BM3.3 T-CELL RECEPTOR ALPHA-CHAIN
B: BM3.3 T-CELL RECEPTOR BETA-CHAIN
H: ALLOGENEIC H-2KBM8 MHC CLASS I MOLECULE
L: Beta-2-microglobulin
P: NATURALLY PROCESSED OCTAPEPTIDE PBM8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8086
Polymers73,5875
Non-polymers2211
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.523, 102.523, 198.381
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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BM3.3 T-CELL RECEPTOR ... , 2 types, 2 molecules AB

#1: Protein BM3.3 T-CELL RECEPTOR ALPHA-CHAIN


Mass: 15570.499 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): myeloma cells / Production host: Mus musculus (house mouse) / References: UniProt: Q5R1F1
#2: Protein BM3.3 T-CELL RECEPTOR BETA-CHAIN


Mass: 13064.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): myeloma cells / Production host: Mus musculus (house mouse) / References: UniProt: P04214

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Protein , 2 types, 2 molecules HL

#3: Protein ALLOGENEIC H-2KBM8 MHC CLASS I MOLECULE


Mass: 32078.799 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS (ALPHA1, ALPHA2, ALPHA3)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01901
#4: Protein Beta-2-microglobulin


Mass: 11835.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887

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Protein/peptide / Sugars / Non-polymers , 3 types, 79 molecules P

#5: Protein/peptide NATURALLY PROCESSED OCTAPEPTIDE PBM8 / RNA-BINDING PROTEIN 5


Mass: 1037.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in mouse / References: UniProt: Q91YE7
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12 % PEG 6000, 100 mM Hepes, pH 7.5, and 150 mM Magnesium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. obs: 22488 / % possible obs: 98.1 % / Rmerge(I) obs: 0.116
Reflection shellResolution: 2.9→3.06 Å

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NAM

1nam


Resolution: 2.9→25 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.866 / SU B: 33.256 / SU ML: 0.341 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.014 / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28352 1214 5.1 %RANDOM
Rwork0.22422 ---
obs0.2272 22488 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.829 Å2
Baniso -1Baniso -2Baniso -3
1-3.14 Å20 Å20 Å2
2--3.14 Å20 Å2
3----6.29 Å2
Refinement stepCycle: LAST / Resolution: 2.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4982 0 14 77 5073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225128
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.956961
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.655610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18623.695249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58115864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4781536
X-RAY DIFFRACTIONr_chiral_restr0.0770.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023941
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2620.22492
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.23521
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2196
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3090.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7221.53129
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.60724957
X-RAY DIFFRACTIONr_scbond_it2.68632311
X-RAY DIFFRACTIONr_scangle_it3.6264.52004
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 85 -
Rwork0.364 1628 -
obs--99.13 %
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)
14.3569-3.06161.19933.9216-3.61936.377-0.23041.0923-0.52140.127-0.31190.6294-0.2463-0.40460.54230.0499-0.18180.03810.4042-0.24160.14431.508316.6126-5.2689
24.2015-0.8221-1.95423.8633-0.56727.8883-0.34590.1374-0.30750.141-0.16990.22610.059-0.46270.51580.1426-0.07380.02570.2683-0.13070.14373.045121.82977.2564
311.3165-2.09441.260910.4646-2.505111.86570.01520.3113-0.69360.1919-0.61260.89061.0347-1.67470.59740.0451-0.31780.1580.3114-0.28150.0733-4.172114.73958.5963
43.46742.56580.51825.17141.133912.8013-0.41450.40290.4203-0.27-0.16250.6331-0.9746-1.90990.5770.00150.07670.01020.3069-0.13340.164-1.481923.2966-2.3204
53.7416.13459.995410.059416.390726.70682.40411.117-2.55651.4175-3.53451.86842.28394.25061.13040.3851-0.02530.48780.48340.08850.370811.576624.013717.8676
65.051-0.13038.22163.62890.976819.9898-0.04620.59470.0152-0.5997-0.31040.2208-0.3603-1.01130.35660.1002-0.08690.03150.3729-0.14-0.10312.700822.5048-6.396
74.63262.4246-5.32023.3472-0.63368.3360.69540.14310.47790.4053-0.28290.2801-0.5621-0.8249-0.41250.21540.02430.04310.14380.08760.100615.717543.70911.0491
811.8388-0.4353-0.17060.6911-4.467329.64950.5478-0.33380.23781.10660.36010.7212-1.6058-1.6354-0.90790.2409-0.01230.17690.0093-0.04130.1662.577343.069314.5744
91.94720.1658-1.8564.52593.9286.81360.17060.16520.02650.1907-0.06880.0611-0.17950.0314-0.10180.1941-0.05310.01520.10270.04430.050614.20932.74959.3725
1025.9599-23.0001-30.798232.008237.768445.98460.3251-0.49660.0071-0.0284-0.1606-0.00230.7163-0.3597-0.16450.38450.0001-0.05270.09860.16760.063722.931435.34915.3224
114.1038-3.0913-3.28875.0641.36343.48510.67480.04870.25920.1354-0.3688-0.1536-0.4512-0.2155-0.3060.2244-0.143-0.00770.08520.00320.079318.797440.197611.6017
125.5534-0.8631-1.99541.7912-0.0070.77770.4166-0.20570.0090.3485-0.3753-0.0018-0.28520.1019-0.04130.1941-0.03030.01960.15710.03770.12519.450436.11722.5275
130.27221.0643-1.43444.1763-5.103524.30960.24640.77850.2425-1.0784-0.37780.3780.3503-0.36580.13140.142-0.10260.03680.2307-0.05090.09933.447831.065816.2095
146.65043.8251-2.60423.361-3.28323.7656-0.20560.7545-0.2529-0.0203-0.1140.3362-0.4692-0.82290.31950.25090.08280.09960.24910.01880.04214.822438.2697-2.5254
152.92411.40750.96544.12432.25882.6725-0.0537-0.3557-0.0726-0.13970.0499-0.2514-0.12630.41070.00380.12460.0250.10280.24770.04990.131310.909623.451440.348
166.54623.3608-1.657613.1467-3.86225.62520.0294-0.512-0.8593-0.6137-0.3811-1.49530.22990.73980.3517-0.13550.14180.1230.15870.05610.195619.427815.771935.688
172.20440.2609-0.33943.0058-0.20611.47260.066-0.03580.0262-0.2151-0.1362-0.2789-0.15850.12490.07020.177-0.01730.05570.2022-0.01130.10955.844629.64334.1139
184.88921.82851.1566.14162.61545.4503-0.1911-0.14350.0396-0.13810.09790.315-0.05130.00430.09320.1823-0.01660.07710.1341-0.00820.0654-4.672929.97635.3915
191.0060.21640.37881.7083-1.68352.73610.0435-0.1842-0.2792-0.0608-0.0823-0.25790.12580.24140.03870.19680.02090.05590.2596-0.03250.22523.06416.521341.5937
202.56331.5252-0.32233.13660.62225.14950.4474-0.5508-0.03850.8699-0.4350.1005-0.3869-0.1301-0.01240.1581-0.08540.02310.23830.140.05932.450515.134172.8963
2118.4826-20.906320.602538.861-31.468335.55550.0410.2939-0.14780.55440.01090.2957-1.6780.0535-0.05190.0525-0.24520.11820.3563-0.17980.09718.637232.710657.9353
224.0116-3.81723.40545.5987-3.820513.3933-0.0473-0.9008-0.72210.87570.2221-0.2395-0.18660.8047-0.1749-0.1325-0.1662-0.07250.39970.15050.114917.44623.884362.4989
235.4343.134.99938.28536.86458.83090.04870.2950.30070.8879-0.0787-1.19230.2581.2470.030.0251-0.2206-0.06420.36780.1690.288122.996231.455557.8182
2486.559242.8666-28.794541.9182-35.136730.6446-0.97911.56841.6753-2.12432.29191.36861.6585-0.842-1.31280.09270.1820.2266-0.0691-0.03370.15943.029827.686346.8728
253.0720.4820.67695.5354-0.57153.23350.1652-0.89240.04520.5427-0.2206-0.7186-0.85180.8570.0553-0.0396-0.2756-0.10130.43770.00430.038118.214831.15164.5152
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 201 - 20
2X-RAY DIFFRACTION2AA21 - 5021 - 51
3X-RAY DIFFRACTION3AA51 - 7552 - 76
4X-RAY DIFFRACTION4AA76 - 9377 - 94
5X-RAY DIFFRACTION5AA95 - 10395 - 103
6X-RAY DIFFRACTION6AA104 - 118104 - 118
7X-RAY DIFFRACTION7BB1 - 231 - 23
8X-RAY DIFFRACTION8BB24 - 3124 - 32
9X-RAY DIFFRACTION9BB32 - 5333 - 54
10X-RAY DIFFRACTION10BB54 - 5955 - 60
11X-RAY DIFFRACTION11BB60 - 7761 - 78
12X-RAY DIFFRACTION12BB78 - 9479 - 93
13X-RAY DIFFRACTION13BB95 - 10794 - 103
14X-RAY DIFFRACTION14BB108 - 117104 - 113
15X-RAY DIFFRACTION15HC1 - 351 - 35
16X-RAY DIFFRACTION16HC36 - 6336 - 63
17X-RAY DIFFRACTION17HC64 - 11164 - 111
18X-RAY DIFFRACTION18HC112 - 140112 - 140
19X-RAY DIFFRACTION19HC141 - 194141 - 194
20X-RAY DIFFRACTION20HC195 - 276195 - 276
21X-RAY DIFFRACTION21LD0 - 111 - 12
22X-RAY DIFFRACTION22LD12 - 3313 - 34
23X-RAY DIFFRACTION23LD34 - 5535 - 56
24X-RAY DIFFRACTION24LD56 - 6157 - 62
25X-RAY DIFFRACTION25LD62 - 9963 - 100

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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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