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- PDB-5nme: 868 TCR in complex with HLA A02 presenting SLYNTVATL -

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Basic information

Entry
Database: PDB / ID: 5nme
Title868 TCR in complex with HLA A02 presenting SLYNTVATL
Components
  • Beta-2-microglobulin
  • Gag protein
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Human T-cell receptor beta chain
  • T-cell receptor Alpha chain
KeywordsIMMUNE SYSTEM / MHC / TCR / CD8+
Function / homology
Function and homology information


Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / 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 ...Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / 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 / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / CD8 receptor binding / Vpr-mediated nuclear import of PICs / antigen processing and presentation of exogenous peptide antigen via MHC class I / viral budding via host ESCRT complex / Early Phase of HIV Life Cycle / beta-2-microglobulin binding / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / 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 / Binding and entry of HIV virion / detection of bacterium / T cell receptor binding / Membrane binding and targetting of GAG proteins / 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 / Assembly Of The HIV Virion / 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 / Budding and maturation of HIV virion / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / host multivesicular body / 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 / positive regulation of cellular senescence / antibacterial humoral response / 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 / viral nucleocapsid / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium
Similarity search - Function
Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / 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 ...Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / 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 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / MHC classes I/II-like antigen recognition protein / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / : / 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 / 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
Gag protein / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Gag polyprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsRizkallah, P.J. / Cole, D.K. / Fuller, A. / Sewell, A.K.
CitationJournal: Front Immunol / Year: 2017
Title: Dual Molecular Mechanisms Govern Escape at Immunodominant HLA A2-Restricted HIV Epitope.
Authors: Cole, D.K. / Fuller, A. / Dolton, G. / Zervoudi, E. / Legut, M. / Miles, K. / Blanchfield, L. / Madura, F. / Holland, C.J. / Bulek, A.M. / Bridgeman, J.S. / Miles, J.J. / Schauenburg, A.J.A. ...Authors: Cole, D.K. / Fuller, A. / Dolton, G. / Zervoudi, E. / Legut, M. / Miles, K. / Blanchfield, L. / Madura, F. / Holland, C.J. / Bulek, A.M. / Bridgeman, J.S. / Miles, J.J. / Schauenburg, A.J.A. / Beck, K. / Evavold, B.D. / Rizkallah, P.J. / Sewell, A.K.
History
DepositionApr 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 17, 2024Group: 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 / 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 1.4Nov 6, 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: Gag protein
D: T-cell receptor Alpha chain
E: Human T-cell receptor beta chain
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Gag protein
I: T-cell receptor Alpha chain
J: Human T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,40826
Polymers189,14710
Non-polymers1,26116
Water75742
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Gag protein
D: T-cell receptor Alpha chain
E: Human T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,11012
Polymers94,5745
Non-polymers5367
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Gag protein
I: T-cell receptor Alpha chain
J: Human T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,29814
Polymers94,5745
Non-polymers7259
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.140, 85.140, 113.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
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
13LYSLYSPROPRODD2 - 2001 - 199
23LYSLYSPROPROII2 - 2001 - 199
14ASPASPARGARGEE1 - 2401 - 240
24ASPASPARGARGJJ1 - 2401 - 240

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


Mass: 31951.316 Da / Num. of mol.: 2
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
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 T-cell receptor Alpha chain


Mass: 22321.721 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 beta chain


Mass: 27440.178 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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Protein/peptide , 1 types, 2 molecules CH

#3: Protein/peptide Gag protein


Mass: 981.101 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: O11793, UniProt: P04591*PLUS

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Non-polymers , 4 types, 58 molecules

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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium Cacodylate, pH 6.0, 15% PEG 4000, 0.2 M Ammonium Sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.94→64.76 Å / Num. obs: 44013 / % possible obs: 99.1 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 12.4
Reflection shellResolution: 2.94→3.01 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3213 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BNU, 2V2W

2bnu

2v2w


Resolution: 2.94→64.76 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.879 / SU B: 42.429 / SU ML: 0.353 / Cross valid method: THROUGHOUT / ESU R Free: 0.448 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26326 2212 5 %RANDOM
Rwork0.1961 ---
obs0.19947 41746 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.995 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å2-0 Å2
2---2.92 Å20 Å2
3---1.17 Å2
Refinement stepCycle: 1 / Resolution: 2.94→64.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13316 0 73 42 13431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01913756
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211914
X-RAY DIFFRACTIONr_angle_refined_deg1.9721.93118670
X-RAY DIFFRACTIONr_angle_other_deg1.116327719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.20351646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57523.862712
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.13152194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2331596
X-RAY DIFFRACTIONr_chiral_restr0.1170.21947
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02115419
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022982
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5833.2966611
X-RAY DIFFRACTIONr_mcbond_other1.5823.2966610
X-RAY DIFFRACTIONr_mcangle_it2.6914.9398248
X-RAY DIFFRACTIONr_mcangle_other2.6914.948249
X-RAY DIFFRACTIONr_scbond_it1.723.4717141
X-RAY DIFFRACTIONr_scbond_other1.6963.4547117
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8125.10410381
X-RAY DIFFRACTIONr_long_range_B_refined5.91736.24314251
X-RAY DIFFRACTIONr_long_range_B_other5.91536.23914249
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A163220.12
12F163220.12
21B57120.12
22G57120.12
31D107440.12
32I107440.12
41E142040.11
42J142040.11
LS refinement shellResolution: 2.936→3.012 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 151 -
Rwork0.281 3055 -
obs--99.81 %
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)
13.5261.13950.81793.8293-0.27695.1036-0.1084-0.0884-0.0821-0.0306-0.0091-0.12810.25160.07990.11760.3640.00110.04270.0056-0.00030.025756.588226.011929.8952
23.1561-0.9367-0.001113.10170.57672.37110.1918-0.0131-0.39890.1559-0.0978-1.3110.36580.2126-0.09410.44430.0129-0.02370.43820.04660.446762.3247-6.086845.4486
32.8610.8916-1.51952.8811-1.81298.8964-0.0681-0.093-0.12250.04120.23190.25910.2142-0.4383-0.16380.3070.0177-0.00180.20910.04610.177842.95836.363643.4427
45.63512.5904-1.3164.5408-3.36252.6032-0.30590.36480.1107-0.0629-0.0513-0.48680.04090.13210.35720.2309-0.0267-0.060.1554-0.04950.198673.59751.145519.4893
58.2526-3.0003-2.28525.931.84366.53440.0864-0.27710.83530.2467-0.1412-0.4376-0.40110.25840.05480.4168-0.1593-0.11720.38960.18890.480776.994582.64328.0365
62.2752-1.20480.63329.4220.45792.5611-0.0927-0.11380.15180.1205-0.00860.3965-0.1761-0.32870.10130.19550.0049-0.03970.21040.02170.057150.99356.280624.9187
75.0349-0.5284-3.36552.67230.38836.8978-0.0205-0.28430.27670.1663-0.1307-0.0712-0.16990.2870.15120.37140.0187-0.18460.11040.04610.226360.823978.79936.6533
85.0038-0.67290.7054.02830.3285.5351-0.27950.53650.3731-0.2094-0.00020.1937-0.2944-0.03410.27970.4824-0.1279-0.20940.69110.17060.336495.077424.4424-6.3573
92.7469-0.45130.65044.552-4.540211.07190.213-0.35190.1904-0.24360.08080.1430.1397-0.2167-0.29380.3534-0.11680.0780.588-0.01270.395196.723223.2035-42.9018
104.97510.25941.91835.3122.25466.6425-0.22340.0437-0.1295-0.3019-0.16750.33340.2478-0.40660.39090.3991-0.2333-0.06760.98130.22480.478380.872815.9259-28.164
116.10952.6073.11551.40531.04515.7395-0.08880.14410.2098-0.18410.1630.1145-0.09740.0826-0.07420.16620.0440.04970.17070.10190.2645115.395228.850618.1651
126.9326-0.575-0.77587.00810.38034.6743-0.048-0.2424-0.4224-0.1652-0.034-0.34930.60510.40.0820.2473-0.00840.0030.4364-0.02330.3044126.706125.475448.9949
132.9061-0.27641.03035.0262-2.64737.1974-0.09290.04520.09830.33040.03610.5507-0.0901-0.60020.05680.2153-0.1090.08450.3189-0.05670.241396.076215.879623.6836
144.92453.79230.67098.22390.71811.9081-0.0148-0.14440.07520.1463-0.05170.14790.4433-0.09710.06640.24770.00310.09460.26990.06040.1298109.956123.614250.7051
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 180
2X-RAY DIFFRACTION1C1 - 10
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D0 - 115
6X-RAY DIFFRACTION5D116 - 210
7X-RAY DIFFRACTION6E0 - 115
8X-RAY DIFFRACTION7E116 - 247
9X-RAY DIFFRACTION8F0 - 180
10X-RAY DIFFRACTION8H1 - 10
11X-RAY DIFFRACTION9F181 - 276
12X-RAY DIFFRACTION10G0 - 99
13X-RAY DIFFRACTION11I0 - 115
14X-RAY DIFFRACTION12I116 - 210
15X-RAY DIFFRACTION13J0 - 115
16X-RAY DIFFRACTION14J116 - 247

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  • 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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