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- PDB-8shi: Valpha3S1 Vbeta13S1 HLA C 0602 VRSRRCLRL -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8shi
TitleValpha3S1 Vbeta13S1 HLA C 0602 VRSRRCLRL
Components
  • (T cell receptor ...T-cell receptor) x 2
  • Beta-2-microglobulinBeta-2 microglobulin
  • MHC class I antigen (Fragment)
  • VAL-ARG-SER-ARG-ARG-ABA-LEU-ARG-LEU
KeywordsIMMUNE SYSTEM / COMPLEX / T cell receptor / psoriasis / TCR HLA-C / HLA-C6:02 / ADAMSTL5
Function / homology
Function and homology information


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 ...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 / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / 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
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.90001719663 Å
AuthorsLittler, D.R. / Anand, S. / Vivian, J.P. / Rossjohn, J.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Complimentary electrostatics dominate T-cell receptor binding to a psoriasis-associated peptide antigen presented by human leukocyte antigen C∗06:02.
Authors: Anand, S. / Littler, D.R. / Mobbs, J.I. / Braun, A. / Baker, D.G. / Tennant, L. / Purcell, A.W. / Vivian, J.P. / Rossjohn, J.
History
DepositionApr 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen (Fragment)
B: Beta-2-microglobulin
C: VAL-ARG-SER-ARG-ARG-ABA-LEU-ARG-LEU
D: MHC class I antigen (Fragment)
E: Beta-2-microglobulin
F: VAL-ARG-SER-ARG-ARG-ABA-LEU-ARG-LEU
G: T cell receptor alpha
H: T cell receptor beta
I: T cell receptor alpha
J: T cell receptor beta


Theoretical massNumber of molelcules
Total (without water)188,02610
Polymers188,02610
Non-polymers00
Water181
1
A: MHC class I antigen (Fragment)
B: Beta-2-microglobulin
C: VAL-ARG-SER-ARG-ARG-ABA-LEU-ARG-LEU
G: T cell receptor alpha
H: T cell receptor beta


Theoretical massNumber of molelcules
Total (without water)94,0135
Polymers94,0135
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: MHC class I antigen (Fragment)
E: Beta-2-microglobulin
F: VAL-ARG-SER-ARG-ARG-ABA-LEU-ARG-LEU
I: T cell receptor alpha
J: T cell receptor beta


Theoretical massNumber of molelcules
Total (without water)94,0135
Polymers94,0135
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.001, 192.963, 211.462
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein MHC class I antigen (Fragment)


Mass: 32202.309 Da / Num. of mol.: 2 / Mutation: C2S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-C / Variant: 06:02 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F6IQM2
#2: Protein Beta-2-microglobulin / 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 BL21(DE3) (bacteria) / References: UniProt: P61769

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T cell receptor ... , 2 types, 4 molecules GIHJ

#4: Protein T cell receptor alpha


Mass: 21604.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCRAV / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Protein T cell receptor beta


Mass: 27182.135 Da / Num. of mol.: 2 / Mutation: S169C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV / Production host: Escherichia coli BL21(DE3) (bacteria)

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Protein/peptide / Non-polymers , 2 types, 3 molecules CF

#3: Protein/peptide VAL-ARG-SER-ARG-ARG-ABA-LEU-ARG-LEU


Mass: 1144.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: ADAMTSL5 / Source: (synth.) Homo sapiens (human)
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.94 Å3/Da / Density % sol: 58.13 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: 20% w/v polyethylene glycol 3350, 0.2M NaSO4.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953728 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953728 Å / Relative weight: 1
ReflectionResolution: 2.9→48.2 Å / Num. obs: 48398 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 66.046152005 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.083 / Net I/σ(I): 8.4
Reflection shellResolution: 2.9→3.06 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7008 / CC1/2: 0.44 / Rpim(I) all: 0.705 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.90001719663→48.2 Å / SU ML: 0.51380713506 / Cross valid method: FREE R-VALUE / σ(F): 1.35179031073 / Phase error: 31.8727937447
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.290914703424 2419 4.99876012564 %random selection
Rwork0.234571561804 45973 --
obs0.237350055406 48392 99.9876027935 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.8752400949 Å2
Refinement stepCycle: LAST / Resolution: 2.90001719663→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12829 0 0 1 12830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011992119733113169
X-RAY DIFFRACTIONf_angle_d1.6445762997717908
X-RAY DIFFRACTIONf_chiral_restr0.07892555587171887
X-RAY DIFFRACTIONf_plane_restr0.01076141560052359
X-RAY DIFFRACTIONf_dihedral_angle_d24.60824026814808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.901-2.95920.4015236560861460.3403751678212660X-RAY DIFFRACTION100
2.9592-3.02350.4187053881161260.3345580398362688X-RAY DIFFRACTION100
3.0235-3.09390.3772407666671520.3338636712662661X-RAY DIFFRACTION100
3.0939-3.17120.4063297065091450.3263778403772670X-RAY DIFFRACTION100
3.1712-3.25690.4163533566221370.3312382632292697X-RAY DIFFRACTION99.9647266314
3.2569-3.35280.3915239671231340.3130224574192660X-RAY DIFFRACTION100
3.3528-3.46090.3592395864431360.2800881440742702X-RAY DIFFRACTION100
3.4609-3.58460.3525170192361570.2569358551652648X-RAY DIFFRACTION100
3.5846-3.72810.3245617470691380.2585565373282713X-RAY DIFFRACTION100
3.7281-3.89770.3106392933671520.2493961327592684X-RAY DIFFRACTION100
3.8977-4.10310.2606299000651250.2268719935232712X-RAY DIFFRACTION100
4.1031-4.360.2367733096651490.1946472293172688X-RAY DIFFRACTION100
4.36-4.69640.2483068682231380.1695382070832692X-RAY DIFFRACTION100
4.6964-5.16850.1983825774271450.1739192939672726X-RAY DIFFRACTION100
5.1685-5.91520.2660071708891490.2036686209282736X-RAY DIFFRACTION100
5.9152-7.44810.2684854418681420.235575228582752X-RAY DIFFRACTION100
7.4481-48.20.2505468115311480.2053346036632884X-RAY DIFFRACTION99.8353638459
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)
13.833240630630.5899995612230.9612670128323.663372856490.1171920883921.507779868910.0706338306267-0.0664186557089-0.1007008637980.279507866702-0.08134823322110.09033486167970.0657781654534-0.07720050540760.0225928308990.3648302291680.0596854209906-0.04566451175520.349823586374-0.05204462933830.424464004032-11.4166640603-17.6276314693-43.2896767615
29.87643399625-6.57242554511-1.665067782415.665369756241.843112778840.8504805003760.3504934111240.522222947467-1.385775147240.175246050857-0.7614035976731.452880296460.211124760597-0.5642495773840.2709664781820.40710575558-0.02015998058780.009076335532570.5439137472130.1250450874950.594542857893-19.369925241-38.5443709431-40.632479982
39.3462593258-2.382917009492.60966874234.92100251053-1.91648719985.033918760340.1014676212130.0346323562256-0.1922787631560.167367816503-0.151455504443-0.0139532424599-0.005592727851440.5618781973020.008055965706190.361468716632-0.0430219549267-0.0953502380630.317668085713-0.009178308587870.3990273582815.03269447805-50.7445272703-38.9267829704
46.824185057714.84589834683.917228937638.099132911714.816023058146.105213201480.133745308327-0.512365000287-0.6913439614860.304464251072-0.160900407096-0.5082807482730.568354698423-0.0143941089007-0.05328817959610.3039256147660.04865524663550.006114423444910.4352932925360.03551208163750.4866170423922.73601481437-40.1572272865-53.4298268401
51.325193678040.585719448256-1.340022116237.266839443485.067608985536.32819682329-0.1875407246390.22634326750.231941766231-0.293810016326-0.226277864970.870325706875-0.396333640799-0.3319397292920.4703323848840.2841367853130.0794914317977-0.01438231929060.3468724247240.03240796259590.533072237105-0.0316888651292-37.8733530387-55.0798193631
63.385346487740.4109254007630.1647716069082.435331902692.075169109832.432757932860.06605516813940.4907290763390.00654063661418-1.210384648010.0813972218285-0.302018003109-1.208813259920.18937324059-0.2071094569880.351409718340.02036594232960.06155710861910.4172653002660.04211903946210.4342220478914.38127544732-28.9888261669-59.0237472497
72.002416351772.001948802660.3791004652312.00131760463-5.712349784434.05081261492-0.7209409754940.4938390032841.990730472491.20630901265-0.120286150698-1.922531905850.144246075827-1.442330134550.7600031927230.449045972329-0.0517764267146-0.1032451591810.522176282142-0.02436373773820.4819858216715.62623753357-37.4389466468-69.1533126118
83.81706214539-6.06963456353-4.614647861729.729670557717.377759712275.60419183923-0.460155368241.0672296355-0.434455605242-1.88143178045-0.7208534007261.437860845-2.40188979973-1.175798993961.157761569210.8492911188040.0360005228506-0.2376473002090.812642354966-0.03034409941230.745257634478-4.12267268057-33.6302743637-64.8923423465
95.507105508996.718518797365.792729379318.346429514826.909937270946.226192507810.518520468374-0.4404732624650.1566557694270.893635402795-0.6515522287780.6534897134980.958386066278-0.471789127692-0.03794549491040.4051898530930.03167858909160.0302652173860.3795323377140.02187681230240.733083674799-3.13894620553-26.0482692594-45.2841323376
103.51776236232-3.77423071324-3.981418382448.202022953826.246962262197.70094590049-0.3248033290720.06437390325820.008390161526290.454590811939-0.03211976711380.02339230482140.483590782037-0.2844370644680.4330638555220.331216224253-0.0116824280261-0.05901079108360.3722839050030.05780429018140.451421479377-2.66272840085-36.2876530514-57.5637563924
112.890975561593.21117503008-4.156634153294.42208310206-3.258647738248.10884845456-0.005919922396770.736048110399-1.348068111620.2932923283280.527684450075-2.022056746390.3991647861780.480345667782-0.4808888151390.530858411754-0.2144123081950.02776292851880.569316079227-0.08883039491430.8045901063566.40989402592-49.6883998517-66.6868453518
122.541529534551.241040502821.91400519437.513241448985.59958659144.58419871016-0.176674205340.1762095542420.705082360678-0.8673159728120.0768930712281-1.6420453923-1.389250382490.533608246670.0127794810560.544418942037-0.0203813302339-0.02168015504190.4703349583580.1305548199670.7970596719477.77787316391-35.4247163811-61.5001615658
136.39368209321.597682903552.377564168073.948291722843.994945667544.156668426680.320914156899-0.7171666232290.597268665238-0.8750252270840.264247879467-1.07746939872-0.9249436484690.909468871569-0.4846138447090.4594631751470.0119574224586-0.02783103055240.519707202035-0.1940359920880.89089127091713.5075009743-25.5431333013-56.3933175082
143.817125756790.831103032450.74434748785.543180940946.040345202066.63788204066-0.210456394293-0.466245756439-0.8983973337981.174339904260.114267223725-0.00412932790991.072653139640.2629872191910.2257675454540.4951962546870.06381053266210.08976529721440.278282406945-0.00378303279420.8507239966168.6454490825-44.6737972547-56.3707645657
155.799408194236.074694308912.042856403746.94695107162.936277775156.250604933720.4869373843570.1164483262640.2084437229530.0986763240528-0.4672044197461.09730471583-0.5074800891-0.257611152168-0.123389760060.4454119737910.154306772082-0.1577658500960.480756548567-0.03670832740990.631702394607-16.6950358198-13.4075783104-41.822544342
162.38277767424-1.00182767413-0.1673555344813.55131857777-0.3255956688084.69766196990.1272716973120.3921905424790.419649372965-0.400750738241-0.232948758009-0.181489455281-0.4631334293420.2367680404840.077763820360.575530562129-0.02792699844850.130527487150.4891339609280.1061378866660.482378314841-23.0839194186-21.5985051705-86.928568476
173.926077736430.756779009581-0.158125936432.58076214826-0.3354620854942.946495542180.1143174609170.4086720699230.108456380571-0.183094981459-0.01020563528520.389346517764-0.349322960154-0.54042097113-0.03753930955740.8096680649310.2343950588610.06833181271310.6591410016940.01131398746310.502038504405-37.9597212647-22.3543354984-90.2860423357
183.1832035271-1.35233470054-0.137213567066.898020860550.1877385239743.788815492430.1883296508320.4395103669870.491748266513-0.718163170685-0.4235228561340.493360641961-1.16789682899-0.7603471082890.231068599410.8795073823860.25161980516-0.03046255655330.634623471063-0.02287672514410.570801840236-36.27418577187.80545821553-70.7335028641
192.896588883171.775340486960.2598809997012.9953710364.356536589859.118423979881.12252113524-1.25622538528-0.540124247801-0.1061456159250.699759015278-0.000434444019021-0.437279857152-0.56892656351-1.228497435020.9807485973630.308532568320.06312018228210.6600672418810.3710978859261.06696529322-26.22974862961.93254236415-88.2167560747
204.2875367634-1.1253658493-3.142309830823.46567753851-1.989526253374.886160971681.05427512499-0.9339484183730.3431503932070.418341842882-0.22474790428-0.676927283207-1.758242785190.958471031906-0.7793066683550.997208012344-0.210183099490.4129241842310.59786140883-0.1181871296990.784021584131-19.0426366282.5169551932-74.6505637471
212.707243831781.75072711732-0.7669685560463.569654553931.553742862592.178119883340.3567247828570.6873881051590.0950247154982-0.1905844952790.4383712530540.0272848354477-1.62574663104-0.539338406157-0.3151985336531.38939545112-0.1687671671170.4351034863630.4038743166150.341328741260.812343115041-17.0684904531-0.841086695089-89.9692067715
224.158714101563.18207436436-0.8439911194523.578690199-2.088710720951.993924239360.0380736824159-0.281985020473-0.251551896947-0.31164870378-0.194528154136-0.425409126568-0.3801802396640.30668024130.01633965901721.32212757033-0.6261524608820.8357715165890.726999336275-0.06750190301191.74627423256-7.306180171556.46626938672-84.0903803828
239.933322514995.64469174433-7.886611367712.00225296299-1.601972852779.8588536781.344029340330.677761775198-2.21801727669-1.18054029282-2.24892801963-1.70185724045-0.1488020935410.7562639012160.2833318333771.157880376590.1000770522150.2888095820640.3898530880460.08815226406771.23708057882-10.4841755993-4.64886217977-81.6875402165
245.599326690711.11166114143.390786601726.24825265275.02182411126.363413547370.426981607383-0.6711073880260.364377447585-1.12444171771-0.409323823158-0.922517927392-0.655684352054-0.5776167283650.07487281197250.7890362752790.0198551255820.236725004350.7463653721360.1951373314160.721740114209-23.2770701489-6.02851381326-83.4645457336
251.606175142940.666447393985-1.303951184561.64673080561.005046557842.78722814012-0.5603917801560.3887703122070.130370390451-1.59535407529-1.64292557535-0.572165453573-1.891750516650.4909214211841.997171122281.990053454890.120818796330.3712281449880.715819914260.1096514579161.4682421273-10.317626511513.5776937352-73.8280751612
269.403237066994.356167200677.668631019464.534613823154.261630883358.167711672430.2563763659870.5036483238440.672640423445-0.37481730853-0.0545447187338-0.198406338837-0.6113687932530.483612971729-0.1882855038611.50599132688-0.03829243749190.2466299081320.6177749447960.1207210471810.770536453256-17.63173761115.06059539826-92.5773290707
277.308921784912.609447832892.202703583762.83530405243.202795568773.75666982430.382043454704-0.4429331644961.715349791290.748107870285-0.3707550710270.3712595144750.807086261421-1.32771380604-0.5528488978771.350286341150.1984247790780.4318254284490.5700284970350.1044234239950.832649007966-20.149210397611.6285624636-79.5610653487
285.834229946682.33787329692.939474442614.22148352634-2.610595301525.840391695510.8310771252360.489658670682-0.226921158732-1.35925832711-0.101418055906-0.953426390946-0.2105700607770.206708865234-0.6888044130260.7550857998230.3038158844490.2785026986870.6963460062010.07902443502830.674183614915-31.2894499367-28.5689263239-90.7283137791
295.38391025127-2.77095231406-2.444462505926.14752473875-1.233224598747.73029515803-0.2346439644330.0611347065601-0.401860385417-0.261315126419-0.1976324824430.09525987456670.730362014928-0.6804220554640.07133134651360.312337173376-0.03070619635680.009297770895290.406946074665-0.1258077551161.00734926292-48.29113796931.30244033099-32.6368109623
305.50987619097-3.95242291518-1.551640666562.906853233551.056674631540.7796929261320.6494226109490.953815795809-0.365941796673-0.696987367061-1.165310958380.51692702435-0.152267532205-0.4216469055010.6378723341370.5330173403040.0470228705437-0.1299951997510.64077829502-0.04126292419550.701889602359-35.1160258888-4.97470963349-42.4743097773
317.71513067495-0.650796454605-1.050142832877.410070548443.64576647533.228546041660.00218539028438-0.483503513225-1.19229098781.04689309385-0.2613165453320.7615073710460.8932416999210.2775146883940.274907583850.577341984590.04717225416380.06819334029850.550763958710.1083915351850.808736215778-36.5173406273-6.81860145184-35.8048334548
322.26696413978-1.88437264569-0.9473149093985.341881619360.3222890680521.275433367310.3038430450460.501276932401-0.606004361307-0.279683868978-0.433267805360.119364376525-0.164135851524-0.101285988570.2028901117130.285104699564-0.0170066197057-0.09915343414130.570427030496-0.1322724215420.84270987458-36.6682559768-2.59113001104-39.6714905496
332.62818183169-2.45156988327-4.248312959985.773246839515.215170074498.422976300070.4528121417941.168155957750.0724337731571-0.721066080688-0.9721730877021.26850918525-0.914198650818-1.602823228990.3967833096230.3314177818960.0956258126639-0.06010244347610.5489923437730.08200928387360.900148724274-41.00157180444.06951881188-40.3459878104
344.55993398674-1.15946876094-1.115389539619.81156381992-2.923453055966.50115244314-0.02902620283580.0920756036452-0.3755457504420.858984701842-0.2265939092060.3934551303890.0745133541869-0.6815504826210.1679417686990.379743421621-0.02815168634050.1017509925640.549639235999-0.1037067228460.650958935862-54.037661201526.3149272967-27.658013944
355.118764825563.846214402160.4907258254325.455859384983.558703820043.97341346292-0.5100386935741.766660540530.57509534257-1.02616364591-1.056811401461.60567012630.246745815617-1.544916166781.532942838620.7147426328940.0960815990227-0.2218874402680.961415688846-0.224289454931.03718319354-54.370010345626.5888805843-42.5767610351
362.68991831938-0.5910001034353.370638104038.13893782172-2.904840007199.09534471193-0.3473102831190.0867778821537-0.5620426738610.494874374793-0.452795580021-0.3451135429430.7459667521160.4310749336160.755911222060.403002073657-0.02662490387680.2359433585240.538849981763-0.01677949626980.987716098767-46.756734691120.2269151169-22.8540339695
372.84873156638-0.778711430491-0.3822455738787.246372490273.630994981318.490458793050.8177536385931.026217146992.858690124-0.952617263967-0.617591910760.864301655312-1.0254147662-2.600437411030.08342570042240.7640361805350.318959101804-0.110582150520.841210918396-0.09046477508261.17151225832-57.974817852933.0324581977-38.4847556547
383.91023923525-0.47590873920.395091188122.63810792415-1.361204605323.68721300730.1992077306690.06388251804780.0210988367226-0.221299412723-0.0540720993332-0.0565423137217-0.0620909380009-0.0864486188692-0.1298730606130.4800046552390.02848086864920.04855476608340.346860557912-0.03509270486510.553820211469-23.74392046578.70706100187-49.4985896039
393.47637600764-0.908605040165-0.0003946100633920.244104074435-0.04699634621940.01727719219621.076984911081.0605441422-0.393159712727-2.91057882836-1.461886635640.763801227687-0.176399360172-0.042465612874-0.07438919429971.416228805270.375406635335-0.02599423626940.517332552029-0.03314661159730.578678307661-33.478468350328.0464013161-52.7117607425
401.9456454254-0.939611595101-0.5776291726463.429569102151.389862212048.79065530247-0.0492113616820.007651577558830.0091274447352-0.108467382209-0.2089699325580.4426151154530.415956230176-0.2904715130760.3301162860990.3547070073380.0009952137305720.03717176007880.3084036002310.05243178629180.634400314619-42.41403809829.1204668668-33.5538534593
411.135006628840.334788679663-0.8276203891113.046531570341.257689559224.96675768664-0.0307192302597-0.184456572279-0.25494466107-0.0249815153773-0.1915066567060.108672764714-0.1933740052850.2119886133210.179894837490.3019406613150.0640173262290.04582739312140.4561612284190.04496208335240.539524059293-35.430385315834.7704483587-34.4139793996
424.041215789263.242876439621.676652187354.754764060770.6904638989842.876240440070.4739111132350.0314732482124-0.1297700493450.241542785162-0.4430811990530.01883176650230.3488703953230.0191575959182-0.08844746931380.4533536203990.1240485929030.1446406703350.53052663468-0.06495131484690.662334735956-29.9889021879-56.6976795573-87.4260577032
434.990235556533.727524448181.720841481879.576534358462.940251094354.61059336880.08642754109810.5343739156220.1785345000620.05510552115380.02611894327670.49222994385-0.169955685538-0.396978584718-0.1310808426150.4141466083660.09584230921340.08994333881240.5759304582320.04378124942950.434323796155-31.8128865851-50.7680225251-87.3268757767
447.980622784175.18237397367-4.181737753084.62086568127-4.57749231786.839617740320.32332654805-0.101608934092-0.438515074892-0.525189180307-1.16559508342-0.3877054142851.193284368580.4450112130990.6105531553140.4965839645790.1683295591310.06522002145760.589603877904-0.05987265438310.519072587982-27.4322126419-58.3494576323-92.6227929361
453.42640064554-1.729955677141.200683769923.685377779322.645455595924.19022867436-0.5695793427580.831813925865-4.009883322770.67493208936-1.535222102920.2445161267342.29557815496-1.473523362051.676356617041.49041140278-0.5161154785430.2179485718291.19808454575-0.6473245409281.83550049842-40.7579811417-83.9730628888-97.9403039495
467.17701703233-1.145255119563.053000584951.64144651776-0.8129230932522.31646286168-0.02629713744321.33782385225-0.05299609284380.505501041473-1.025571570610.2816594403010.1927043470840.8916757706420.5294543239130.811615895777-1.46192378991.016224678191.52853230851-0.7540828184792.25900881027-31.3309308097-84.8344369549-111.804116558
471.89434696643-1.191410960641.205763125285.43736916721.944268642693.05892148469-1.125935311833.70315392849-4.428508839430.997129847543-1.00912368772-1.472344549260.689984446301-2.533894512292.179905578681.07926489084-0.0560825221762-0.1284168706661.52835968743-0.4499726393411.70185890675-25.1993945631-81.513527039-97.7711971988
481.2673941228-2.63006409787-0.7930416891518.91692886783-1.891024169933.776384572910.2933586835052.05697115746-2.04986635163-1.71494936619-0.5594538193790.2162590857390.821184577452-1.093540157660.384313448831.35957543908-0.0664982871979-0.267294866061.18536906971-0.6434596832051.88050938944-36.4018327935-77.0457887808-103.449364664
499.8567087031-3.44190865686-5.994260415862.041873743031.826807728044.8282687214-1.457824664960.465653583064-4.103598523290.1898053540230.0558012906029-2.321861304323.263283694360.4191265323971.775554467261.75541746420.04750036987120.4889865361320.9797420769330.06853790792922.8413351407-23.5946128113-89.4275256537-105.199490251
502.42951795539-0.455519413363-1.016718860263.610004474891.74389607543.344750580740.1440701000560.714351113398-0.328271335095-0.953842304342-0.220174793409-0.205339283765-0.7218546031920.02219600877230.1068085554460.7895817948350.09316204581360.1780242134580.768346165439-0.04117301731270.45247406482-21.2946426814-43.9879550836-107.15583189
516.93844716758-2.00916913633-4.12174188826.933330178110.6415474736656.06020026909-0.4238223518640.06687246209350.08563171753570.1483808876320.5548874532310.0494647107441-0.596742862273-0.437737612088-0.3308632315890.4789805284880.06545212003510.06321794085680.591754089639-0.02668888997350.341613333079-22.9689524193-45.8160829085-104.501814576
521.573406584380.09252760836131.466340112419.382314300791.964217132711.901468959330.2082129503631.266571379430.333725603392-0.304563137296-0.860738195347-1.209567608630.909319752471-1.80337253538-0.162355201531.27581353442-0.2009627753880.1161428025411.71397887867-0.953757889620.505474071455-21.9963256192-68.2717225113-117.968731945
535.34557478391.81978010204-1.32171930149.04508319397-2.926579644435.816853168180.0958894939890.284982512383-0.814574272792-0.617550297077-0.5527515154650.1096615547910.837513090354-0.9401278121860.3353143867210.840748832863-0.0520649878360.1333106260281.18114973141-0.4675288802790.869251176578-32.1473181726-73.0013086829-112.219922873
540.726197979771.618321752191.225230956867.95785133446-0.7576226842174.83967761093-0.4346059102432.65757917716-0.399259924022-0.5805292959570.4685699621381.474158519970.31139232506-2.5960588859-0.177383752561.09167388025-0.5260928025380.1808711479151.81199274485-0.6572586546791.40006944519-40.3242485203-77.5530543152-112.267302499
558.67263729941-0.300181900791-0.4195066630744.54125295913-3.349928512942.51554949877-1.474572402613.51660289478-1.19913430467-1.78516487451.995106639950.50296861329-0.417530065136-1.39598091146-0.6410864223041.09349784097-0.2501709888110.0515573418422.45922417844-0.35884145930.904037793068-40.6003022978-72.3801906622-121.065435855
563.22169542263.92918174696-2.890432841728.64705734136-1.839874830253.60066427691-1.39817230452-0.5774770809570.0819005756593-2.591767973550.601316268518-0.3390779449250.249594663821-0.5958459025970.6507669414971.51123559903-0.08942149515970.08251582927872.20243120394-0.4424731092960.839605379355-25.4221839801-66.3841586844-126.321130803
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 162 )
2X-RAY DIFFRACTION2chain 'A' and (resid 163 through 188 )
3X-RAY DIFFRACTION3chain 'A' and (resid 189 through 274 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 19 )
5X-RAY DIFFRACTION5chain 'B' and (resid 20 through 30 )
6X-RAY DIFFRACTION6chain 'B' and (resid 31 through 41 )
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 46 )
8X-RAY DIFFRACTION8chain 'B' and (resid 47 through 51 )
9X-RAY DIFFRACTION9chain 'B' and (resid 52 through 61 )
10X-RAY DIFFRACTION10chain 'B' and (resid 62 through 71 )
11X-RAY DIFFRACTION11chain 'B' and (resid 72 through 77 )
12X-RAY DIFFRACTION12chain 'B' and (resid 78 through 83 )
13X-RAY DIFFRACTION13chain 'B' and (resid 84 through 90 )
14X-RAY DIFFRACTION14chain 'B' and (resid 91 through 99 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 9 )
16X-RAY DIFFRACTION16chain 'D' and (resid 2 through 84 )
17X-RAY DIFFRACTION17chain 'D' and (resid 85 through 174 )
18X-RAY DIFFRACTION18chain 'D' and (resid 175 through 274 )
19X-RAY DIFFRACTION19chain 'E' and (resid 1 through 11 )
20X-RAY DIFFRACTION20chain 'E' and (resid 12 through 30 )
21X-RAY DIFFRACTION21chain 'E' and (resid 31 through 41 )
22X-RAY DIFFRACTION22chain 'E' and (resid 42 through 46 )
23X-RAY DIFFRACTION23chain 'E' and (resid 47 through 51 )
24X-RAY DIFFRACTION24chain 'E' and (resid 52 through 71 )
25X-RAY DIFFRACTION25chain 'E' and (resid 72 through 77 )
26X-RAY DIFFRACTION26chain 'E' and (resid 78 through 90 )
27X-RAY DIFFRACTION27chain 'E' and (resid 91 through 99 )
28X-RAY DIFFRACTION28chain 'F' and (resid 1 through 9 )
29X-RAY DIFFRACTION29chain 'G' and (resid 18 through 33 )
30X-RAY DIFFRACTION30chain 'G' and (resid 34 through 46 )
31X-RAY DIFFRACTION31chain 'G' and (resid 47 through 79 )
32X-RAY DIFFRACTION32chain 'G' and (resid 80 through 110 )
33X-RAY DIFFRACTION33chain 'G' and (resid 111 through 123 )
34X-RAY DIFFRACTION34chain 'G' and (resid 124 through 160 )
35X-RAY DIFFRACTION35chain 'G' and (resid 161 through 170 )
36X-RAY DIFFRACTION36chain 'G' and (resid 171 through 188 )
37X-RAY DIFFRACTION37chain 'G' and (resid 189 through 201 )
38X-RAY DIFFRACTION38chain 'H' and (resid 3 through 107 )
39X-RAY DIFFRACTION39chain 'H' and (resid 108 through 122 )
40X-RAY DIFFRACTION40chain 'H' and (resid 123 through 186 )
41X-RAY DIFFRACTION41chain 'H' and (resid 187 through 242 )
42X-RAY DIFFRACTION42chain 'I' and (resid 18 through 46 )
43X-RAY DIFFRACTION43chain 'I' and (resid 47 through 110 )
44X-RAY DIFFRACTION44chain 'I' and (resid 111 through 123 )
45X-RAY DIFFRACTION45chain 'I' and (resid 124 through 135 )
46X-RAY DIFFRACTION46chain 'I' and (resid 136 through 152 )
47X-RAY DIFFRACTION47chain 'I' and (resid 153 through 165 )
48X-RAY DIFFRACTION48chain 'I' and (resid 166 through 190 )
49X-RAY DIFFRACTION49chain 'I' and (resid 191 through 204 )
50X-RAY DIFFRACTION50chain 'J' and (resid 3 through 74 )
51X-RAY DIFFRACTION51chain 'J' and (resid 75 through 107 )
52X-RAY DIFFRACTION52chain 'J' and (resid 108 through 130 )
53X-RAY DIFFRACTION53chain 'J' and (resid 131 through 186 )
54X-RAY DIFFRACTION54chain 'J' and (resid 187 through 201 )
55X-RAY DIFFRACTION55chain 'J' and (resid 202 through 213 )
56X-RAY DIFFRACTION56chain 'J' and (resid 214 through 242 )

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  • 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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