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- PDB-7n6d: HLA peptide complex -

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Basic information

Entry
Database: PDB / ID: 7n6d
TitleHLA peptide complex
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Spike protein S1
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / peptide HLA complex / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / : / : / negative regulation of receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane ...antigen processing and presentation of peptide antigen via MHC class I / : / : / negative regulation of receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / 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 / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / positive regulation of protein binding / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / 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 / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / iron ion transport / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / amyloid fibril formation / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / intracellular iron ion homeostasis / membrane fusion / entry receptor-mediated virion attachment to host cell / learning or memory / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / immune response / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / Golgi membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / focal adhesion / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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, alpha chain, C-terminal / MHC_I C-terminus / 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 / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Spike glycoprotein / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChaurasia, P. / Petersen, J. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)#1194036 Australia
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural basis of biased T cell receptor recognition of an immunodominant HLA-A2 epitope of the SARS-CoV-2 spike protein.
Authors: Chaurasia, P. / Nguyen, T.H.O. / Rowntree, L.C. / Juno, J.A. / Wheatley, A.K. / Kent, S.J. / Kedzierska, K. / Rossjohn, J. / Petersen, J.
History
DepositionJun 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 22, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Spike protein S1
E: MHC class I antigen
F: Beta-2-microglobulin
G: Spike protein S1
I: MHC class I antigen
J: Beta-2-microglobulin
K: Spike protein S1
M: MHC class I antigen
N: Beta-2-microglobulin
O: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,68029
Polymers180,62512
Non-polymers1,05517
Water3,603200
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4047
Polymers45,1563
Non-polymers2484
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-8 kcal/mol
Surface area19000 Å2
MethodPISA
2
E: MHC class I antigen
F: Beta-2-microglobulin
G: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4047
Polymers45,1563
Non-polymers2484
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-7 kcal/mol
Surface area18930 Å2
MethodPISA
3
I: MHC class I antigen
J: Beta-2-microglobulin
K: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4678
Polymers45,1563
Non-polymers3105
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-13 kcal/mol
Surface area19170 Å2
MethodPISA
4
M: MHC class I antigen
N: Beta-2-microglobulin
O: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4047
Polymers45,1563
Non-polymers2484
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-6 kcal/mol
Surface area18860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.197, 85.197, 442.850
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Space group name HallP312(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: -y,-x,-z+2/3
#5: -x+y,y,-z+1/3
#6: x,x-y,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 13 or resid 18...
d_2ens_1(chain "E" and (resid 1 through 13 or resid 18...
d_3ens_1(chain "I" and (resid 1 through 13 or resid 18...
d_4ens_1(chain "M" and (resid 1 through 13 or resid 18...
d_1ens_2(chain "B" and (resid 1 through 40 or (resid 41...
d_2ens_2(chain "F" and (resid 1 through 40 or (resid 41...
d_3ens_2(chain "J" and (resid 1 through 40 or (resid 41...
d_4ens_2(chain "N" and (resid 1 through 44 or resid 46...
d_1ens_3(chain "C" and (resid 1 through 4 or resid 6 through 9))
d_2ens_3(chain "G" and (resid 1 through 4 or resid 6 through 9))
d_3ens_3(chain "K" and (resid 1 through 4 or resid 6 through 9))
d_4ens_3(chain "O" and (resid 1 through 4 or resid 6 through 9))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYSERA1 - 13
d_12ens_1GLYALAA18 - 40
d_13ens_1SERGLNA42 - 43
d_14ens_1METILEA45 - 52
d_15ens_1GLUPROA55 - 57
d_16ens_1TYRSERA59 - 71
d_17ens_1THRHISA73 - 74
d_18ens_1VALTYRA76 - 85
d_19ens_1GLNGLNA87
d_110ens_1GLYLEUA91 - 110
d_111ens_1GLYLYSA112 - 127
d_112ens_1ASPLEUA129 - 130
d_113ens_1SERALAA132 - 140
d_114ens_1THRLYSA142 - 144
d_115ens_1LYSGLYA146 - 175
d_116ens_1GLUVALA177 - 231
d_117ens_1THRGLUA233 - 254
d_118ens_1ARGHISA256 - 263
d_119ens_1GLYPROA265 - 267
d_120ens_1PROGLUA269 - 275
d_21ens_1GLYSERD1 - 13
d_22ens_1GLYALAD18 - 40
d_23ens_1SERGLND42 - 43
d_24ens_1METILED45 - 52
d_25ens_1GLUPROD55 - 57
d_26ens_1TYRSERD59 - 71
d_27ens_1THRHISD73 - 74
d_28ens_1VALTYRD76 - 85
d_29ens_1GLNGLND87
d_210ens_1GLYLEUD91 - 110
d_211ens_1GLYLYSD112 - 127
d_212ens_1ASPLEUD129 - 130
d_213ens_1SERALAD132 - 140
d_214ens_1THRLYSD142 - 144
d_215ens_1LYSGLYD146 - 175
d_216ens_1GLUVALD177 - 231
d_217ens_1THRGLUD233 - 254
d_218ens_1ARGHISD256 - 263
d_219ens_1GLYPROD265 - 267
d_220ens_1PROGLUD269 - 275
d_31ens_1GLYSERG1 - 13
d_32ens_1GLYALAG18 - 40
d_33ens_1SERGLNG42 - 43
d_34ens_1METILEG45 - 52
d_35ens_1GLUPROG55 - 57
d_36ens_1TYRSERG59 - 71
d_37ens_1THRHISG73 - 74
d_38ens_1VALTYRG76 - 85
d_39ens_1GLNGLNG87
d_310ens_1GLYLEUG91 - 110
d_311ens_1GLYLYSG112 - 127
d_312ens_1ASPLEUG129 - 130
d_313ens_1SERALAG132 - 140
d_314ens_1THRLYSG142 - 144
d_315ens_1LYSGLYG146 - 175
d_316ens_1GLUVALG177 - 231
d_317ens_1THRGLUG233 - 254
d_318ens_1ARGHISG256 - 263
d_319ens_1GLYPROG265 - 267
d_320ens_1PROGLUG269 - 275
d_41ens_1GLYSERJ1 - 13
d_42ens_1GLYALAJ18 - 40
d_43ens_1SERGLNJ42 - 43
d_44ens_1METILEJ45 - 52
d_45ens_1GLUPROJ55 - 57
d_46ens_1TYRSERJ59 - 71
d_47ens_1THRHISJ73 - 74
d_48ens_1VALTYRJ76 - 85
d_49ens_1GLNGLNJ87
d_410ens_1GLYLEUJ91 - 110
d_411ens_1GLYLYSJ112 - 127
d_412ens_1ASPLEUJ129 - 130
d_413ens_1SERALAJ132 - 140
d_414ens_1THRLYSJ142 - 144
d_415ens_1LYSGLYJ146 - 175
d_416ens_1GLUVALJ177 - 231
d_417ens_1THRGLUJ233 - 254
d_418ens_1ARGHISJ256 - 263
d_419ens_1GLYPROJ265 - 267
d_420ens_1PROGLUJ269 - 275
d_11ens_2ILEGLUB1 - 44
d_12ens_2ILEILEB46
d_13ens_2VALSERB49 - 57
d_14ens_2ASPTHRB59 - 73
d_15ens_2LYSSERB75 - 88
d_16ens_2PROPROB90
d_17ens_2ILEASPB92 - 96
d_18ens_2ASPMETB98 - 99
d_21ens_2ILEGLUE2 - 45
d_22ens_2ILEILEE47
d_23ens_2VALSERE50 - 58
d_24ens_2ASPTHRE60 - 74
d_25ens_2LYSSERE76 - 89
d_26ens_2PROPROE91
d_27ens_2ILEASPE93 - 97
d_28ens_2ASPMETE99 - 100
d_31ens_2ILEGLUH2 - 45
d_32ens_2ILEILEH47
d_33ens_2VALSERH50 - 58
d_34ens_2ASPTHRH60 - 74
d_35ens_2LYSSERH76 - 89
d_36ens_2PROPROH91
d_37ens_2ILEASPH93 - 97
d_38ens_2ASPMETH99 - 100
d_41ens_2ILEGLUK2 - 45
d_42ens_2ILEILEK47
d_43ens_2VALSERK50 - 58
d_44ens_2ASPTHRK60 - 74
d_45ens_2LYSSERK76 - 89
d_46ens_2PROPROK91
d_47ens_2ILEASPK93 - 97
d_48ens_2ASPMETK99 - 100
d_11ens_3TYRPROC1 - 4
d_12ens_3THRLEUC6 - 9
d_21ens_3TYRPROF1 - 4
d_22ens_3THRLEUF6 - 9
d_31ens_3TYRPROI1 - 4
d_32ens_3THRLEUI6 - 9
d_41ens_3TYRPROL1 - 4
d_42ens_3THRLEUL6 - 9

NCS ensembles :
ID
ens_1
ens_2
ens_3

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Components

#1: Protein
MHC class I antigen


Mass: 32125.473 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: Q861F7
#2: Protein
Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 4
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/peptide
Spike protein S1


Mass: 1151.377 Da / Num. of mol.: 4 / Fragment: epitope YLQPRTFLL (UNP residues 269-277) / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, 0.2 M sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 293.15 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953731 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953731 Å / Relative weight: 1
ReflectionResolution: 2.3→49.21 Å / Num. obs: 82685 / % possible obs: 99.89 % / Redundancy: 14 % / Biso Wilson estimate: 47.21 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.06 / Rrim(I) all: 0.16 / Net I/σ(I): 10.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 14.4 % / Rmerge(I) obs: 1.782 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4473 / CC1/2: 0.997 / Rpim(I) all: 0.482 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GSO

3gso


Resolution: 2.3→44.28 Å / SU ML: 0.3318 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.202
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.247 4268 5.17 %
Rwork0.2126 78222 -
obs0.2144 82490 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12605 0 68 200 12873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003313092
X-RAY DIFFRACTIONf_angle_d0.653717747
X-RAY DIFFRACTIONf_chiral_restr0.04461804
X-RAY DIFFRACTIONf_plane_restr0.00492318
X-RAY DIFFRACTIONf_dihedral_angle_d12.53994774
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.577916167592
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.685958479241
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.685986718605
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.444035557059
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.635947547816
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS0.629070908292
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.901345627026
ens_3d_3CX-RAY DIFFRACTIONTorsion NCS0.416944994572
ens_3d_4CX-RAY DIFFRACTIONTorsion NCS0.137806723033
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.36081220.32872536X-RAY DIFFRACTION99.77
2.33-2.350.37771470.33382585X-RAY DIFFRACTION99.78
2.35-2.380.35681320.32112585X-RAY DIFFRACTION100
2.38-2.410.36331390.30462590X-RAY DIFFRACTION99.82
2.41-2.440.33531340.29112600X-RAY DIFFRACTION99.85
2.44-2.480.35081530.2912546X-RAY DIFFRACTION99.82
2.48-2.510.3541570.28122597X-RAY DIFFRACTION100
2.51-2.550.28431440.28292570X-RAY DIFFRACTION99.89
2.55-2.590.30911210.28012635X-RAY DIFFRACTION99.82
2.59-2.630.32621290.32554X-RAY DIFFRACTION99.96
2.63-2.680.36551860.2852581X-RAY DIFFRACTION99.93
2.68-2.730.35281510.28742576X-RAY DIFFRACTION99.93
2.73-2.780.3511340.27582584X-RAY DIFFRACTION100
2.78-2.840.30321380.25932640X-RAY DIFFRACTION99.78
2.84-2.90.25961240.26132570X-RAY DIFFRACTION99.93
2.9-2.970.32341190.25282606X-RAY DIFFRACTION99.93
2.97-3.040.28931690.25232595X-RAY DIFFRACTION99.86
3.04-3.120.27371510.25022597X-RAY DIFFRACTION99.93
3.12-3.210.31321390.26012568X-RAY DIFFRACTION100
3.21-3.320.29671520.26232624X-RAY DIFFRACTION100
3.32-3.440.28241370.22822608X-RAY DIFFRACTION99.96
3.44-3.570.24861510.21012639X-RAY DIFFRACTION100
3.57-3.740.23591280.1962599X-RAY DIFFRACTION100
3.74-3.930.24831290.19722623X-RAY DIFFRACTION100
3.93-4.180.21391410.17832629X-RAY DIFFRACTION100
4.18-4.50.17061220.15492680X-RAY DIFFRACTION100
4.5-4.950.17381720.14952605X-RAY DIFFRACTION100
4.95-5.670.19211510.16232653X-RAY DIFFRACTION99.96
5.67-7.140.21681500.18792691X-RAY DIFFRACTION100
7.14-44.280.16571460.16212756X-RAY DIFFRACTION99.45
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)
13.272102637080.1024787664440.14615024162.85156430417-0.5048784174061.09099754926-0.163320466671-0.2258818547880.3402577755630.2277092922140.165238885444-0.483301519973-0.1089447279180.0352602196632-0.002603283283780.4586286511910.202689697628-0.1101707777460.377859778003-0.06590418300090.619908897649-18.8437379758-24.09298931357.0980741697
23.587640781140.330734727097-0.08220669584454.299974739850.5652903992894.064619563320.04079132227940.0394495396730.3801550797670.1165059818630.147697160102-0.436338828405-0.524958066962-0.337445897029-0.07940462625680.5344553287790.1337965749320.02891757624290.3207042185940.07190822052230.645130175017-28.52259365848.5998649833250.8577379876
32.00000911986.319984538342.000083201261.999926460271.999954027041.99994281117-0.191939730827-4.3951470495-1.423872488234.94960950185-0.458632621987-0.00810694035856-4.6034294081-6.158702323550.7291238903410.908454433449-0.297123588741-0.4405133194650.9890297647180.09301323701211.64717849717-29.532600282323.040248176946.8146936018
45.10841880630.768428552214-0.8721397813392.503162709810.9793422987672.06920140762-0.0118352096333-0.407784698191-0.378594399166-0.1066364211450.02755885204820.03105673623340.243159498077-0.0738197656050.05617574123610.3816681485090.154085962797-0.005607160775090.5033507421950.09719131835880.523241707589-32.9404364555-9.976299301243.0124045067
55.187874263332.10751773309-0.3400981935345.30156605063-0.2330312937676.553901923580.1162174851220.1677507058030.907989954168-0.590770682999-0.166195118785-0.437495004041-1.015534369960.641816876392-0.03471337936650.5753019859240.06566249502060.07806059195780.3285864930850.1266572525860.817609423429-21.4142243374-1.4812042807536.7566177898
64.293891681410.59460675659-2.842710785353.95884954831.853319464394.576609868-0.3381544956970.4471002332760.0204880400936-0.4542462980840.337932295755-0.2117662004480.389731011412-0.006499712242550.1726438701520.3931702786080.128944419404-0.09547143577150.3110847146290.006780240446190.497438412826-29.3018171925-15.382583219835.6874898333
75.13593007781-1.023559776034.375024630034.550786585-4.311522198726.83440007331-0.4292620158511.68579742118-0.04184851464340.21163184356-0.267376215991-0.782747988692-1.014227816170.05759986663050.6199653817950.5589086783760.07111068752730.1530991283540.5680267783290.2038460778170.752053563975-26.7187190016-9.1705727794723.7066907234
85.18702773-1.917707229231.310031991424.03882631607-2.327772545469.941123195170.5832171753270.6551850988990.000634500653359-0.399000348556-0.0143511071787-0.452450199039-0.1543629052470.583603413195-0.3889656442050.4677609356280.1749218749420.04333705245570.401519367947-0.005235033718340.768866936397-20.2130069278-15.036972697138.6101013884
93.859704068872.16627614989-1.885801102628.34344720233-5.025324288863.72598318774-0.09943096330380.7070999092830.369551055976-0.008154473718410.473602515657-0.172103612267-0.521087814263-0.634617933777-0.3102993038970.4707892796550.121547417389-0.01008844299270.372474607465-0.07953283307660.582728282092-24.0333245162-11.084017156442.9647253535
107.823412022353.24470380811-1.542145969012.561370043770.9672087275752.54761616215-0.3289546341480.7854910535940.713536358282-1.068896582330.383880424672-0.1772450975040.224028985323-0.0699200719097-0.02688416042940.50186121430.173098604399-0.04018578278240.5041800182720.1188928246130.689868173545-31.8306336997-7.644595428130.5167658898
115.02652269665-0.433393466104-1.947378002342.067210388712.404092022017.43769688706-0.0460667296792-1.033155070231.30517325756-0.5045510025010.087626496799-0.364074688034-1.87042767126-0.2465018906710.03649487519320.731156697710.315578144668-0.1448133569430.5707530735590.1377741637150.901639378655-30.83242573271.1553506035233.6851559292
120.3934394546320.425592056197-0.02548099052350.504817652188-0.127449012210.726048046486-0.216971122373-0.0397561622420.3513591322350.5282659895940.1063251687-0.3435944427390.04497889808650.02576046072390.1666309424620.5239442605380.326266603803-0.1858425365270.318790098487-0.1764923082970.764264420357-15.5003545625-29.996935274561.09598953
133.196944515980.6677332559071.153767530464.612686852511.966557073314.17283028411-0.188674957561-0.0117826279983-0.3323738519890.2831977305440.1532920092550.03973414646810.06924350857220.1719967216750.1360449904180.277982451890.08606434738110.01736095147060.4930388116190.0845411955450.684979146556-29.847729186-47.868650236226.0551585424
141.90919954947-0.381323694423-0.7801325879442.635136475-0.484028279281.875582653750.014151566050.4128810306140.0267965315429-0.0454254875026-0.0486868416879-0.166244945188-0.0128900005728-0.028825906240.08358256689190.2488804818640.0667794652273-0.004794398054490.6343563940670.1059253116260.745685239097-28.9262835987-38.54012421216.4513092994
153.678629512330.106179453635-0.9230660873632.35605346765-0.9412896224342.09761391549-0.1193035049850.467152337938-0.375308754763-0.0941400217891-0.0387894910484-0.3602118657290.1768263645110.08117072579140.2152809209340.2743190454370.0588784674148-0.1033824911860.594275766626-0.06157649807220.396687394699-38.3484379337-47.998129700915.1286467957
162.183357574630.496027836939-0.6007824230082.466342406290.08305212308872.885275470110.1253121926730.20453603823-0.175591558094-0.01358881573690.03845845108240.181401056835-0.100933053864-0.648313421986-0.07291232553610.2965879157390.0316783141364-0.00424505975140.6406094382760.08774657897110.703009304809-62.9869200091-49.496436851622.8423677005
175.282110710067.25896178534-0.5321238874229.96405345068-0.7304093744630.06257031728920.1098505877510.321505909530.5105494214550.3054846414230.1130566955950.3828431342350.1897002658970.074227708125-0.3651824104880.5556950632910.1503195181120.07100739751860.611353616120.2295899568910.710079595858-43.2333749632-28.314878398127.6801247486
183.83655381155-1.29387972771-0.813225160510.839784902550.1241563823053.420776819110.0341276919356-0.298769312364-0.1874872057780.154442830446-0.06939290612110.2903797592450.2502262606370.05563440171240.01648643187270.347349586290.0263949133548-0.04846861837040.4304561795930.1100467332460.536733100083-46.5349510486-45.725691585139.7431186952
193.15950373931.82060763956-2.025203857074.79022848309-3.510501156183.189272139070.02406093925590.172714915849-0.152725555310.223749874046-0.0845153779376-0.3355437873980.172418418630.2283939649290.02907151910230.3288559568410.0866590555897-0.05057179031630.4454225561660.04309906803190.559005262161-41.5341900392-44.172533777630.9834031801
204.33873531021-0.266424300775-1.29399803835.91428700394-2.965875153598.66379611656-0.270438017181-0.131372935514-0.3960909855620.4386701728530.09239698979680.706166292859-0.0680582083977-1.16871270190.01990676082740.3266735565780.11397834570.02885138947720.513894984937-0.001979543508290.703918121081-52.3976180698-40.936934547542.7861324954
210.4947725229781.91012920868-0.7237842255628.32359778162-3.176816468631.198319764180.09456912144260.1251807513660.359704468746-0.263811873453-0.430210667161-1.269244323930.00989085348820.2415744512260.4763887820160.3217732133850.09450822040550.009479252549650.5965628836090.04674358311740.828149223161-21.8844183602-41.976391602514.5766328252
221.04418377198-0.7276860160460.1156444087774.45132454701-2.696789987855.56393388759-0.04477302203930.0603129219949-0.124149134376-0.1350117809750.1712332107030.6550825094540.0199006642128-0.674619449587-0.1322173413050.3269373174860.129307745762-0.08580332784440.426546235498-0.01302123091810.676793822729-26.7894961826-56.928937931960.2030385518
232.63162803786-0.67744950630.1805936154213.69980494044-0.9003560622452.002588341990.0737423370134-0.02114474993750.512356805590.02468125851660.0398379459835-0.147071579127-0.1136213842210.0995569610797-0.07100877184090.4525019209010.171628735405-0.07217970576550.347816449211-0.01999963804990.65273265133-14.7528368194-48.767258776962.5862586203
245.35790994723-4.61139307748-2.777280803154.993550219914.787258601596.8897546196-0.831995370198-0.410730345703-1.157443627711.072887301580.3222594892861.577094326551.330647308830.5268550212770.13542766720.7651332958170.1223494158420.1745638531570.5035703111610.2509469629860.964686991502-17.402675235-84.071289903466.7814459723
256.05101737589-3.530537204910.2151411584543.766624019041.745640460692.08177468036-0.516655602199-0.595975196462-0.6946290295180.4996811525820.6357642263310.932318920180.583478172520.607296673312-0.1165568565850.5572024791640.2192774323640.03370306358350.5715404791910.1263155477120.718469704539-8.88988256727-85.146396122563.1380922537
260.573901580760.16417680492-0.1119033298743.58667687203-0.7902904942610.827581550040.121551436487-0.280359499840.000379517103288-0.46582354068-0.143829015461-0.533193051823-0.012193398276-0.277646330473-0.2210862722931.294126229171.216941879310.2405635832810.8351622363960.4151353996380.788482863821-11.1476487699-87.507855993972.8935110646
272.20662117159-0.6449301147370.732742106264.58977811748-0.03730038809182.754450391060.1860658857590.137426241955-0.629791937425-0.670295629929-0.1561705211330.9641453132460.456693014667-0.5672185901790.2735552263070.5875290292620.133758775464-0.1948216213250.40676543702-0.08417002710240.88500071312-21.8469966418-76.441050141553.1787856973
284.022141394780.723328567579-1.044690260543.85656011521-0.04521268054134.54480003150.1804948482710.412608861327-0.640385876477-0.694938186924-0.4085021789510.6656341069080.302972013235-1.065210130830.05178348837840.6867574073450.184842249614-0.3311457476460.662725384573-0.1692747927410.782690131798-27.2384840878-70.600796272847.1366552404
295.57088379822.31470193194-1.499542964978.137586067771.292234985173.21177664873-0.1127485467710.463674556496-0.940814023011-0.8386714254830.008579403719560.2595653720710.106935715061-0.2499953822430.2346219777880.4953944529340.162893678609-0.2523236424670.3847206455910.02550404733820.738798387338-21.4167590214-68.677316989654.4359003863
303.708661214810.183030234275-1.974963482357.163549830760.1789284047915.04269190835-0.3254581383220.904837235899-1.62303220243-1.29955512135-0.4900837844090.7964239820921.07578150464-1.340326690380.5367420462161.158295457460.199998519953-0.3456890810920.778274462632-0.3048007788531.1603656313-23.0505841467-81.050351179245.0129776573
310.4726273596810.674383994959-0.3254109988882.00373413046-1.142392500693.174327995580.3822529956230.4403550397780.5998420105640.0597890085410.219009917789-0.670812062803-0.650910288461-0.001476191193-0.09806020690280.3446660762830.203907850643-0.1208411625870.3965134047760.02455023235190.678076094887-19.4008326192-43.874246882363.4293136545
325.26777128465-0.356907707478-0.8755911307422.82006344943-1.432015532463.94271273801-0.0309196324666-0.1857688919560.7761490109130.4255318861660.09238280816680.373106761862-0.757192001673-0.315615340887-0.05451303111030.3566357617180.143090881273-0.02568267647850.527690010781-0.01706801936030.867046044389-4.15080162057-20.100739133912.0462026319
333.70454375268-0.665132352801-1.728714185176.67683766458-5.265170868986.788376653780.13853419228-0.06409479860210.2471031627660.06220811536380.3403862854961.01667784709-0.035577543975-0.455029861458-0.3109598436780.2892839814620.0728554419470.007459203047570.6753522376310.008725853248670.886391533302-12.822898804-27.595031658614.6572300742
343.25970224794-0.09923475992250.8100832016863.07197400229-0.7560246577073.85357618978-0.230656424545-0.255693202695-0.802271357996-0.01588840349060.1771045597970.2470287022910.39061934882-0.08757568538190.07431111894320.2636856612070.0819930282620.03394361014140.576224469132-0.02716259814350.768195458958-2.68294681576-39.070975674711.475897893
356.945046838330.001379709519121.859801228022.02791167368-0.6547442161682.65589692385-0.3050633654761.246815243691.20282581766-0.205676188141-0.001278735304430.408850070916-0.404347334955-0.1969454717240.2783781290520.3645776015360.122961966398-0.01958993386230.7096975673470.09777014672460.7325850089352.42660809009-20.5266324529-4.07317237444
362.72996825512-1.747370373352.729795416094.225609421390.2622431188585.104799756810.07100883720680.8029493470751.220014463940.287830692886-0.055535317748-0.2690176084340.00345113636210.9721188491730.131163846670.3931737624620.0896309050697-0.02746755602380.771622506180.1894066502450.95175113337230.2874471455-17.972102773811.2758619775
373.545206065850.703606434022-0.7385347589812.532541376622.188858902342.328917304630.3642516039641.363111802950.766916892349-0.198211018199-0.231087501967-0.228904825321-0.1103978394770.756835041389-0.1747363059880.3784703525810.1425831475910.01587421422580.9154789184720.2495962361290.83221168544530.2593934125-21.02686079868.75084421781
386.111531298121.68565551275-2.641768209460.739781060247-0.6853585494512.43630748659-0.0271064344294-1.439177014370.7551477497450.498260713716-0.231016437140.111110186068-0.868817015051-0.2267152384780.4575647046350.2861296550230.0856532350037-0.1436771303410.843533228004-0.1844695961120.73948901138613.1229776959-23.034713015824.6375250153
394.626080893650.656374780501-0.4702207131665.1707896069-2.064707074494.80330675223-0.0411351238837-0.9144984208721.425583045830.168157591626-0.70799657504-0.0780874476414-0.7712289498180.4560370356380.2640808192740.5396474980940.0419016037968-0.1650395333930.651463144532-0.2568117498541.2262197415512.7655980148-11.150220595521.0523328547
403.45942340734-0.917907062447-2.095080346624.74369734444-2.707293537294.010037172050.15583078154-0.92121697299-0.1783325834691.03238924446-0.0909262541868-0.689166022303-1.230798896070.439087940146-1.054317643630.8088391149540.136585128449-0.1316901186621.02623032742-0.3211879569091.623967314487.81917220638-4.4243314251726.6221512717
415.71519996042.885202609170.8169569353111.55661450360.03116485722244.69489309452-0.268804121898-0.7363888854550.8538096193540.02096927182050.0417327871811-0.0117383561926-0.5926655002020.04748922570840.07434616805240.3352223185720.152355814969-0.04944103019320.611644967336-0.2002281310420.8719470606087.40018452435-18.273183795218.1767199841
425.709229834284.138321147941.499089856667.51935819306-0.2874916152726.13980132335-0.86619695322-0.8296217889142.172472696410.3392743328940.3781222616560.245785966252-1.207153163680.05013137082410.2967777250120.6646889873750.103740238178-0.3167508760890.894514714141-0.3270163874321.3063572720818.2880896779-11.175158663627.8504308
432.781088706513.81296205114-4.014818511346.41105782505-4.619771905346.61699153873-0.09656339901730.638911515311-0.207799383315-0.0116304157220.6135351406250.4374411613320.0821548286315-1.42900539773-0.2303264412150.269648606780.08356387819540.02668501025340.63979398192-0.01028056536750.65831004096-11.7516174394-33.30810732668.64338234944
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 174 )AA1 - 1741 - 174
22chain 'A' and (resid 175 through 274 )AA175 - 274175 - 274
33chain 'A' and (resid 275 through 275 )AA275275
44chain 'B' and (resid 1 through 11 )BB1 - 111 - 11
55chain 'B' and (resid 12 through 30 )BB12 - 3012 - 30
66chain 'B' and (resid 31 through 41 )BB31 - 4131 - 41
77chain 'B' and (resid 42 through 46 )BB42 - 4642 - 46
88chain 'B' and (resid 47 through 56 )BB47 - 5647 - 56
99chain 'B' and (resid 57 through 71 )BB57 - 7157 - 71
1010chain 'B' and (resid 72 through 90 )BB72 - 9072 - 90
1111chain 'B' and (resid 91 through 99 )BB91 - 9991 - 99
1212chain 'C' and (resid 1 through 9 )CC1 - 91 - 9
1313chain 'E' and (resid 1 through 56 )ED1 - 561 - 56
1414chain 'E' and (resid 57 through 137 )ED57 - 13757 - 137
1515chain 'E' and (resid 138 through 197 )ED138 - 197138 - 197
1616chain 'E' and (resid 198 through 276 )ED198 - 276198 - 276
1717chain 'F' and (resid 0 through 5 )FE0 - 51 - 6
1818chain 'F' and (resid 6 through 51 )FE6 - 517 - 52
1919chain 'F' and (resid 52 through 71 )FE52 - 7153 - 72
2020chain 'F' and (resid 72 through 99 )FE72 - 9973 - 100
2121chain 'G' and (resid 1 through 9 )GF1 - 91 - 9
2222chain 'I' and (resid 1 through 56 )IG1 - 561 - 56
2323chain 'I' and (resid 57 through 174 )IG57 - 17457 - 174
2424chain 'I' and (resid 175 through 197 )IG175 - 197175 - 197
2525chain 'I' and (resid 198 through 262 )IG198 - 262198 - 262
2626chain 'I' and (resid 263 through 276 )IG263 - 276263 - 276
2727chain 'J' and (resid 0 through 30 )JH0 - 301 - 31
2828chain 'J' and (resid 31 through 56 )JH31 - 5632 - 57
2929chain 'J' and (resid 57 through 70 )JH57 - 7058 - 71
3030chain 'J' and (resid 71 through 99 )JH71 - 9972 - 100
3131chain 'K' and (resid 1 through 9 )KI1 - 91 - 9
3232chain 'M' and (resid 1 through 56 )MJ1 - 561 - 56
3333chain 'M' and (resid 57 through 84 )MJ57 - 8457 - 84
3434chain 'M' and (resid 85 through 162 )MJ85 - 16285 - 162
3535chain 'M' and (resid 163 through 185 )MJ163 - 185163 - 185
3636chain 'M' and (resid 186 through 219 )MJ186 - 219186 - 219
3737chain 'M' and (resid 220 through 276 )MJ220 - 276220 - 276
3838chain 'N' and (resid 0 through 11 )NK0 - 111 - 12
3939chain 'N' and (resid 12 through 41 )NK12 - 4113 - 42
4040chain 'N' and (resid 42 through 51 )NK42 - 5143 - 52
4141chain 'N' and (resid 52 through 71 )NK52 - 7153 - 72
4242chain 'N' and (resid 72 through 99 )NK72 - 9973 - 100
4343chain 'O' and (resid 1 through 9 )OL1 - 91 - 9

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