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- PDB-6pug: Structure of human MAIT A-F7 TCR in complex with human MR1-2`OH-E... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6pug
TitleStructure of human MAIT A-F7 TCR in complex with human MR1-2`OH-Ethyl-5-OP-U
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Human TCR alpha chain
  • Human TCR beta chain
  • Major histocompatibility complex class I-related gene protein
KeywordsIMMUNE SYSTEM / MAIT / MR1 / Metablite presentation
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 / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / innate immune response / Neutrophil degranulation / endoplasmic reticulum membrane / 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-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. ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-OZD / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAwad, W. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Nat.Immunol. / Year: 2020
Title: The molecular basis underpinning the potency and specificity of MAIT cell antigens.
Authors: Awad, W. / Ler, G.J.M. / Xu, W. / Keller, A.N. / Mak, J.Y.W. / Lim, X.Y. / Liu, L. / Eckle, S.B.G. / Le Nours, J. / McCluskey, J. / Corbett, A.J. / Fairlie, D.P. / Rossjohn, J.
History
DepositionJul 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: 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.year
Revision 1.2Mar 18, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)188,91515
Polymers188,1008
Non-polymers8157
Water38,4802136
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)94,4057
Polymers94,0504
Non-polymers3553
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)94,5108
Polymers94,0504
Non-polymers4604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)212.620, 69.266, 142.055
Angle α, β, γ (deg.)90.000, 103.677, 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 / 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, 2143 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-OZD / 6-[(2-hydroxyethyl)amino]-5-[(E)-(2-oxopropylidene)amino]pyrimidine-2,4(1H,3H)-dione


Mass: 240.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12N4O4
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2136 / 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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM BTP (pH 6.0 - 6.5), 8-20% PEG3350 and 200 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→47.03 Å / Num. obs: 185974 / % possible obs: 99.93 % / Redundancy: 5 % / Biso Wilson estimate: 22.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09636 / Rpim(I) all: 0.04744 / Net I/σ(I): 11.96
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 5 % / Rmerge(I) obs: 0.8326 / Mean I/σ(I) obs: 1.96 / Num. unique obs: 18582 / Rpim(I) all: 0.4102 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PHENIX1.16_3549-000refinement
PHENIX1.16_3549-000refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L4T

4l4t


Resolution: 1.8→47.03 Å / SU ML: 0.2081 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.6509
RfactorNum. reflection% reflection
Rfree0.1941 9336 5.02 %
Rwork0.1596 --
obs0.1614 185962 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.92 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12796 0 52 2137 14985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008913770
X-RAY DIFFRACTIONf_angle_d0.98418861
X-RAY DIFFRACTIONf_chiral_restr0.06222023
X-RAY DIFFRACTIONf_plane_restr0.0062477
X-RAY DIFFRACTIONf_dihedral_angle_d16.08958388
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.820.333302588199.97
1.82-1.840.3057319580399.98
1.84-1.860.3214320595799.97
1.86-1.890.3046281576699.9
1.89-1.910.3066339582899.97
1.91-1.940.2539316584899.94
1.94-1.970.2528305588099.98
1.97-20.2557290590099.94
2-2.030.2525304587699.98
2.03-2.060.2377334581899.95
2.06-2.10.2229313589499.94
2.1-2.130.2221300584499.95
2.13-2.180.24311582899.93
2.18-2.220.2136300591599.98
2.22-2.270.2149307584099.97
2.27-2.320.2318341586999.9
2.32-2.380.2128320587299.98
2.38-2.440.2228284587899.98
2.44-2.510.2081307586799.95
2.51-2.60.2116333588499.94
2.6-2.690.2117302587799.97
2.69-2.80.2196287594199.98
2.8-2.920.2029307588999.98
2.92-3.080.1811315589599.97
3.08-3.270.1676315592199.98
3.27-3.520.1782278591999.95
3.52-3.880.15983320.12135935100
3.88-4.440.12813320.1102594399.97
4.44-5.590.12843330.1097594399.94
5.590.1809309611599.46
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)
11.0207915264-0.3667587652060.05957641440220.928984928460.2279452302790.7190826432170.01387373036440.04525825134930.0768403315569-0.04954601550030.0403510877934-0.04012241219560.03272167362920.00663218938727-0.03560256942840.110582254768-0.0142030413356-0.01251213985730.1403781005690.01925741993020.15429664180952.446495053376.9505162318223.171606888
20.878721154096-0.295820852562-0.1651834547141.692539211560.1543299440610.315363986942-0.0153013826328-0.08275205096370.1079898939580.123106303988-0.03085929570920.160034750523-0.00755777701026-0.08046393744260.04414288979950.1335308699610.005906171438920.007831578171190.146207572777-0.007209752704380.17790588555340.027966011380.6393905219233.507366783
31.053664304670.1367066296870.4997059368850.3652508198440.2853294822540.7835020502970.0492780750047-0.0433882084071-0.2247537219020.07815067955320.0210228249042-0.07806657820440.1724676072280.166647010011-0.04386452519880.1787683534690.0238902294311-0.02486632346870.1978110914950.008526586590470.16784328542756.8487725363.2175376146235.090545976
40.7749581586790.2543256876280.09563150684030.734878984862-0.00232192334191.20392993519-0.0774790111272-0.2544275001010.3758340496350.16547175185-0.0149026355476-0.000831410933009-0.27123449367-0.1124398578130.0357109604250.2571443390380.0674483552502-0.08668580028120.387242877684-0.08309460274290.30666416605169.87288817379.9588774069255.209230541
52.07845484858-0.979943452857-0.1804478258411.484928209940.02064318950660.587001983394-0.113293969719-0.1165045877450.4249015707050.285526993626-0.02616666286510.0404072512606-0.2624012038190.106618952984-0.007402829627040.219173448059-0.0231554874932-0.07168812071240.22757722498-0.03660233830060.49723963914663.39660679792.357898197236.887699382
61.947608471380.886637274442-0.258656842750.5095537176690.2027809595190.885764566254-0.0436962366233-0.267930179911-0.1151926339130.231599675939-0.0444645400143-0.5710136674020.1336222975580.547547939355-0.02441053296850.2156823395820.0498844321414-0.2487442858450.5678064815960.1567993164510.84054709042284.330373808979.4902430556240.584768843
72.09847267428-0.2010190353450.01350853502430.5171485635840.04308958734490.592903171583-0.1190216714480.2008766490460.479084747355-0.014207343322-0.0517062311776-0.291955177017-0.06389903361410.2236300340970.02178059255820.165435042196-0.0445682560687-0.05283262698160.2876293684980.0714863409510.39500293271970.09970401788.779156166231.638103132
83.024346305612.649561653720.3671901985042.305103546560.3159900084050.0721181910229-0.1898406041960.4019522643420.0846689220342-0.361624517141-0.0240321013182-0.0505134496924-0.1099638156570.1296466237590.02742772669580.268839793041-0.1164153845230.0620230470860.6304599334640.04556764732640.64983659464578.483020662288.7735657969226.2127244
99.805469444770.607023596529-2.86917212722.5331313863-1.216768552843.83074335546-0.04928061371140.352632318245-0.341143436134-0.1846890068190.0900747847022-0.23646013207-0.118359053041-0.04643374637830.03664873892230.2066129135570.02668717926970.002793566369450.216375351341-0.02178022012580.20197044943861.177578113381.9317052114228.281902499
105.052083680540.208622604220.2719709537550.629322416639-0.09177022196430.619058128552-0.1740924038690.01393938680340.167921158364-0.004967081619840.018437965086-0.2656207146640.1031961425660.2972637220770.04470545130190.1499174602160.0204359280996-0.02137480373090.2494468307420.0268428397110.31837504085766.704426521484.1277461701232.648093536
110.2591106073260.02748655929510.02006095451670.00406479188011-0.00164173569765-0.00811046307133-0.0845152183742-0.1122183439580.2158292043430.1247673218560.017730556281-0.285739356783-0.1354050416810.2274044816320.0244603313578-0.165810956304-0.309078809631-0.3703623003780.666943340340.03673941965051.2266178573388.808273807590.6650838733237.285146351
122.511837609870.9019754290350.2972002656540.3952085102230.3680431298451.003519253240.244646272910.2680228931190.231319522553-0.211642147637-0.0588880373379-0.258652687198-0.216793964851-0.01027407414750.007822257834390.0356883707028-0.243174821849-0.1733716285290.3629015125360.1892805054980.89510367190674.78273280994.3371296297231.731227833
131.522083567961.13103970911-0.3665304385330.849836289463-0.2690804206820.09230990525510.00427966311388-0.05063701459480.479180338078-0.0551999413643-0.0279707329618-0.419695427571-0.3819212099020.2689765229290.000995669100650.343673899621-0.134158251527-0.0938490827510.3225748233090.084969873250.55468401933664.4932066409101.350888831230.881806639
142.5077494006-1.02574855379-0.2643925153392.488489329970.2297662567031.5978198635-0.124490798389-0.3638688310160.04461342364380.3909284561810.231017306489-0.1038071953720.01181801934260.2980251799530.04010564164250.433371377768-0.143429301846-0.1963140318510.528612441929-0.06955698147140.64165089170277.755916696193.114539575239.643635146
150.827086697783-0.0434425517929-0.06147513817341.289877968250.1326278676911.096249782960.06604366089290.1640699459020.0177422010666-0.0950277484257-0.02411407411070.0893800813601-0.06155946899930.000191910575196-0.02111444151680.167433904982-0.01748150760560.01089369394180.175390473767-0.01761224527740.152856044177-3.3661236278663.5714666765159.511143333
160.9943692804910.0257727836888-0.003283142978131.23459331402-0.4627008843590.5590200541480.06911777255330.0350789358723-0.1098221286920.189759151632-0.087469382858-0.03609659638730.04144233824590.1049561454450.01430183210440.18376460993-0.03610171896130.002739423434880.172380750189-0.01104193654240.1319860052984.3895538770355.6362374744169.730137764
171.19730404690.203800106208-0.38626961431.208443754840.3635441123280.7714078849880.044617528107-0.15211316089-0.1200522896570.0984160935596-0.05047779805180.108685917083-0.004332615161870.0118847145885-0.007032087404550.201632327627-0.0203985420380.02839365947350.1260817730490.01111962772260.195072440154-18.803333858271.8277166612188.944024383
181.291900407790.396808335380.1995828277061.685010406020.02257902634851.313861489540.0104480493786-0.223302043015-0.03088943698920.201760254282-0.03309129830710.07903297858180.0717109592258-0.1513232329320.001240810277970.180789113088-0.001998110458280.04649163378090.170456061560.007128683788640.213626786428-18.296045141472.9256650958194.929138412
191.86502884370.2563971653680.2394400401970.759458914311-0.4034702428161.17894914496-0.180981776936-0.0007509951886840.002159654478150.1172070970790.1896126446580.129143987599-0.1000470493530.192142473715-0.03213810844560.199003409389-0.0149339742645-0.002350790653590.3864898639440.02544446663110.16969363437836.621594700666.663733169156.35477808
201.003688002580.107823591605-0.3094692898520.511019540286-0.09400083342740.874728465024-0.01986388457620.08840292564080.0521295163665-0.02496151992360.0576607779972-0.02522557085830.008868395952960.0693835103426-0.03736625911490.171483230963-0.0269773288955-0.005743095429190.2766934499610.02650649739950.13200494168226.325442530261.7178041847157.488544062
212.63050947663-0.874734993072-1.116940216541.214520895230.1157128097771.69866468252-0.0195038770056-0.154051062709-0.07044610420150.01162273151310.0440828114639-0.03972372146160.1231612566360.2010964136060.005722960601340.181596302327-0.0149175860908-0.007739408623070.3207320547980.002118908420440.15028969146730.774134137459.6651109285165.208016537
222.49519519155-0.830080431037-0.6374416716570.9631035799370.3608518515461.22987844784-0.1407414972210.0658116682035-0.2067568310640.1120269440570.0782181694362-0.01593465764430.1382917010540.1583733666720.001746772505450.196594983542-0.004015099644810.0139077909720.314277186292-0.001705711380990.12202401771834.976452850358.2415310867154.634276568
234.13663456627-0.193115650579-2.043929957820.05183817802590.2295951902921.169770836510.103499129680.03167677063810.343867349720.07249341811270.00136412741872-0.00764431011920.07944305389780.008037478763860.004669903479080.228138310497-0.0374570512354-0.005268129817380.3404365358030.04480398990250.14189708660917.853420182467.2906423095154.699558059
244.65123191453-0.568305917714-1.400592859220.04047749330070.1969612486960.420115964794-0.122390568892-0.165615040838-0.1734214425580.019737477230.0984810509566-0.1969817032450.06421824900840.38344313376-0.01793990750790.1770451034270.0339680041263-0.0103994718450.510808569392-0.01606008904140.23660782659551.904072039958.9138650209150.294287654
251.00937274090.1161421957490.277186638581.18490435060.4727202840710.9886872255870.2172727708550.7374115312490.0751239263696-0.280012321529-0.146486899677-0.1457249289550.03285648303870.240722970747-0.002450452320690.3240903236720.1048452260250.08558368748790.6225416174840.008386609862890.37460114079458.95934698459.0768465253130.156896633
260.897777067789-0.1908566360140.3382094517720.9144177395930.5084923690491.99893242284-0.0759517832027-0.2858414846340.543802251352-0.07500066347120.00336635291999-0.0279019333929-0.5142882138630.06882160491520.08328318606370.3134357886440.03036792482670.04598592508060.400656791135-0.07990130231360.46251357655454.410387991568.0359504509140.890695158
272.05230795165-0.1405616473530.1458592215421.227300375260.144746520031.81996721710.0890600197320.03680161708070.226087833398-0.175452715623-0.0119592989037-0.254937492980.09075038996160.303598089694-0.137226455930.2320041826160.03025940184590.06196328847220.3177257726630.0299104358220.31000366093854.22740914160.4523408574136.608948627
282.37246658736-0.6285315598570.03423103460652.468641320050.7816175492792.11050095728-0.0980964131868-0.04915815439780.3912756778790.0833026654456-0.0327415832825-0.232102208366-0.2585408971760.426292626824-0.02361047196630.220641570586-0.05119277712180.0220149126240.513765662019-0.03842522418110.55813328198563.87897699266.6970048079139.9596303
291.33594199941-0.254033093391-0.7078314506560.583368912853-0.1013271061.140394151680.002469296373630.207579981126-0.0553996549109-0.102192598791-0.07677864532430.02721768381120.0925362082883-0.236219672210.05513819451210.23912925674-0.0241855984759-0.02102707841470.353883013732-0.006029757091560.14279843285414.920754992461.213923853138.841972068
301.214466334940.108561217284-0.431130136091.06018256769-0.4079383188071.177856016340.09040576481040.0852412596393-0.008704389982260.03361336419190.0005211225382830.102853675581-0.0879037222915-0.238713090814-0.08788215289790.187966414338-0.00539719508468-0.01556905123360.274501936450.0004469332187210.11775956614816.970588500660.7371904549142.171889188
311.59281137552-0.0935333561343-1.137082852040.7082754491070.0949631499780.9637695714420.1290440700630.264496903180.219648453814-0.0620612718-0.03112525781670.0708751794934-0.0776403210935-0.182187027339-0.05325890802910.3893702102540.04333274113950.01399789567220.3152575820120.02695082420160.19285293094929.682427347866.7901440941123.333822042
321.796694268280.2213746470020.8733974343380.724876172229-0.1574569225241.333931086990.2992733007960.17579983641-0.343832091286-0.0639067330595-0.0317974658433-0.05776884934960.2938906231420.29138799851-0.1607569832330.3794219639890.1267516317330.004883233476090.265119489834-0.05811788664490.2419965127548.041748454654.5102197158130.600655999
331.833496011720.01132244451230.4698607614431.43783157869-0.244001785851.697266725940.3627408537580.48081880419-0.23764295328-0.411612490546-0.06999911603010.1059282553130.4329822698580.0911590963616-0.153880667520.5092050140150.116323985707-0.04122353544210.322146197428-0.06471665757890.24300737310436.074293061756.4997340126117.908072336
341.286559034390.4215524557430.198937426041.03903896729-0.5070099908641.056531280580.01286325297960.0934922676070.073640446221-0.0165452482944-0.121741731529-0.00736157094185-0.031915647335-0.1156492123080.05337124440390.164936830566-0.0186701825431-0.005345560189560.10462228223-0.01110968135850.219273906735-25.224632075866.6127108795174.901005062
351.13760197522-0.505695089319-0.04407159783861.004486524350.173521152710.713449707821-0.07553442326630.1919102032790.0225939488123-0.2036921104530.0208418688830.113244544142-0.113107226738-0.09215856503670.0734515268330.208277434084-0.0230616764795-0.02018093530590.16582164573-0.0007051332741540.212597263947-24.493542338465.3156698696168.136176674
363.81968307727-0.01903682351840.0729069150577-0.0003953717328110.02330686774210.207158077368-0.07488877058330.3850885222130.13077381923-0.40882354285-0.104641830750.0818250146505-0.35364416332-0.01641042540050.02073218073570.34500758346-0.00184456085321-0.08812296552950.3844102407520.06945852204740.275801607802-30.6240972371.1161273515162.278804872
372.85094452067-2.329450420990.8830500869183.3297956278-0.8487010777150.883951979355-0.0925962220735-0.002245409080460.0818170065911-0.09277217542280.148951811473-0.0804374989749-0.07493853216590.05794058601640.04725227712310.139746892465-0.0522637240130.04008189069040.110164945968-0.04652973883510.166431339483-11.148844130560.7295466095168.72542167
383.30457781302-2.44286999447-0.2083291365411.990788406330.1914772197960.5114702117940.05485880616590.3622825147820.210610592922-0.191626191627-0.109819739019-0.0522634074627-0.143322461739-0.0759759254613-0.007596607451210.268881316624-0.010208094246-0.03784183255150.193093133743-0.01893274402750.235788349564-23.241037777970.5776594656168.183404303
391.21240776013-0.753254038257-0.4014750877412.385646666630.6518263552621.11677646655-0.01821752397980.06056472623410.0121189431913-0.124943533832-0.1086556833640.343659121804-0.086880235489-0.2338746752620.07660323452790.210666131179-0.0344360940384-0.04135089320540.225236689487-0.0647049395520.293662428815-33.183246443264.0971064111171.52214557
402.73991845330.439598275074-0.06431625663251.318714082930.06167236670831.06141957755-0.0456145328522-0.0710021187325-0.0690483098229-0.09225759130710.0879459788247-0.1226882041660.03206341037060.0803079169589-0.06823141980770.159372685929-0.0174262858260.02257445673180.140536080907-0.001282260951190.17707500103222.455713628550.6101631278218.895604227
410.8180414767620.3276989984310.2305860684810.7618695943870.2776225370670.809746233733-0.04629486167290.0222254865194-0.0767935210025-0.01705284239730.07945008088470.0128090456076-0.0002369341708360.0079065507754-0.02334814284750.125929312432-0.01516274045460.012527380590.12785360460.01823390251120.16129684856827.394594106860.4938312732220.273953002
423.448598027370.09901231896551.402423300250.956131232410.1826668526781.83354631670.0319569373551-0.358981003799-0.00793102059230.113726412347-0.06082462101010.04958870578950.0154677471087-0.2403777615840.08144345684590.165438424246-0.03668295223310.02584949661810.1576631149720.00878188704290.19508024245723.084739689458.9523950392228.398968731
433.323444158770.6243269167840.4977205864520.846238370372-0.0451978320071.13250820661-0.08140999041420.0238030277220.139099913333-0.0339108494240.04549328498630.153915752367-0.0540156983502-0.0674306457892-0.01209334401710.143887251179-0.01008989166240.003783294073360.1019802139440.01594031607580.15820278030318.600628049158.5433498122217.95933465
442.617390467730.6269486179390.4878031601810.7769451754920.1289404820820.662466979153-0.1018599060150.0917711730118-0.263382833659-0.05939462830740.070881750475-0.157344659579-0.05263261882580.1007852475290.02291373348630.139797536713-0.01608779230240.009743725939850.1910515433010.006001997802010.11886145807430.541062550257.6714173733216.71305446
452.324493690030.6702845518570.7892372786081.4134704217-0.3715343916920.4752620933760.0674675707014-0.2727827792560.143891647838-0.00748450227615-0.08799702671990.1518856208760.00970256012251-0.448275860596-0.002058430022930.164132291432-0.01637926433720.004132770753910.1567646701060.02078570726630.226962703316-3.803697972645.6497276866206.915165372
460.5506797868530.21036447157-0.7325419158390.213931530522-0.419494738693.03427292236-0.0070301106280.164609885327-0.0424807081071-0.2655923920180.05965765266530.110360656380.112625529022-0.091712561959-0.001195134403220.309311965828-0.0460216557619-0.02871477585710.1373507219850.01175792345990.1506061607520.74482561724546.2457432208188.856458069
473.1090960096-1.47937307946-0.887289616492.219711718210.5844219695812.162400412770.00617809025607-0.197849692578-0.007046097541140.164863412934-0.0563231409645-0.1291625508070.3196809136950.3647044624590.06214020010780.182766757877-0.01483619156960.006803412623720.1818663987540.05585281267120.2309517103154.2974461207742.1562988712208.966998273
481.555655721360.336154553423-0.03092034239511.35440664005-0.04722687122782.37918637636-0.0207777444204-0.2060978266280.0482575871335-0.1539321458740.0714555277720.0263465388641-0.02501656937030.142776626260.01509151315190.204941067063-0.008118698398240.009671539276050.1058285581520.02515056129820.1720449204324.7981973924647.9548647369200.958714237
491.062836094630.517912368162-2.131602539640.245691032655-1.008749192564.16387592139-0.01525028996890.213490149184-0.476463282264-0.300540018681-0.0402638515334-0.05086294588160.62457224289-0.1806590914550.08693923000120.520664059391-0.06763269968210.03964957786970.1953477021-0.0384198668290.3707771805112.7878816329235.5724018805189.903596407
503.08662038237-0.4197871544850.613184860621.48758090148-0.3945027235241.669604330490.0448938304049-0.0826489992898-0.447678005735-0.3315445295950.04595437049730.1794316417680.511709505984-0.0984144374592-0.0438650562270.336387356981-0.0206737984162-0.006273462819620.1488711285380.06397616773930.294678317155-2.1081686733135.8719062389201.798395705
511.029220649690.4979976625140.05634437873760.8810665782340.4923785186541.22822612181-0.06136264870760.1568486953560.0729477669537-0.0450904443216-0.0372695109470.0446968723916-0.1625058896370.09018553626830.08807897734620.179798000255-0.04999753031510.004465821092850.1873797669440.01016466563190.14418498253936.293834941767.7693536479201.863524828
520.902440210710.0686874646311-0.4802475633881.310924491940.5466559691261.41688447131-0.07586076046120.05029229298720.01102897524470.06741756577690.0522387592313-0.075472050732-0.0637744349040.153531903850.04295691728460.167611300397-0.0327819575244-0.009385738889430.1633324427780.004806972995720.15205806276734.381775748566.8957844225205.499086589
531.687259687840.554783149631.007918545480.4790005179540.1613700233160.7251553383420.0206150709430.0680558318409-0.1867494607350.108286957193-0.01049524891810.02781371195440.2362607402230.1210097173120.01318678895670.184402424468-0.01380240186920.02191540666520.24070134953-0.00652072686350.18313733310328.337773147654.0447408821186.98829881
541.559084400570.0156463136977-0.5318381026720.69822114569-0.3919153054730.9524294472170.07461938283160.01262918623880.0304481659721-0.08670576327380.04484529600990.0240653568883-0.152068739301-0.0248509241514-0.07722488276760.181341244569-0.0376310551090.01870896783550.1189213651690.01507901390430.1579870747223.5101310177953.7378448212193.171367901
551.311287207030.592729020122-0.5334114641741.09642854076-0.1490195641381.708655439260.0531589883889-0.1935880669250.01678814901250.006358822081670.00517116294522-0.181453580244-0.05319086005850.191223868573-0.02098226670130.199199079588-0.03216480617460.01920145430570.1206841675780.01630596239260.1751386726168.3208847449753.6459284963195.948790802
564.48208341764-0.401958306781-0.2135253738990.2871094896920.09592105673780.2369146340560.09682007895660.2624422964490.240129029991-0.05754923152820.05160855563510.151925915381-0.189614669178-0.0662933627787-0.1010961594410.23799255807-0.01792636805650.04316003430530.176872366330.06066040146240.2495943002950.68193604419661.7482586662189.166128012
572.66672143833-0.150016655708-0.9705341509040.848949862219-0.2247092951591.342061190350.122822065669-0.00438849132272-0.0705002520902-0.0335512922271-0.03747585379620.0316211972485-0.0600257681720.0589988649251-0.08061091455250.146774128398-0.0505665609958-0.02227285007740.1501256994160.02911269857570.11465925610116.787377408559.1404993862181.204261101
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 182 )
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 270 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 11 )
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 19 )
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 41 )
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 51 )
9X-RAY DIFFRACTION9chain 'B' and (resid 52 through 56 )
10X-RAY DIFFRACTION10chain 'B' and (resid 57 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 97 )
15X-RAY DIFFRACTION15chain 'C' and (resid 0 through 83 )
16X-RAY DIFFRACTION16chain 'C' and (resid 84 through 171 )
17X-RAY DIFFRACTION17chain 'C' and (resid 172 through 237 )
18X-RAY DIFFRACTION18chain 'C' and (resid 238 through 270 )
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 17 )
20X-RAY DIFFRACTION20chain 'D' and (resid 18 through 52 )
21X-RAY DIFFRACTION21chain 'D' and (resid 53 through 75 )
22X-RAY DIFFRACTION22chain 'D' and (resid 76 through 91 )
23X-RAY DIFFRACTION23chain 'D' and (resid 92 through 102 )
24X-RAY DIFFRACTION24chain 'D' and (resid 103 through 116 )
25X-RAY DIFFRACTION25chain 'D' and (resid 117 through 135 )
26X-RAY DIFFRACTION26chain 'D' and (resid 136 through 150 )
27X-RAY DIFFRACTION27chain 'D' and (resid 151 through 185 )
28X-RAY DIFFRACTION28chain 'D' and (resid 186 through 199 )
29X-RAY DIFFRACTION29chain 'E' and (resid 3 through 73 )
30X-RAY DIFFRACTION30chain 'E' and (resid 74 through 109 )
31X-RAY DIFFRACTION31chain 'E' and (resid 110 through 124 )
32X-RAY DIFFRACTION32chain 'E' and (resid 125 through 215 )
33X-RAY DIFFRACTION33chain 'E' and (resid 216 through 244 )
34X-RAY DIFFRACTION34chain 'F' and (resid 0 through 19 )
35X-RAY DIFFRACTION35chain 'F' and (resid 20 through 41 )
36X-RAY DIFFRACTION36chain 'F' and (resid 42 through 51 )
37X-RAY DIFFRACTION37chain 'F' and (resid 52 through 61 )
38X-RAY DIFFRACTION38chain 'F' and (resid 62 through 71 )
39X-RAY DIFFRACTION39chain 'F' and (resid 72 through 99 )
40X-RAY DIFFRACTION40chain 'G' and (resid 1 through 17 )
41X-RAY DIFFRACTION41chain 'G' and (resid 18 through 52 )
42X-RAY DIFFRACTION42chain 'G' and (resid 53 through 75 )
43X-RAY DIFFRACTION43chain 'G' and (resid 76 through 91 )
44X-RAY DIFFRACTION44chain 'G' and (resid 92 through 108 )
45X-RAY DIFFRACTION45chain 'G' and (resid 109 through 120 )
46X-RAY DIFFRACTION46chain 'G' and (resid 121 through 135 )
47X-RAY DIFFRACTION47chain 'G' and (resid 136 through 145 )
48X-RAY DIFFRACTION48chain 'G' and (resid 146 through 175 )
49X-RAY DIFFRACTION49chain 'G' and (resid 176 through 185 )
50X-RAY DIFFRACTION50chain 'G' and (resid 186 through 200 )
51X-RAY DIFFRACTION51chain 'H' and (resid 1 through 73 )
52X-RAY DIFFRACTION52chain 'H' and (resid 74 through 109 )
53X-RAY DIFFRACTION53chain 'H' and (resid 110 through 124 )
54X-RAY DIFFRACTION54chain 'H' and (resid 125 through 162 )
55X-RAY DIFFRACTION55chain 'H' and (resid 163 through 202 )
56X-RAY DIFFRACTION56chain 'H' and (resid 203 through 215 )
57X-RAY DIFFRACTION57chain 'H' and (resid 216 through 244 )

+
About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

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Aug 12, 2020. Covid-19 info

Covid-19 info

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