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- PDB-6pvd: Structure of human MAIT A-F7 TCR in complex with human MR1-NV18.1 -

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Basic information

Entry
Database: PDB / ID: 6pvd
TitleStructure of human MAIT A-F7 TCR in complex with human MR1-NV18.1
Components
  • Beta-2-microglobulin
  • Human TCR alpha chain
  • Human TCR beta chain
  • Major histocompatibility complex class I-related gene protein
KeywordsIMMUNE SYSTEM / MAIT / MR1
Function / homology
Function and homology information


positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / 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 / 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 / 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 / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / 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 / 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 / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / defense response to Gram-negative bacterium / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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 / MHC classes I/II-like antigen recognition protein / : ...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 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-N18 / Beta-2-microglobulin / Major histocompatibility complex class I-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsAwad, W. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Ligand-dependent downregulation of MR1 cell surface expression.
Authors: Salio, M. / Awad, W. / Veerapen, N. / Gonzalez-Lopez, C. / Kulicke, C. / Waithe, D. / Martens, A.W.J. / Lewinsohn, D.M. / Hobrath, J.V. / Cox, L.R. / Rossjohn, J. / Besra, G.S. / Cerundolo, V.
History
DepositionJul 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2May 13, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 27, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 11, 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
C: Major histocompatibility complex class I-related gene protein
D: Human TCR alpha chain
E: Human TCR beta chain
F: Beta-2-microglobulin
G: Human TCR alpha chain
H: Human TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,84914
Polymers188,1008
Non-polymers7496
Water21,0421168
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: Human TCR alpha chain
H: Human TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5348
Polymers94,0504
Non-polymers4844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Major histocompatibility complex class I-related gene protein
D: Human TCR alpha chain
E: Human TCR beta chain
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3146
Polymers94,0504
Non-polymers2642
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)216.057, 70.112, 142.874
Angle α, β, γ (deg.)90.000, 103.970, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 4 types, 8 molecules ACBFDGEH

#1: Protein Major histocompatibility complex class I-related gene protein / MHC class I-related gene protein / Class I histocompatibility antigen-like protein


Mass: 31711.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95460
#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
#3: Protein Human TCR alpha chain


Mass: 22781.268 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)
#4: Protein Human TCR beta chain


Mass: 27677.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 1174 molecules

#5: Chemical ChemComp-N18 / methyl N-(2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carbonyl)-beta-alaninate


Mass: 241.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11N3O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1168 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: BTP (pH 6.0 - 6.5), PEG3350 and sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.14→53.49 Å / Num. obs: 113315 / % possible obs: 98.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 42.56 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.15
Reflection shellResolution: 2.14→2.216 Å / Num. unique obs: 11169 / CC1/2: 0.799

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L4T

4l4t


Resolution: 2.14→53.49 Å / SU ML: 0.2255 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.1671
RfactorNum. reflection% reflection
Rfree0.1977 5592 4.94 %
Rwork0.1683 --
obs0.1697 113270 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.42 Å2
Refinement stepCycle: LAST / Resolution: 2.14→53.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12705 0 51 1168 13924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003113494
X-RAY DIFFRACTIONf_angle_d0.616518441
X-RAY DIFFRACTIONf_chiral_restr0.04461969
X-RAY DIFFRACTIONf_plane_restr0.00372413
X-RAY DIFFRACTIONf_dihedral_angle_d16.45378151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.160.2641820.23723515X-RAY DIFFRACTION98.19
2.16-2.190.23151860.23053574X-RAY DIFFRACTION98.2
2.19-2.220.24791940.22263517X-RAY DIFFRACTION98.12
2.22-2.240.29531760.22713544X-RAY DIFFRACTION98.18
2.24-2.270.28361940.22483594X-RAY DIFFRACTION98.26
2.27-2.310.26871780.22873494X-RAY DIFFRACTION98.23
2.31-2.340.28222080.21983550X-RAY DIFFRACTION98.33
2.34-2.370.22711920.21473539X-RAY DIFFRACTION98.39
2.37-2.410.27981820.20863605X-RAY DIFFRACTION98.41
2.41-2.450.25361820.2133532X-RAY DIFFRACTION98.54
2.45-2.490.2541800.20993567X-RAY DIFFRACTION98.53
2.49-2.540.26351800.20873577X-RAY DIFFRACTION98.56
2.54-2.590.26391680.20223609X-RAY DIFFRACTION98.67
2.59-2.640.27081720.20883559X-RAY DIFFRACTION98.65
2.64-2.70.26671870.20183605X-RAY DIFFRACTION98.62
2.7-2.760.23351810.19843528X-RAY DIFFRACTION98.85
2.76-2.830.22361870.19983620X-RAY DIFFRACTION98.88
2.83-2.90.23122030.18593583X-RAY DIFFRACTION98.88
2.9-2.990.20751960.18863572X-RAY DIFFRACTION98.92
2.99-3.090.22591930.1773589X-RAY DIFFRACTION99.08
3.09-3.20.19751780.17593607X-RAY DIFFRACTION99.08
3.2-3.320.20861930.17163616X-RAY DIFFRACTION99.06
3.32-3.480.18391770.15743598X-RAY DIFFRACTION99.03
3.48-3.660.16561910.14883619X-RAY DIFFRACTION98.83
3.66-3.890.16811980.14663601X-RAY DIFFRACTION98.86
3.89-4.190.18491660.13953644X-RAY DIFFRACTION99.14
4.19-4.610.14011980.1173628X-RAY DIFFRACTION99.38
4.61-5.280.13691840.12593648X-RAY DIFFRACTION99.25
5.28-6.650.17881980.16513667X-RAY DIFFRACTION99
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)
11.92166706286-0.7114206020280.355771247872.165070360960.4565773677741.832990755250.0462993855630.2695773714020.203724704823-0.4010219736850.00250993013557-0.2337387733410.1168033510350.170718962237-0.04742279623790.276529154753-0.06698271752970.05364794165040.3526032731550.01240851062280.2897435343851.45282206977.456660549224.067286732
21.47923368247-0.649312676045-0.03272505500042.334354895560.2503157733020.8109262422490.0309093504506-0.07635043973220.1124929889220.0668763145922-0.02924738624790.285682954395-0.0149635833404-0.06795605581060.01183927603910.231890161415-0.0160500360318-0.003432632046880.294917535567-0.008035385304260.29651757276939.409907736980.6677665815234.767976772
31.960602942390.3566698312541.097857565581.14448247938-0.06176368254771.337700456380.05415121725980.0120425751929-0.07807776436590.1425975104880.126270991998-0.3608777307640.1052717968110.207104432165-0.1175413540280.2695782340080.0802072822201-0.04122637830330.405397419244-0.1082175863950.39856400561664.336140801670.197216694243.410734626
41.137063619620.669236053199-0.2470027462820.876494253287-0.1503309676221.451123521190.0220423084859-0.2465724538050.4508709847020.309444885930.050609445865-0.114493186752-0.37264497073-0.115918548047-0.08702752737640.409248249520.135733260673-0.1006742738880.600119706912-0.2142216193710.5798899593968.776568439179.5672952361256.87627829
52.46752225718-0.447733830730.7082502261082.64149628013-0.5730564259311.982841392320.2040166638290.2756612576260.6883591791030.1311113434470.39108097082-0.192671087173-0.4220399087420.201207975917-0.6047315766750.468336702595-0.02081197591470.02040807916250.357352101496-0.0538137903010.72841261564454.875918592696.8444288735235.827409578
60.789020554383-0.6351070968971.010425615092.45645839752-0.9632020321281.2740495475-0.02720520930350.0898372270480.02671172239040.356341795273-0.0638504974964-0.087147226408-0.1092993605420.1973958812450.04325258414190.386828367916-0.0459968571845-0.08695822220.566370347866-0.1132425356920.74479902410771.06598480987.8812434016240.623442176
71.22400782999-0.1096714680540.239383250202-0.00089268446576-0.05566609740321.34349493294-0.33477283758-0.12532638682-0.1734049067870.160257097583-0.0850527551815-0.7061566015790.01995568972620.8728085159240.2755460622110.3324326807570.0289842089333-0.1356739303410.953662885788-0.03511007427320.96956643855883.980963884379.444681254241.411587304
82.214672760.191702588428-0.1359905053560.1589276606630.1951020589151.28421449420.09682173927810.2719078199210.255569686221-0.2881130953820.0844680788283-0.306641247404-0.03627861300380.354697778313-0.1372976441950.371708538838-0.142454087485-0.02481859912020.6367872338930.02730835741310.73083866764769.608557057988.8616158733232.813948479
92.648430034921.734079385720.06293407098941.205242404710.03036459197450.0840268006016-0.1862985261320.335426051570.0835071106208-0.294476992956-0.148898294765-0.4139596170880.1670731380910.1987961916940.1525592608770.516484119457-0.3439247180910.03574095594751.180298107240.05674821804261.0570405236977.793730336388.9379074017227.128597818
107.74405887601-0.757707440799-2.28510434771.54893281533-0.2140480956382.155842182590.424045184270.1912189643870.1918444062380.1326221650150.00902226333078-0.379046953509-0.03873795910480.270264682431-0.3536297432260.296208021987-0.039399164469-0.01806060715860.357823593396-0.02924374030380.40284106925156.423028978883.7573050598233.428736302
114.328987757340.0745894195384-0.3224510526540.46164489994-0.08096817595950.808352269110.002317079255350.415600452925-0.153062284413-0.1925995878820.0767896485016-0.2347074300110.1112970144410.406727214279-0.05785825297540.284541580777-0.04448419875570.04858353283970.605807181473-0.03749092778660.57777960554972.164497778583.7508349152232.484217132
120.753861235942-0.5254244909480.3813192807360.366049518317-0.2656908873520.176431351381-0.05671417928190.00714093648987-0.063053344857-0.00132554720391-0.0119435871825-0.207321063962-0.05266596935390.2033778674780.07063182130740.474566319229-0.113371463547-0.1313813371961.416779225960.01529504296381.1970253486788.712657099989.7451491244238.522119461
132.942931772670.818462825538-0.525030555730.4575230806630.389229745551.310612846560.4927130883340.1094026430510.256620977803-0.08416395767780.0537815893038-0.277189203099-0.1640072657370.253663673267-0.4713789735120.471111760617-0.159416939472-0.03797088304770.7086652083420.08343588856851.2484478458574.242956356294.4429478251232.939562677
140.6110644883320.8465035918390.02216304678211.15977757607-0.02809282620210.2844568153110.219805499125-0.002320969774330.563604056865-0.0342182973869-0.00656103696891-0.697718858388-0.5723548616270.427709404969-0.2481181332950.544407766447-0.194313865873-0.008109052256820.6913105010290.09002104015120.97657123610263.4535883599101.049675762232.312621362
153.352666456140.65301357732-1.120828984752.019369903691.055696960873.02912401779-0.154157753557-0.09696727491720.003170583945970.5985244586190.501801804284-0.1117751112960.09955775902090.694720394931-0.370587390160.601800673738-0.126754895939-0.1895145988030.812717170774-0.1275862359450.92280395341677.3160099293.0267397997240.815468111
161.40719594869-0.0390315681535-0.06136161248371.82399945018-0.5669894954692.001536413460.06913505770790.1550546247760.0330186154616-0.0697974519384-0.07886534968430.0908685535379-0.127469616360.02713969988810.01289008993670.255649151256-8.1679408136E-50.0005365966302620.264516672842-0.0144843014580.283130784764-3.2440009265263.0127963303160.222005635
171.41402439907-0.421002989253-0.05462521406542.13644612258-1.059562258281.107253366330.06438601540370.0079676455468-0.02489229261110.181209599063-0.189370245035-0.102306399480.04155222877980.08744235845880.1314416324920.293110131152-0.0455695277602-0.008062568118180.290826083258-0.01071955811780.2421778921614.38110693255.9110597777170.620354638
181.62676136419-0.0825236141747-0.142207265391.204219189340.3338446534881.18569306635-0.0274541724736-0.178580314718-0.128941930661-0.0508564367886-0.06465192340780.098920125417-0.171942049698-0.07612553215520.1028032823010.3552007543450.004815673347590.01131984030780.253861024125-0.02118487248750.337307494007-19.314455346172.1971956954189.01731743
191.415505267980.01775544370310.4925659043762.39180748930.2786329592261.755477300450.185031108307-0.208922825745-0.1141669618770.398521195403-0.01684202340580.1519988545210.00501776583662-0.230646634338-0.13477961030.4143309403340.004562253238130.01035756062890.2832935626850.0006080115384030.374368216586-18.776738907573.3341903954195.429788081
202.21403598602-0.6737858263510.0608231547311.33594591852-0.09300326881621.14424998657-0.172021082507-0.192854088493-0.3134617391430.01312753779490.2904147923320.448729124536-0.05289372395880.0596634541767-0.1207975170370.311915576209-0.0698158921459-0.02532259393190.5030291346420.1550918810150.41487431444636.740007091966.6712396245156.748007
211.261888793740.310792117582-0.3109798301140.546278280715-0.1012690434361.03500686565-0.06294703536020.06432417806450.1456092763410.02429237314690.0643180694546-0.0142132995333-0.125649826657-0.116884555052-0.02432314052720.346906025237-0.03385274707580.03448923350410.4512826423830.08780560519640.33035314111226.362281111564.8901735584159.901299749
220.9334008513220.011694567432-0.1433709087150.716682536638-0.3016528341181.112084488480.2294571596680.1111713501960.0617922420337-0.1483508250530.236892327114-0.0673032642029-0.261518434965-0.0918604985922-0.4112962922730.393939358184-0.10243454570.007910679335630.4385525652280.09828018463870.31891199996626.534225440257.0508489129156.317090867
233.12898329173-1.05446831459-1.374493374251.91028341560.1109935046862.257162937460.0280629203722-0.04602843147960.06850721808160.02332575310080.0906620650897-0.05018306674110.1348423604280.0395161023966-0.1354490353970.330168311305-0.0386106177384-0.003743072106960.3857563411130.08665290772330.30285578310330.377820023560.236745722166.253087138
242.10197651334-0.336517648616-0.3226740404220.8867155320830.1609010145431.58881444082-0.1305651642910.1410718605040.05042736595190.009501288057070.124726721092-0.03606027572590.0193436051140.0223010175237-0.02777081140740.324821968783-0.07011132491740.004958791399190.4470448385750.1249783037380.30470830680628.327326211661.6279288404155.674313504
253.784824194030.0972628276436-1.076447065390.4191678333240.1857628298730.468507328642-0.00284463069759-0.4706200510610.1139968774390.1618133973140.0882860746944-0.4120326207040.1156861372090.608648592955-0.07564568304380.339070510781-0.0006224801847-0.01905387248310.857191497260.1095504093450.49486752162651.88716399358.7471118287151.01370464
261.3534419039-0.247901257731-0.1262431451610.9282782205470.2340563070552.474961325460.09749064157320.0544667057170.0402613893978-0.354666654754-0.207829886629-0.0399295724068-0.4652283738170.3978643245450.08439393956250.630493410510.03046535965120.09306048597840.8349886003930.009928542066970.63370245559256.978323391663.387378464136.150959964
272.08624513965-0.4896059267090.1402794096681.383058241770.04194511451391.771240683680.0473399938759-0.137222516378-0.109654832713-0.1864337790740.197569748978-0.2626406945940.2120613491860.214584773042-0.2207592329120.634950693213-0.03335833826240.04449433686840.6382340681430.1226346860930.53547716446352.298391034157.969778671139.938236391
281.39032445952-0.386438760351-0.5872206891141.765972457340.5684728279350.313110440703-0.03112205502530.3625850681810.765827992946-0.4761503074890.327642862899-0.640337970014-0.4672479442990.678184954525-0.3062841992750.762206713279-0.09906079518780.2314276662220.9727818977390.09590051667910.92365770180562.669121147567.6000274604136.756750168
291.10909727696-0.218806170034-0.5947675044140.7044051901980.3214549222361.267084903480.03408189902920.347876391194-0.165125071113-0.2514036826390.1605130500390.02418529684820.262049436127-0.691732156637-0.2321640516160.58641177005-0.179365958113-0.07418369970030.7226139577150.1117835716240.39434278713417.501019859757.8759408048137.445398566
300.902498506336-0.348175995565-0.1815790109291.002885727250.09860607304720.9303411553940.09025575172670.03568354372970.295662865201-0.164942689701-0.1393630334240.127805054148-0.200312457775-0.1860999739910.05414034373610.416039100967-0.0201003352615-0.01904869005960.6181094588750.09719954750850.38384113196413.874302170466.9583966647144.329850991
311.57835267349-0.300087963152-0.9477757992580.4164896953880.3105735733540.505736403238-0.1575353470050.363456249524-0.00393030884039-0.492218767180.3556356090520.2891139844830.421788970288-0.725258143647-0.07872073064940.54984694273-0.13166309681-0.08438468090490.6602473064410.1333359786470.36473937931514.470750108861.9054384865137.261727244
321.190248015290.4832940530740.121773828671.06237800913-1.010770544671.308259581590.287405583301-0.10641324234-0.1911953236190.01527445400030.03659751371970.355861369616-0.503713770074-0.654273715262-0.3235499497540.37941678502-0.03643391161150.04438754756120.4745967132810.07110475669420.4231991058616.555644822855.5614959662152.000037764
331.564152291610.0109902466564-0.8211218634440.6931406618910.06920905459691.404854917930.305370018770.1433600780490.493234028587-0.2503626829740.1772140235240.12135457888-0.0733470342632-0.150939356418-0.3166552882990.6152066576140.00509780199120.09030594792630.4755764813680.09546574653170.37460436593530.101019939966.0370133835125.097449116
342.21588442334-0.7527829783310.6795274962341.46330949635-0.5446484398211.582983017780.5353980262730.372758939388-0.414801183879-0.42648101088-0.175107150673-0.02170063793980.3667363721360.417008528467-0.3254741275860.5714289347770.09033462201370.06020751270540.444104560336-0.01922236104170.40842839847649.908355742154.769093909130.658869813
351.172337982660.02543875449880.4454745142630.8886901059-0.5194666129670.9764870538050.0730741499206-0.0765884491469-0.283168742136-0.03365485783420.2917738786060.3925563120030.0249471195765-0.0424966714928-0.3654873272960.6854592032020.02405674760390.03499909573110.5006426806470.02936437695180.47950218004742.806138529560.6520011828132.444367583
362.22013861037-0.7965526062971.040614970641.19487538792-0.4349117332850.9166341068560.427162008505-0.107814739015-0.585221681412-0.619303336874-0.0890164144173-0.0153322586120.2485144808130.238914316232-0.2730022459420.6180127928760.1387606500520.08877407601670.499060485580.0725886924570.50358233164353.125798607850.9305707988133.523904547
370.5225957848180.74460200158-0.7635020175471.75319376047-0.2191335025041.675270512570.5945586654320.83661301651-0.536895205213-0.70612366093-0.1064101367040.1599878735360.7884333881090.147289628542-0.4227278649550.8432806049630.0416539896045-0.08543536209630.593487807841-0.07204489914760.50246067255638.346998424852.5531842603122.838890174
382.123563271220.5203534915840.1098068890980.6187437445030.4322360491770.7295645218980.4991211689180.935889308247-0.431576850829-0.736380412345-0.150771158533-0.1951227197250.4557280300940.773317998463-0.2852318115360.9350703710870.1313792447-0.03880905259380.702189707117-0.1126593230690.53675683088841.428404373154.3168780844118.950951732
391.45177028737-1.30702146525-0.1959036622391.62684296552-0.3570492695431.18991037232-0.1332372282410.186867703826-0.2393003468670.2871826257490.0991782699375-0.3986142675810.1194810880070.007123185384970.05644019938520.301363843506-0.0640009340199-0.03048258640880.258900130515-0.03518517592130.447509440509-21.966444427257.5248557005173.71295928
403.36124359078-0.3608794581560.6506214423072.16502615469-0.4141726108791.5759140487-0.484560160221-0.1606503637410.3815348088230.134678854195-0.1950630320120.326827511068-0.785529916756-0.7373371790750.658327562080.5573179296410.16299989866-0.04369684124660.458175660579-0.05763681787710.608341885576-31.085719827880.6380057466178.577145259
411.00889355063-0.1195268177310.03710638747640.96795994213-0.01297538531960.895684143389-0.09554351693060.246111689650.00862942213598-0.335989683754-0.02526573401470.124573329252-0.313377613364-0.23688768680.1211081564540.3636285224550.00753999842373-0.06486067828110.336598169715-0.03869478834650.334658831343-24.750674063264.9529240876168.616929124
421.83465751598-0.757798989274-0.05545344357091.36722312158-0.01375394180560.6337826613530.03985023772290.251416400360.157951554406-0.3403781910940.0107261260890.0990163371081-0.0632349222597-0.162234985383-0.05520298788140.420309086417-0.0076642459679-0.03273719149980.435241949866-0.02888125332620.389612035424-21.034771531865.8452119408166.031102106
434.54955439788-2.091116081550.1311980485443.02603028437-0.06032123289192.004516684910.03461677744820.4548788274920.564798176658-0.344140434115-0.108333672651-0.181018237371-0.455191613192-0.03953052996930.07764504682440.424411498259-0.0100641897708-0.02300293446060.378297439792-0.005464796602850.342767854037-23.375564464370.3012527391168.822326421
441.35144033164-0.212714006036-0.3404562242982.25801327732-0.1407067634290.695082304048-0.03753398175540.0400621748393-0.01483770525620.00724858796349-0.05073094041250.462964755493-0.0568456069406-0.2338949597750.1064975837630.349176958949-0.00219733031719-0.0396827144730.396108285631-0.07416582248710.451206465627-33.235397101563.4973718827171.988069098
451.049750389090.7242347952570.05716918429581.755862514550.5144965341671.32437267626-0.1148037153170.192050343114-0.0111423198188-0.01599275430620.244205908754-0.1336194627020.1004316696820.116115428129-0.1241593523280.295626059229-0.0247404176103-0.03051938992690.2600594285530.0004992718225970.29924801713224.958825771257.2923514516221.273751193
461.542056836970.8992264695711.194916001211.329491652370.6743793873351.360930956920.00125963558838-0.06035099909840.08496293908660.08375126983640.007744738992110.03939336960970.0151156639921-0.0170259607841-0.02992879641670.296026573991-0.016776499341-0.002038942640780.230664616628-0.001566506343050.25679310004418.642493326356.1660070529220.6748806
472.151082165950.633858738892-0.5723454333671.37347462695-1.202105658132.76998230716-0.0345287464154-0.0513686731383-0.260478598498-0.364281693899-0.002099898004570.01114657067810.2892495714070.04448191765010.006129376422210.364272201992-0.00827449568606-0.01598286652560.2203948609690.02605015803340.3455292676471.4965490789842.7957915229199.235182987
481.59102481547-0.2251446315140.1224186462411.202096479381.659573429922.415033307580.03739298279950.267305284620.387465798246-0.2764805872840.219693689857-0.341690660161-0.484919006050.529903757208-0.2283355101520.373980193154-0.1596006034990.04529045891870.4613941847880.007585810502090.39910588378235.234802973866.9619158918202.520217523
490.5768801951470.154099680528-0.7562597410152.196714693870.5080287988441.3699690192-0.2886204328010.1793867797810.3574420378010.3261922464030.22227494529-0.0984718112261-0.07938649655080.728535522410.02010366623880.409827877936-0.0454863446249-0.09799513920280.387249264435-0.02898012389510.42849877582331.299100341171.8393066488215.827670617
501.752018802420.5498258942411.015880511120.3252723307620.07666205719860.898028184150.298077547363-0.135648925533-0.1660193785140.201919685074-0.0409629744168-0.0997824287190.3419272014890.602825964257-0.1881058523820.3175187557060.0185495254356-0.01420980254360.421385992390.00326157319310.2671262743627.091957031453.6925800189187.86254593
511.3653141589-0.613950289909-0.4171473454310.94575386288-0.6244553039110.9658469581230.0926160093061-0.08527168813440.154364085086-0.0330854908571-0.03350275894940.047605135644-0.06375305360970.0466457733328-0.04997400062150.312493741827-0.0436559639284-0.00879414288490.233141571378-0.01490068996990.2862860383633.2594734212653.5753912656194.010737546
522.222450811470.284565211721-0.514994758271.05090279962-0.5383442534352.075426167320.15380895044-0.3136766512810.0248851974823-0.0551073691673-0.0878436792842-0.159158278677-0.1365523889090.274727670247-0.03397327579290.36871608479-0.05806628139890.001772959290320.2773675516330.0055452245380.3070067862657.4821196905453.4340388888196.61413114
531.87948752014-0.4524809305330.4017735740550.4265317075590.08934859240230.5303385709060.2579425262320.3777755284250.565820859526-0.2888611335850.0574426623630.261664220288-0.169151770505-0.0849209117134-0.2893969805150.475572490984-0.0429907207486-7.5617795599E-50.354502752890.09453664342990.424281438423-0.76706952978562.0511676612189.757751238
541.665257426-0.330734481596-0.6035912374471.03555137958-0.06280208912051.488065429990.163504541794-0.127994597774-0.04023316825330.0189381630415-0.107226973306-0.0973285260063-0.1460910593120.104188666744-0.0279735310070.37756700612-0.0342417305488-0.03314285120740.3334221892820.06354351502590.28940606008116.236005745458.656080823182.020693829
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 158 )
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 205 )
4X-RAY DIFFRACTION4chain 'A' and (resid 206 through 270 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 5 )
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 11 )
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 19 )
8X-RAY DIFFRACTION8chain 'B' and (resid 20 through 41 )
9X-RAY DIFFRACTION9chain 'B' and (resid 42 through 51 )
10X-RAY DIFFRACTION10chain 'B' and (resid 52 through 61 )
11X-RAY DIFFRACTION11chain 'B' and (resid 62 through 71 )
12X-RAY DIFFRACTION12chain 'B' and (resid 72 through 77 )
13X-RAY DIFFRACTION13chain 'B' and (resid 78 through 83 )
14X-RAY DIFFRACTION14chain 'B' and (resid 84 through 90 )
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 97 )
16X-RAY DIFFRACTION16chain 'C' and (resid 0 through 84 )
17X-RAY DIFFRACTION17chain 'C' and (resid 85 through 171 )
18X-RAY DIFFRACTION18chain 'C' and (resid 172 through 237 )
19X-RAY DIFFRACTION19chain 'C' and (resid 238 through 270 )
20X-RAY DIFFRACTION20chain 'D' and (resid 2 through 17 )
21X-RAY DIFFRACTION21chain 'D' and (resid 18 through 37 )
22X-RAY DIFFRACTION22chain 'D' and (resid 38 through 52 )
23X-RAY DIFFRACTION23chain 'D' and (resid 53 through 75 )
24X-RAY DIFFRACTION24chain 'D' and (resid 76 through 102 )
25X-RAY DIFFRACTION25chain 'D' and (resid 103 through 116 )
26X-RAY DIFFRACTION26chain 'D' and (resid 117 through 150 )
27X-RAY DIFFRACTION27chain 'D' and (resid 151 through 175 )
28X-RAY DIFFRACTION28chain 'D' and (resid 176 through 198 )
29X-RAY DIFFRACTION29chain 'E' and (resid 3 through 37 )
30X-RAY DIFFRACTION30chain 'E' and (resid 38 through 63 )
31X-RAY DIFFRACTION31chain 'E' and (resid 64 through 94 )
32X-RAY DIFFRACTION32chain 'E' and (resid 95 through 109 )
33X-RAY DIFFRACTION33chain 'E' and (resid 110 through 124 )
34X-RAY DIFFRACTION34chain 'E' and (resid 125 through 162 )
35X-RAY DIFFRACTION35chain 'E' and (resid 163 through 188 )
36X-RAY DIFFRACTION36chain 'E' and (resid 189 through 203 )
37X-RAY DIFFRACTION37chain 'E' and (resid 204 through 225 )
38X-RAY DIFFRACTION38chain 'E' and (resid 226 through 243 )
39X-RAY DIFFRACTION39chain 'F' and (resid 0 through 11 )
40X-RAY DIFFRACTION40chain 'F' and (resid 12 through 19 )
41X-RAY DIFFRACTION41chain 'F' and (resid 20 through 41 )
42X-RAY DIFFRACTION42chain 'F' and (resid 42 through 61 )
43X-RAY DIFFRACTION43chain 'F' and (resid 62 through 71 )
44X-RAY DIFFRACTION44chain 'F' and (resid 72 through 99 )
45X-RAY DIFFRACTION45chain 'G' and (resid 2 through 52 )
46X-RAY DIFFRACTION46chain 'G' and (resid 53 through 120 )
47X-RAY DIFFRACTION47chain 'G' and (resid 121 through 201 )
48X-RAY DIFFRACTION48chain 'H' and (resid 1 through 94 )
49X-RAY DIFFRACTION49chain 'H' and (resid 95 through 109 )
50X-RAY DIFFRACTION50chain 'H' and (resid 110 through 124 )
51X-RAY DIFFRACTION51chain 'H' and (resid 125 through 162 )
52X-RAY DIFFRACTION52chain 'H' and (resid 163 through 202 )
53X-RAY DIFFRACTION53chain 'H' and (resid 203 through 215 )
54X-RAY DIFFRACTION54chain 'H' and (resid 216 through 244 )

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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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