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- PDB-6bj3: TCR55 in complex with HIV(Pol448-456)/HLA-B35 -

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Basic information

Entry
Database: PDB / ID: 6bj3
TitleTCR55 in complex with HIV(Pol448-456)/HLA-B35
Components
  • Beta-2-microglobulin
  • HIV Pol B35 peptide
  • HLA class I histocompatibility antigen, B-35 alpha chain
  • TCR 55 alpha chain
  • TCR 55 beta chain
KeywordsIMMUNE SYSTEM / non-agonist / complex
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / integrase activity / regulation of T cell anergy / regulation of interleukin-6 production / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / integrase activity / regulation of T cell anergy / regulation of interleukin-6 production / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / TAP binding / protection from natural killer cell mediated cytotoxicity / Binding and entry of HIV virion / detection of bacterium / viral life cycle / secretory granule membrane / 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 I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / 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 / response to bacterium / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / Assembly Of The HIV Virion / 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 / retroviral ribonuclease H / exoribonuclease H / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / Budding and maturation of HIV virion / response to molecule of bacterial origin / MHC class I peptide loading complex / exoribonuclease H activity / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / protein processing / positive regulation of T cell cytokine production / MHC class I protein complex / host multivesicular body / multicellular organismal-level iron ion homeostasis / defense response / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / viral genome integration into host DNA / RNA-directed DNA polymerase / positive regulation of T cell mediated cytotoxicity / establishment of integrated proviral latency / viral penetration into host nucleus / specific granule lumen / RNA stem-loop binding / recycling endosome membrane / phagocytic vesicle membrane / symbiont-mediated suppression of host gene expression / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / RNA-directed DNA polymerase activity / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / host cell / positive regulation of T cell activation / Interferon alpha/beta signaling / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / peptidase activity / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway
Similarity search - Function
: / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 ...: / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / MHC classes I/II-like antigen recognition protein / Integrase, catalytic core / Integrase catalytic domain profile. / Immunoglobulin V-set domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / : / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Human nkt tcr beta chain / HLA class I histocompatibility antigen, B alpha chain / Gag-Pol polyprotein / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / TRA@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 Å
AuthorsJude, K.M. / Sibener, L.V. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI103867 United States
CitationJournal: Cell / Year: 2018
Title: Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding.
Authors: Sibener, L.V. / Fernandes, R.A. / Kolawole, E.M. / Carbone, C.B. / Liu, F. / McAffee, D. / Birnbaum, M.E. / Yang, X. / Su, L.F. / Yu, W. / Dong, S. / Gee, M.H. / Jude, K.M. / Davis, M.M. / ...Authors: Sibener, L.V. / Fernandes, R.A. / Kolawole, E.M. / Carbone, C.B. / Liu, F. / McAffee, D. / Birnbaum, M.E. / Yang, X. / Su, L.F. / Yu, W. / Dong, S. / Gee, M.H. / Jude, K.M. / Davis, M.M. / Groves, J.T. / Goddard III, W.A. / Heath, J.R. / Evavold, B.D. / Vale, R.D. / Garcia, K.C.
History
DepositionNov 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
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
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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, B-35 alpha chain
B: Beta-2-microglobulin
D: TCR 55 alpha chain
H: TCR 55 beta chain
C: HIV Pol B35 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,65013
Polymers94,9845
Non-polymers6678
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12360 Å2
ΔGint-106 kcal/mol
Surface area37360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.996, 61.414, 92.064
Angle α, β, γ (deg.)90.00, 105.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 4 molecules ABDH

#1: Protein HLA class I histocompatibility antigen, B-35 alpha chain / MHC class I antigen B*35


Mass: 31940.246 Da / Num. of mol.: 1 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P30685, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1 / 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: Trichoplusia ni (cabbage looper) / References: UniProt: P61769
#3: Protein TCR 55 alpha chain


Mass: 22890.752 Da / Num. of mol.: 1 / Mutation: T161C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6IRV4
#4: Protein TCR 55 beta chain


Mass: 27390.535 Da / Num. of mol.: 1 / Mutation: A187C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: K7N5M4

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Protein/peptide , 1 types, 1 molecules C

#5: Protein/peptide HIV Pol B35 peptide


Mass: 1014.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04585*PLUS

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Non-polymers , 3 types, 372 molecules

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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: PEG4000, 0.1 M sodium cacodylate, pH 6.0, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99995 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99995 Å / Relative weight: 1
ReflectionResolution: 1.898→50 Å / Num. obs: 83485 / % possible obs: 97.79 % / Redundancy: 3.4 % / Biso Wilson estimate: 34.9 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.1382 / Rpim(I) all: 0.0853 / Rrim(I) all: 0.1628 / Net I/σ(I): 4.67
Reflection shellResolution: 1.898→1.966 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.313 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 7910 / CC1/2: 0.406 / Rpim(I) all: 0.8382 / Rrim(I) all: 1.563 / % possible all: 92.69

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1A1N, 4LFH, 4PJ5

1a1n

4lfh

4pj5


Resolution: 1.898→48.094 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.16
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 2000 2.4 %random
Rwork0.1876 ---
obs0.1883 83459 97.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.898→48.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6575 0 37 364 6976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036837
X-RAY DIFFRACTIONf_angle_d0.5999312
X-RAY DIFFRACTIONf_dihedral_angle_d11.1824085
X-RAY DIFFRACTIONf_chiral_restr0.045984
X-RAY DIFFRACTIONf_plane_restr0.0031217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8977-1.94510.43881310.37475306X-RAY DIFFRACTION89
1.9451-1.99770.31621420.30445822X-RAY DIFFRACTION99
1.9977-2.05650.31011440.26025844X-RAY DIFFRACTION98
2.0565-2.12290.25921420.23835778X-RAY DIFFRACTION98
2.1229-2.19880.26711410.22385765X-RAY DIFFRACTION98
2.1988-2.28680.27231410.21815757X-RAY DIFFRACTION97
2.2868-2.39090.2531420.20975720X-RAY DIFFRACTION97
2.3909-2.51690.2691410.20855782X-RAY DIFFRACTION97
2.5169-2.67460.2391410.20025777X-RAY DIFFRACTION97
2.6746-2.88110.22751450.20615842X-RAY DIFFRACTION99
2.8811-3.1710.25131460.19635980X-RAY DIFFRACTION100
3.171-3.62970.20011460.17845954X-RAY DIFFRACTION100
3.6297-4.57250.15521480.14885998X-RAY DIFFRACTION100
4.5725-48.10980.17781500.15676134X-RAY DIFFRACTION100
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)
13.0880.0725-0.96061.2413-0.00972.5801-0.1405-0.3572-0.3991-0.01080.05380.05920.311-0.1267-0.11160.2823-0.0252-0.02880.41710.09510.2761-30.424228.4271-2.711
24.13110.3653-1.93491.0309-0.31483.93460.16020.1181-0.135-0.00080.04450.09930.1999-0.4269-0.0930.2283-0.0179-0.07350.29180.03160.2601-32.598332.499-13.6163
32.49430.0586-0.76522.29680.62363.90560.187-0.22220.0370.35680.0386-0.14640.15090.1043-0.05920.241-0.0156-0.04940.37490.01470.2552-20.42937.5111-7.3675
41.7637-0.61380.12051.7014-0.46761.10160.0371-0.12860.1085-0.04950.0685-0.1877-0.14130.36720.01970.2369-0.0303-0.00160.3731-0.04350.3132-16.632943.2334-15.1134
52.04480.5353-0.40381.8632-1.19173.45190.0721-0.57110.23680.22550.12110.1442-0.4773-0.0663-0.15230.28640.0391-0.00810.4279-0.04170.2873-31.361845.5522-0.4068
61.377-0.26911.3391.3806-0.72851.5808-0.0609-0.4684-0.53010.08820.2350.08440.0871-0.4305-0.12550.4795-0.0902-0.01790.69740.11010.4506-14.149124.944621.96
73.312-0.09940.53770.97260.02541.8033-0.2038-0.28260.00850.08180.1472-0.04610.0543-0.2477-0.02510.3295-0.0425-0.06250.51920.0510.3441-6.719627.181220.8856
81.8633-0.153-0.45511.5899-1.02864.57660.15270.059-0.5155-0.2214-0.3793-0.10280.5254-0.1015-0.04870.622-0.0160.0320.40030.01610.6108-11.421318.5181.7166
91.2832-0.26030.12230.6956-0.42210.7119-0.0831-0.1589-0.75340.5547-0.28380.17770.5196-0.662-0.18220.8492-0.30620.09450.67840.08530.6081-19.73414.301813.2514
101.09510.39680.06124.2367-3.28173.1158-0.18790.3209-0.0855-0.1424-0.1151-0.04730.8293-0.1137-0.30671.0241-0.2380.15420.6627-0.09830.7189-17.962212.1123-2.0617
110.31670.18480.04643.6389-1.1970.38690.15120.1416-0.37170.4135-0.29260.85840.7512-1.0322-0.29840.9529-0.3350.091.0934-0.09620.7139-23.737412.11262.7719
121.3883-0.5228-0.37922.4043-2.02853.148-0.0726-0.0343-0.77780.0803-0.30020.08790.5861-0.8981-0.2460.6266-0.31960.00540.67370.00140.6679-19.238516.00116.8859
130.2119-0.16870.44531.6341-1.89622.5481-0.7118-0.2256-0.68380.4911-0.0148-0.19791.13010.1433-0.06711.374-0.10690.18760.4976-0.04480.7206-12.14829.234-1.7996
142.5111-0.08540.75233.4951.68354.3408-0.3953-0.694-0.09110.4650.0497-0.11830.15470.0473-0.16471.20690.0206-0.05370.60150.04380.8494-10.24810.444711.934
151.3048-0.54110.50551.8822-1.24411.2286-0.0717-0.22850.16490.17870.08890.0455-0.225-0.0353-0.03870.32820.03910.05410.2821-0.0430.2433-46.305358.3794-16.5114
162.39270.05120.2132.80.25821.91780.0505-0.02040.07470.1133-0.03990.4974-0.076-0.2132-0.01980.2577-0.00930.07080.24220.00260.4174-64.488976.251-38.6321
172.30270.07990.99651.36290.02531.3209-0.0677-0.1712-0.233-0.05480.07610.12920.1513-0.0722-0.19570.2481-0.00130.02630.18840.02060.2281-48.038639.793-28.9061
181.8039-1.92921.80422.0705-2.03743.89120.0281-0.2207-0.4896-0.02290.3890.53650.0296-0.5255-0.28910.3143-0.0484-0.05420.28030.06310.4225-65.346745.6731-41.2334
191.1458-0.24120.48511.3429-0.17920.7380.00030.09760.0561-0.1270.10650.2749-0.1085-0.0994-0.06080.2818-0.01180.04080.18390.00380.2908-59.305368.3682-46.8686
201.9781-0.45010.23811.70640.14821.98510.139-0.3977-0.36230.3139-0.17090.28260.0269-0.1057-0.06750.3077-0.03430.06680.27720.00860.3485-60.159561.6412-40.2138
211.0428-0.13430.1231.7869-0.98591.08430.11930.0882-0.0784-0.2361-0.02790.24750.1194-0.1044-0.10.29080.0001-0.00650.2181-0.01210.2734-58.139761.0285-51.562
220.8216-0.06780.59110.7237-0.57170.83030.20160.02010.0986-0.2174-0.05770.0201-0.3796-0.2966-0.07550.2956-0.01110.00430.4036-0.00050.2773-30.563539.3172-11.968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 118 )
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 150 )
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 174 )
6X-RAY DIFFRACTION6chain 'A' and (resid 175 through 197 )
7X-RAY DIFFRACTION7chain 'A' and (resid 198 through 276 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 11 )
9X-RAY DIFFRACTION9chain 'B' and (resid 12 through 30 )
10X-RAY DIFFRACTION10chain 'B' and (resid 31 through 41 )
11X-RAY DIFFRACTION11chain 'B' and (resid 42 through 56 )
12X-RAY DIFFRACTION12chain 'B' and (resid 57 through 77 )
13X-RAY DIFFRACTION13chain 'B' and (resid 78 through 90 )
14X-RAY DIFFRACTION14chain 'B' and (resid 91 through 99 )
15X-RAY DIFFRACTION15chain 'D' and (resid 2 through 112 )
16X-RAY DIFFRACTION16chain 'D' and (resid 113 through 203 )
17X-RAY DIFFRACTION17chain 'H' and (resid 3 through 108 )
18X-RAY DIFFRACTION18chain 'H' and (resid 109 through 123 )
19X-RAY DIFFRACTION19chain 'H' and (resid 124 through 161 )
20X-RAY DIFFRACTION20chain 'H' and (resid 162 through 187 )
21X-RAY DIFFRACTION21chain 'H' and (resid 188 through 243 )
22X-RAY DIFFRACTION22chain 'C' and (resid 1 through 9 )

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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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