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- PDB-8bbn: SARS-CoV-2 Delta-RBD complexed with BA.2-10 and EY6A Fabs -

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Basic information

Entry
Database: PDB / ID: 8bbn
TitleSARS-CoV-2 Delta-RBD complexed with BA.2-10 and EY6A Fabs
Components
  • BA.2-10 heavy chain
  • BA.2-10 light chain
  • EY6A Heavy chain
  • EY6A light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-CoV-2 / BA.2 mAb / RBD / BA.2-36 / BA.2-10
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.58 Å
AuthorsZhou, D. / Ren, J. / Stuart, D.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CitationJournal: Cell Rep / Year: 2023
Title: Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses.
Authors: Aiste Dijokaite-Guraliuc / Raksha Das / Daming Zhou / Helen M Ginn / Chang Liu / Helen M E Duyvesteyn / Jiandong Huo / Rungtiwa Nutalai / Piyada Supasa / Muneeswaran Selvaraj / Thushan I de ...Authors: Aiste Dijokaite-Guraliuc / Raksha Das / Daming Zhou / Helen M Ginn / Chang Liu / Helen M E Duyvesteyn / Jiandong Huo / Rungtiwa Nutalai / Piyada Supasa / Muneeswaran Selvaraj / Thushan I de Silva / Megan Plowright / Thomas A H Newman / Hailey Hornsby / Alexander J Mentzer / Donal Skelly / Thomas G Ritter / Nigel Temperton / Paul Klenerman / Eleanor Barnes / Susanna J Dunachie / / Cornelius Roemer / Thomas P Peacock / Neil G Paterson / Mark A Williams / David R Hall / Elizabeth E Fry / Juthathip Mongkolsapaya / Jingshan Ren / David I Stuart / Gavin R Screaton /
Abstract: In November 2021, Omicron BA.1, containing a raft of new spike mutations, emerged and quickly spread globally. Intense selection pressure to escape the antibody response produced by vaccines or ...In November 2021, Omicron BA.1, containing a raft of new spike mutations, emerged and quickly spread globally. Intense selection pressure to escape the antibody response produced by vaccines or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection then led to a rapid succession of Omicron sub-lineages with waves of BA.2 and then BA.4/5 infection. Recently, many variants have emerged such as BQ.1 and XBB, which carry up to 8 additional receptor-binding domain (RBD) amino acid substitutions compared with BA.2. We describe a panel of 25 potent monoclonal antibodies (mAbs) generated from vaccinees suffering BA.2 breakthrough infections. Epitope mapping shows potent mAb binding shifting to 3 clusters, 2 corresponding to early-pandemic binding hotspots. The RBD mutations in recent variants map close to these binding sites and knock out or severely knock down neutralization activity of all but 1 potent mAb. This recent mAb escape corresponds with large falls in neutralization titer of vaccine or BA.1, BA.2, or BA.4/5 immune serum.
History
DepositionOct 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: EY6A Heavy chain
N: EY6A light chain
J: EY6A Heavy chain
K: EY6A light chain
E: EY6A Heavy chain
F: EY6A light chain
R: Spike protein S1
L: BA.2-10 light chain
H: BA.2-10 heavy chain
Y: Spike protein S1
D: BA.2-10 light chain
C: BA.2-10 heavy chain
X: Spike protein S1
B: BA.2-10 light chain
A: BA.2-10 heavy chain


Theoretical massNumber of molelcules
Total (without water)356,01115
Polymers356,01115
Non-polymers00
Water00
1
M: EY6A Heavy chain
N: EY6A light chain
Y: Spike protein S1
D: BA.2-10 light chain
C: BA.2-10 heavy chain


Theoretical massNumber of molelcules
Total (without water)118,6705
Polymers118,6705
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
J: EY6A Heavy chain
K: EY6A light chain
X: Spike protein S1
B: BA.2-10 light chain
A: BA.2-10 heavy chain


Theoretical massNumber of molelcules
Total (without water)118,6705
Polymers118,6705
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: EY6A Heavy chain
F: EY6A light chain
R: Spike protein S1
L: BA.2-10 light chain
H: BA.2-10 heavy chain


Theoretical massNumber of molelcules
Total (without water)118,6705
Polymers118,6705
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.655, 171.691, 176.991
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 128 or resid 130 through 225 or resid 227 through 228))
d_2ens_1(chain "C" and (resid 2 through 128 or resid 130 through 225 or resid 227 through 228))
d_3ens_1(chain "H" and (resid 2 through 128 or resid 130 through 225 or resid 227 through 228))
d_1ens_2(chain "B" and (resid 2 through 3 or resid 5...
d_2ens_2(chain "D" and (resid 2 through 3 or resid 5...
d_3ens_2(chain "F" and (resid 2 through 3 or resid 5...
d_4ens_2(chain "K" and (resid 2 through 3 or resid 5...
d_5ens_2(chain "L" and (resid 2 through 3 or resid 5...
d_6ens_2(chain "N" and (resid 2 through 3 or resid 5...
d_1ens_3chain "E"
d_2ens_3chain "J"
d_3ens_3chain "M"
d_1ens_4(chain "R" and (resid 334 through 465 or resid 467 through 527))
d_2ens_4(chain "X" and (resid 334 through 465 or resid 467 through 527))
d_3ens_4(chain "Y" and (resid 334 through 465 or resid 467 through 527))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1VALTHRO2 - 128
d_12ens_1GLYPROO130 - 225
d_13ens_1SERCYSO227 - 228
d_21ens_1VALTHRL1 - 127
d_22ens_1GLYPROL130 - 225
d_23ens_1SERCYSL227 - 228
d_31ens_1VALTHRI2 - 128
d_32ens_1GLYPROI130 - 225
d_33ens_1SERCYSI227 - 228
d_11ens_2ILEGLNH2 - 3
d_12ens_2THRVALH5 - 15
d_13ens_2ASPCYSH17 - 23
d_14ens_2ALAILEH25 - 29
d_15ens_2TYRPROH32 - 44
d_16ens_2LEUASPH46 - 82
d_17ens_2ALACYSH84 - 88
d_18ens_2GLNGLNH90
d_19ens_2TYRSERH92 - 93
d_110ens_2THRGLYH97 - 99
d_111ens_2GLYVALH101 - 104
d_112ens_2LYSASPH107 - 122
d_113ens_2GLNSERH124 - 168
d_114ens_2ASPARGH170 - 211
d_21ens_2ILEGLNK2 - 3
d_22ens_2THRVALK5 - 15
d_23ens_2ASPCYSK17 - 23
d_24ens_2ALAILEK25 - 29
d_25ens_2TYRPROK32 - 44
d_26ens_2LEUASPK46 - 82
d_27ens_2ALACYSK84 - 88
d_28ens_2GLNGLNK90
d_29ens_2TYRSERK92 - 93
d_210ens_2THRGLYK97 - 99
d_211ens_2GLYVALK101 - 104
d_212ens_2LYSASPK107 - 122
d_213ens_2GLNSERK124 - 168
d_214ens_2ASPARGK170 - 211
d_31ens_2ILEGLNN2 - 3
d_32ens_2THRVALN5 - 15
d_33ens_2ASPCYSN17 - 23
d_34ens_2ALAILEN25 - 29
d_35ens_2TYRPRON32 - 44
d_36ens_2LEUASPN46 - 82
d_37ens_2ALACYSN84 - 88
d_38ens_2GLNGLNN90
d_39ens_2TYRSERN92 - 93
d_310ens_2THRGLYN97 - 99
d_311ens_2GLYVALN101 - 104
d_312ens_2LYSASPN107 - 122
d_313ens_2GLNSERN124 - 168
d_314ens_2ASPARGN170 - 211
d_41ens_2ILEGLND2 - 3
d_42ens_2THRVALD5 - 15
d_43ens_2ASPCYSD17 - 23
d_44ens_2ALAILED25 - 29
d_45ens_2TYRPROD32 - 44
d_46ens_2LEUASPD46 - 82
d_47ens_2ALACYSD84 - 88
d_48ens_2GLNGLND90
d_49ens_2TYRSERD92 - 93
d_410ens_2THRGLYD98 - 100
d_411ens_2GLYVALD102 - 105
d_412ens_2LYSASPD108 - 123
d_413ens_2GLNSERD125 - 169
d_414ens_2ASPARGD171 - 212
d_51ens_2ILEGLNB2 - 3
d_52ens_2THRVALB5 - 15
d_53ens_2ASPCYSB17 - 23
d_54ens_2ALAILEB25 - 29
d_55ens_2TYRPROB32 - 44
d_56ens_2LEUASPB46 - 82
d_57ens_2ALACYSB84 - 88
d_58ens_2GLNGLNB90
d_59ens_2TYRSERB92 - 93
d_510ens_2THRGLYB98 - 100
d_511ens_2GLYVALB102 - 105
d_512ens_2LYSASPB108 - 123
d_513ens_2GLNSERB125 - 169
d_514ens_2ASPARGB171 - 212
d_61ens_2ILEGLNF2 - 3
d_62ens_2THRVALF5 - 15
d_63ens_2ASPCYSF17 - 23
d_64ens_2ALAILEF25 - 29
d_65ens_2TYRPROF32 - 44
d_66ens_2LEUASPF46 - 82
d_67ens_2ALACYSF84 - 88
d_68ens_2GLNGLNF90
d_69ens_2TYRSERF92 - 93
d_610ens_2THRGLYF98 - 100
d_611ens_2GLYVALF102 - 105
d_612ens_2LYSASPF108 - 123
d_613ens_2GLNSERF125 - 169
d_614ens_2ASPARGF171 - 212
d_11ens_3GLUPROE1 - 221
d_21ens_3GLUPROC1 - 221
d_31ens_3GLUPROA1 - 221
d_11ens_4ASNGLUG8 - 139
d_12ens_4ASPLYSG141 - 201
d_21ens_4ASNGLUM8 - 139
d_22ens_4ASPLYSM141 - 201
d_31ens_4ASNGLUJ8 - 139
d_32ens_4ASPLYSJ141 - 201

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixVector
1given(-0.351885305428, -0.529239251457, 0.772063822842), (-0.546194125525, -0.553742461742, -0.628523080966), (0.760163606776, -0.642864760881, -0.0942135348643)-72.9889744912, -87.59281854, 4.71076285071
2given(0.623882537037, -0.403077757909, 0.669551268432), (-0.440270687995, 0.526572453164, 0.727243544393), (-0.645702951265, -0.748498345121, 0.151056036224)-73.089592152, 8.62958602084, -27.9325604702
3given(-0.36599728123, -0.52069186296, 0.771314445593), (-0.53928535908, -0.556801901174, -0.631777606703), (0.758430808719, -0.64718747415, -0.0770135162733)-74.6361764796, -86.8438379207, 4.6131273558
4given(-0.207290081392, 0.970945693842, -0.119562877876), (-0.764760799321, -0.0846169620474, 0.638733817451), (0.610058802066, 0.223840187061, 0.76008146187)-89.7414229734, -74.2179444047, 98.392516208
5given(-0.0559123064501, 0.384227819079, -0.921543703268), (-0.793013484804, -0.577881616916, -0.192827512946), (-0.606632860061, 0.720015152532, 0.337008535823)-47.6255223311, -133.576609414, -45.1529175923
6given(0.621432015009, -0.395459503323, 0.676338696183), (-0.450515441749, 0.525895415522, 0.721435962979), (-0.640982127261, -0.753024430656, 0.148647634918)-73.2887628356, 8.0930767113, -27.9367216213
7given(0.0342719250778, 0.619294050937, 0.784410806673), (0.888581170755, -0.378122539429, 0.259705310216), (0.457437359789, 0.688112072013, -0.563252020165)-21.7640477129, 45.0443897421, 55.7898191191
8given(0.49539090703, -0.590133194507, -0.637440712516), (-0.365914381985, 0.523767419054, -0.769268714946), (0.787841680979, 0.614337450819, 0.0435313936413)17.0329837584, -52.0117542184, 66.8426967575
9given(0.496973959309, 0.44345278824, 0.745899797809), (-0.575584563986, -0.474805830383, 0.665779117377), (0.649399178834, -0.760203293887, 0.0192784463392)-19.0678307802, -107.450529778, 55.8149595481
10given(0.515943304761, -0.533887759916, -0.669900265774), (-0.378511834673, 0.559453664805, -0.737387542578), (0.768460342038, 0.634015344253, 0.0865635371647)21.5871544019, -53.870798096, 62.6752200721
11given(0.489825488812, 0.425397779601, 0.76099127434), (-0.582522902079, -0.48973209558, 0.648713760539), (0.64864324483, -0.76105138044, 0.00792068600654)-21.5385702682, -107.597343379, 56.2210287366

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Components

#1: Antibody EY6A Heavy chain


Mass: 24346.273 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody EY6A light chain


Mass: 23315.855 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Spike protein S1


Mass: 22935.734 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#4: Antibody BA.2-10 light chain


Mass: 23441.947 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody BA.2-10 heavy chain


Mass: 24630.637 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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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: 3.64 Å3/Da / Density % sol: 66.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% (v/v) 2-propanol, 0.1 M BICINE, pH 8.5 and 30% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 3.58→57 Å / Num. obs: 61670 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 130.09 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.467 / Rpim(I) all: 0.13 / Net I/σ(I): 4.1
Reflection shellResolution: 3.58→3.65 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 2966 / CC1/2: 0.301 / % possible all: 97.2

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Processing

Software
NameVersionClassification
GDA1.20.1_4487data collection
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NX6

7nx6


Resolution: 3.58→55.79 Å / SU ML: 0.6303 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.3325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3139 2840 5.14 %
Rwork0.2654 52453 -
obs0.268 55293 89.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 173.83 Å2
Refinement stepCycle: LAST / Resolution: 3.58→55.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24330 0 0 0 24330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002224942
X-RAY DIFFRACTIONf_angle_d0.52333930
X-RAY DIFFRACTIONf_chiral_restr0.04263771
X-RAY DIFFRACTIONf_plane_restr0.00444356
X-RAY DIFFRACTIONf_dihedral_angle_d10.34388880
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CX-RAY DIFFRACTIONTorsion NCS0.709455831758
ens_1d_3HX-RAY DIFFRACTIONTorsion NCS0.501651387941
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.487978805974
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS1.0041097187
ens_2d_4KX-RAY DIFFRACTIONTorsion NCS0.962930520231
ens_2d_5NX-RAY DIFFRACTIONTorsion NCS0.317206534726
ens_2d_6FX-RAY DIFFRACTIONTorsion NCS0.966815366342
ens_3d_2JX-RAY DIFFRACTIONTorsion NCS0.34182708602
ens_3d_3MX-RAY DIFFRACTIONTorsion NCS0.345870210144
ens_4d_2XX-RAY DIFFRACTIONTorsion NCS0.0946277387367
ens_4d_3YX-RAY DIFFRACTIONTorsion NCS0.0344548969342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.58-3.650.4535280.5258670X-RAY DIFFRACTION22.89
3.65-3.710.5575350.41351043X-RAY DIFFRACTION35.48
3.71-3.780.5411660.40351423X-RAY DIFFRACTION48.84
3.78-3.860.35981610.38012572X-RAY DIFFRACTION90.2
3.86-3.940.39731610.37082873X-RAY DIFFRACTION99.28
3.94-4.040.38111480.372897X-RAY DIFFRACTION99.51
4.04-4.140.41511330.35382877X-RAY DIFFRACTION99.27
4.14-4.250.38691720.33752879X-RAY DIFFRACTION99.51
4.25-4.370.30921590.29692874X-RAY DIFFRACTION99.57
4.37-4.520.33241980.26862850X-RAY DIFFRACTION99.38
4.52-4.680.29731500.2682903X-RAY DIFFRACTION99.38
4.68-4.860.33431460.26032886X-RAY DIFFRACTION99.21
4.86-5.080.32991400.26012929X-RAY DIFFRACTION99.68
5.09-5.350.30151350.26332943X-RAY DIFFRACTION99.45
5.35-5.690.3452000.25622873X-RAY DIFFRACTION99.74
5.69-6.130.33281280.26312976X-RAY DIFFRACTION99.74
6.13-6.740.33131620.27552911X-RAY DIFFRACTION99.87
6.74-7.710.34941250.2623017X-RAY DIFFRACTION99.84
7.72-9.710.25291690.20782985X-RAY DIFFRACTION100
9.71-55.790.25582240.19863072X-RAY DIFFRACTION99.79
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)
17.62483076353-0.6916318105082.172592685672.767632446720.9981627663310.9907325338860.05762959481850.188150364934-2.345382349771.591470363330.449125645650.9258902388611.13914372396-0.9211974663480.3077830816221.24432756690.03558055634350.1392840331571.347093835450.7592826959460.947061495719-39.2671809592-35.08724549913.9436192666
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944.242247900850.419825361839-2.387575523770.2008018011230.03791652530263.12825555990.645188518787-1.19520509786-1.71841124576-1.067245205440.0457493711210.07681853616210.0345963625506-0.7524421966750.1077222056231.72155172888-0.313120821005-0.1992955563481.163816179590.3739297358281.50549090753-42.8638092703-52.7189573873-41.4045648431
952.273289440584.325663411940.772326695332.06995917943.128513151471.518011279280.41729574651-2.61168084339-1.495679591541.11809692130.780196590626-2.06721882273-0.6175335566480.2739071755072.724583125971.44358129115-0.05124989174110.387143457831.24580242021-0.0466252536548-0.00733777434682-39.9776154731-43.4618662091-39.5608370228
965.94908667827-1.05867501513-1.100020121173.426269482011.386436392340.67253893602-0.4803100911950.6964832402941.343125049280.0455280587248-1.224928680181.242770117450.305691090816-0.2376810618860.8442794688871.166860073580.1077566432830.05287499632492.22458674025-0.06274946960470.939297459728-46.1309311425-45.6707830435-33.8610269995
975.543657026266.04266966981-2.291301505591.994423435075.545210039182.028244373521.472483402880.136708571140.107975640999-0.6621815431620.942739154391-3.17956516038-1.04500987132.54920751413-0.6608542089381.309593185060.1262792119470.103478559870.8955442200270.3765643299941.1696542671-35.7104825265-41.416969553-43.4810264229
985.33690877464-1.897223091670.9239869064941.128385610621.324892571155.92426810627-0.223832525223-1.34550489432-0.899617368728-0.860300107665-1.12650228490.4030267383265.20287199478-2.151892901980.1487237499532.1858975994-0.076331619812-0.2082406231281.959331753420.03413220324830.67056483308-53.6224562517-58.8550448397-48.6541236707
990.941231487668-0.8770298204910.2147806811570.63181241049-0.08515035635950.875963608573-0.2134466641390.436663160386-0.266391269433-1.38036391165-0.559406879194-0.9228042459140.5385594827360.103237689480.6159754676313.12060097323-0.324024273448-0.1786422228261.049696042140.4038457873631.92511930804-54.118864358-56.6477016565-71.6314860879
1008.995813907-0.369517197892-1.936073135080.338808473729-0.8656693358243.143875173351.09925787388-2.21460688137-1.682844153030.403448941222-1.782183531130.3718825794341.38123200151-1.87388060449-0.1931462957852.8405290729-0.6851877283620.2933649358972.32389225441-1.194177365791.99905379276-43.6614932911-63.7008602666-72.2656879151
1011.910271110450.813029239899-0.5940502177050.52165820043-0.426409933770.966524944129-0.535332329420.670686985560.779289619946-0.7910553425180.323351171335-0.403126583681-0.07765748996590.548313727012-1.519696699792.62942471296-0.837304389858-0.281722456378-1.51689334943-1.456313370381.17332601028-52.6961622153-53.8987480571-59.5586814879
1027.067131682730.153506709063-1.454116115492.7459350396-0.1027611908370.3034418508630.370346290653-0.635437009897-1.10373780754-1.387216782530.1821931420880.0856968552554-2.120493670351.559731008040.7404066389823.12890242338-0.92061184647-0.1184223314971.095153081870.3780814224261.24790530564-49.4211204942-62.7776525532-75.0499752564
1037.10498342338-2.60475197754-4.639455795543.90976922472-0.0650473668644.00742096199-1.80171843019-0.253245235544-1.58957511645-0.264662590305-0.0147386222636-0.802706055870.8579539384850.23456453973-1.651617354471.96500882546-0.35219308810.182761469940.710152799761-0.01925146436231.56849397534-42.4690868359-22.7393522662-52.5150231993
1043.65459214492-2.21443638712-1.803263253593.73917597557-2.046161975354.67936491456-1.5722726719-1.096081326890.0296770445231-0.7697114044430.956968022433-1.3877935462-0.0818983509705-0.298099480043-0.4264991022992.02827928001-0.4404759617360.3767828543830.158111098154-0.4776863436921.58042553733-36.8468091661-28.8357225745-49.8647466099
1050.6503999493550.06687955409390.005427245733320.3906908125950.0326458151352.60757608338-1.019991942730.271490379344-1.44109232177-3.616074635270.994711286223-0.03494427092921.249772535790.7736390372790.9958166646353.69812271313-1.12314121659-0.1273738784780.94173552790.5247756074311.67698063909-55.4062157151-46.819913714-76.6254959246
1062.37907247085-1.487046216321.774144700433.684305788933.442960253758.583059059940.8389483198330.2689567970030.0960859257175-1.21729518894-1.397949732141.90602880476-0.393901614054-2.36272454829-0.07331473879992.46345674725-0.261700176364-0.1786253734342.03745272677-0.08678037450581.1885694314-57.4959346764-45.98912346-69.2880496338
1070.0655278743823-0.401681165717-0.7765850050461.352059321322.302503233084.12179348827-0.2591781209440.2558863376330.501138913316-0.907685322224-0.5167407940150.320895620409-2.35433032712-0.492936874176-0.09328738615573.0821219775-0.58639943369-0.3952816283781.43855853150.124325991391.79017383242-64.7672379336-48.8559275278-74.2162177945
1083.8644644687-0.144517397759-0.1199926247790.01821154289250.1781957451343.17921950155-0.707213522732-0.726425906872-0.942856288817-0.2199588298-0.0258679865505-0.1209746498210.068129358693-0.5621309716231.150235655641.062797580710.0728512367049-0.2650330920062.403793017650.2132462528761.55313248271-71.1653039366-40.030740803-19.2323514444
1090.0352606035493-0.1661008537510.383815370980.756007262224-2.41702123837.920989664621.824101606593.09894237756-0.0527624312293-1.5856534851-0.652988542068-2.62798954244-1.840288033442.82681807923-0.7242797325762.274828152290.2991392217160.1503085906262.6320456221-0.128184715832.83753323496-58.57677912-40.6625583888-13.6847683019
1101.940613556751.49517277889-0.3019206365876.51093661081-0.7316121618752.19972506268-0.246114300379-0.885912008249-0.91037628390.0315918781659-0.323417616629-0.08413521859190.376708955977-0.04848448603450.03150267168551.07748899239-0.1269174791050.1001044988581.7432822720.3302735633521.21553775203-68.3979176224-50.1223288431-11.5889810415
1113.48272678539-0.974949641245-0.6111152278750.424012856810.3477845012551.48238318422-0.02207142208040.252307797404-0.7127757209062.204031095691.14946771629-0.8536856344090.9595750421630.273439399764-0.1240300480341.1896991171-0.109391131493-0.04783089618771.801623405670.2764959320271.25888285402-83.615505687-44.4761095599-1.78702367761
1121.04973945861-0.0411594824058-1.43263766557-0.04276863386720.0208313557893.05622977149-0.293410728216-2.05448469766-0.166295391816-0.655242533515-0.3536297271030.424800737433-0.08663031468190.2981404027930.15453414941.34724530627-0.0761901087098-0.02022092596131.668235333850.1363160510041.59027999338-89.5929309028-54.4876989461-9.59728834492
1132.774919066613.16635227504-1.468792199053.29550341904-0.1724023014471.35425168660.84043719601-0.237119004475-0.05486023366830.850223456619-0.0751637150477-0.424962044504-0.437328917230.6132601841960.1560778952961.4787769516-0.1468792535330.04187767650541.764319764330.3101704342091.19860604683-78.0616618125-46.997746982-8.02490705451
1142.276688977670.716249091759-3.783671438664.357938804970.9720241373356.749912305550.9537958250550.1302664130980.02480461715421.33221974287-0.0808065464121-0.996080033834-1.69501173202-0.485574469277-0.1807551547841.363799032550.149331616624-0.03744474154751.740389299490.07015547608411.73965180561-65.2040698226-5.690294887116.59214162751
1153.97626171574-1.25957330336-1.241825236873.788555134713.521995242613.268252442970.9231423109120.836304331957-1.0457694918-0.306344148684-1.59979569733-0.3619653578821.728045405881.896023881170.06701986554191.341925554910.0135959977224-0.0006197806964521.638495577270.173573692351.34676159888-69.6955330198-13.54248843012.64357152803
1162.39167924430.8273054611452.070580366563.100526172931.978466036166.299142990130.5582255813840.334025320952-0.836548848366-0.469565041790.1195758696860.1745381619840.306622741280.731078031486-0.5232341112731.049852536050.2759366377340.1111280258861.342966653320.3577362111161.44671527873-61.751135803-12.8449365496-0.782807411269
1172.50772406522-0.6023810350050.5175864427172.015328079640.329841490667-0.347771774557-0.396839967578-1.378249517820.3284502340690.654365792120.827204775381-0.138475813171-0.624381614749-0.445470564215-0.01350934760881.916853868490.5122132978070.3077504066422.318615231750.2061570291921.51254823099-76.53819774994.957245015213.01663902424
1184.589217189321.40157915731-0.6453107435041.85355034967-0.08579811869169.008012833620.457422566912-0.5870609475760.5430382229751.517534316650.700092221387-0.66008858698-0.3958998071180.0274346728205-1.07458991631.55378974150.242612859970.008831938340741.599116722590.1680445263721.93670187883-79.550815138317.40791975118.75375733769
1190.6657597500470.417626899718-0.2617911924853.17633393744-1.756239497860.9786989813061.509135030291.010751586960.265025933502-1.70838818431-3.035975465970.1036998898563.46937731627-3.11219945823-0.09787093085311.843534155830.292270865372-0.09022857519812.0134891161-0.6806640445461.62300742372-68.131574324110.9999833972-3.74851771641
1200.383907665002-0.2449961681250.7830473176111.8399245217-2.289047283364.960039346790.336130298849-0.3770488122590.754963659762-1.54066742722-0.9741514861811.68635928020.401027172037-0.665024322658-1.006504915881.151380350510.2125763317750.2490771862510.749045424326-0.5362804894382.4731329292-91.249707072322.97471899948.71492442158
1210.0801080976812-0.2758361700080.154814668722.286576250080.5242502062251.495936297430.5965148271521.20678193241-0.892143011686-0.08130446210030.6789995209211.551778278510.220540708449-1.10817185226-1.298411353451.01688552676-0.08336514530050.5302601812753.14834007388-0.2429661003413.20381757563-80.080191127824.409691584112.3804835421
1220.0905848659875-0.0203241416544-0.0328351970702-0.0187778170005-0.00166671777933-0.0112484351812.06252208884-0.739620275050.00507260112344-0.640833034376-1.823971088671.1790170684-0.06721871299630.1068406719030.287416166971.615914206520.441300197589-0.4031749147582.6179726547-0.4903515230112.33247889041-75.894306368327.246968970410.5016084529
1233.77252766968-1.34438058372-3.965792546415.44844128731-1.870910091766.95089905709-0.6828488736530.198290108835-1.259950746610.3144909961630.3874584994090.9161287541741.41810897089-0.4561007156821.05433149331.354842344820.234335459365-0.1843492761082.48719833439-0.05451060963351.1700415449-89.3005095653-14.8371699071-11.9814912516
1240.5274882006781.07988525247-0.6109593225964.043393573081.299555044336.425400727450.3387634500690.490736574528-0.270161901227-0.4590912094890.03663978903980.1132103268340.2707778386460.05126795716410.07067587737861.28287249946-0.0312513218046-0.09646056324072.07189569621-0.08581075316481.60663451778-86.3534423379-16.4697742288-3.95867389564
1250.2440102129151.49050024214-0.6522016838084.07017944471-2.26960681873.6509290726-1.08835141748-0.8783093342112.32440425293-0.5697871643840.6923058077651.7787311747-0.280047359644-0.09783583963370.4074742900811.585977075990.470468575635-0.4018263943422.20503671529-0.1079330625552.50962141508-85.31737957920.4335596935-8.0445396227
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'M' and (resid 1 through 17 )MA1 - 171 - 17
22chain 'M' and (resid 18 through 40 )MA18 - 4018 - 40
33chain 'M' and (resid 41 through 83 )MA41 - 8341 - 83
44chain 'M' and (resid 84 through 119 )MA84 - 11984 - 119
55chain 'M' and (resid 120 through 143 )MA120 - 143120 - 137
66chain 'M' and (resid 144 through 153 )MA144 - 153138 - 147
77chain 'M' and (resid 154 through 183 )MA154 - 183148 - 177
88chain 'M' and (resid 184 through 201 )MA184 - 201178 - 195
99chain 'M' and (resid 202 through 221 )MA202 - 221196 - 215
1010chain 'N' and (resid 1 through 38 )NB1 - 381 - 38
1111chain 'N' and (resid 39 through 61 )NB39 - 6139 - 61
1212chain 'N' and (resid 62 through 90 )NB62 - 9062 - 90
1313chain 'N' and (resid 91 through 114 )NB91 - 11491 - 114
1414chain 'N' and (resid 115 through 151 )NB115 - 151115 - 151
1515chain 'N' and (resid 152 through 212 )NB152 - 212152 - 212
1616chain 'J' and (resid 1 through 83 )JC1 - 831 - 83
1717chain 'J' and (resid 84 through 119 )JC84 - 11984 - 119
1818chain 'J' and (resid 120 through 143 )JC120 - 143120 - 137
1919chain 'J' and (resid 144 through 162 )JC144 - 162138 - 156
2020chain 'J' and (resid 163 through 183 )JC163 - 183157 - 177
2121chain 'J' and (resid 184 through 201 )JC184 - 201178 - 195
2222chain 'J' and (resid 202 through 221 )JC202 - 221196 - 215
2323chain 'K' and (resid 1 through 18 )KD1 - 181 - 18
2424chain 'K' and (resid 19 through 38 )KD19 - 3819 - 38
2525chain 'K' and (resid 39 through 61 )KD39 - 6139 - 61
2626chain 'K' and (resid 62 through 75 )KD62 - 7562 - 75
2727chain 'K' and (resid 76 through 90 )KD76 - 9076 - 90
2828chain 'K' and (resid 91 through 114 )KD91 - 11491 - 114
2929chain 'K' and (resid 115 through 129 )KD115 - 129115 - 129
3030chain 'K' and (resid 130 through 140 )KD130 - 140130 - 140
3131chain 'K' and (resid 141 through 151 )KD141 - 151141 - 151
3232chain 'K' and (resid 152 through 164 )KD152 - 164152 - 164
3333chain 'K' and (resid 165 through 183 )KD165 - 183165 - 183
3434chain 'K' and (resid 184 through 199 )KD184 - 199184 - 199
3535chain 'K' and (resid 200 through 212 )KD200 - 212200 - 212
3636chain 'E' and (resid 1 through 17 )EE1 - 171 - 17
3737chain 'E' and (resid 18 through 40 )EE18 - 4018 - 40
3838chain 'E' and (resid 41 through 60 )EE41 - 6041 - 60
3939chain 'E' and (resid 61 through 73 )EE61 - 7361 - 73
4040chain 'E' and (resid 74 through 83 )EE74 - 8374 - 83
4141chain 'E' and (resid 84 through 119 )EE84 - 11984 - 119
4242chain 'E' and (resid 120 through 153 )EE120 - 153120 - 147
4343chain 'E' and (resid 154 through 165 )EE154 - 165148 - 159
4444chain 'E' and (resid 166 through 183 )EE166 - 183160 - 177
4545chain 'E' and (resid 184 through 201 )EE184 - 201178 - 195
4646chain 'E' and (resid 202 through 221 )EE202 - 221196 - 215
4747chain 'F' and (resid 1 through 38 )FF1 - 381 - 38
4848chain 'F' and (resid 39 through 90 )FF39 - 9039 - 90
4949chain 'F' and (resid 91 through 114 )FF91 - 11491 - 114
5050chain 'F' and (resid 115 through 164 )FF115 - 164115 - 164
5151chain 'F' and (resid 165 through 212 )FF165 - 212165 - 212
5252chain 'R' and (resid 334 through 364 )RG334 - 3641 - 31
5353chain 'R' and (resid 365 through 375 )RG365 - 37532 - 42
5454chain 'R' and (resid 376 through 459 )RG376 - 45943 - 126
5555chain 'R' and (resid 460 through 479 )RG460 - 479127 - 146
5656chain 'R' and (resid 480 through 527 )RG480 - 527147 - 194
5757chain 'L' and (resid 1 through 7 )LH1 - 71 - 7
5858chain 'L' and (resid 8 through 18 )LH8 - 188 - 18
5959chain 'L' and (resid 19 through 32 )LH19 - 3219 - 32
6060chain 'L' and (resid 33 through 48 )LH33 - 4833 - 48
6161chain 'L' and (resid 49 through 61 )LH49 - 6149 - 61
6262chain 'L' and (resid 62 through 75 )LH62 - 7562 - 75
6363chain 'L' and (resid 76 through 90 )LH76 - 9076 - 90
6464chain 'L' and (resid 91 through 107 )LH91 - 10791 - 107
6565chain 'L' and (resid 108 through 113 )LH108 - 113108 - 113
6666chain 'L' and (resid 114 through 128 )LH114 - 128114 - 128
6767chain 'L' and (resid 129 through 137 )LH129 - 137129 - 137
6868chain 'L' and (resid 138 through 150 )LH138 - 150138 - 150
6969chain 'L' and (resid 151 through 155 )LH151 - 155151 - 155
7070chain 'L' and (resid 156 through 163 )LH156 - 163156 - 163
7171chain 'L' and (resid 164 through 174 )LH164 - 174164 - 174
7272chain 'L' and (resid 175 through 204 )LH175 - 204175 - 204
7373chain 'L' and (resid 205 through 213 )LH205 - 213205 - 213
7474chain 'H' and (resid 2 through 25 )HI2 - 251 - 24
7575chain 'H' and (resid 26 through 33 )HI26 - 3325 - 32
7676chain 'H' and (resid 34 through 44 )HI34 - 4433 - 43
7777chain 'H' and (resid 45 through 83 )HI45 - 8344 - 82
7878chain 'H' and (resid 84 through 99 )HI84 - 9983 - 98
7979chain 'H' and (resid 100 through 111 )HI100 - 11199 - 110
8080chain 'H' and (resid 112 through 125 )HI112 - 125111 - 124
8181chain 'H' and (resid 126 through 136 )HI126 - 136125 - 135
8282chain 'H' and (resid 137 through 146 )HI137 - 146136 - 141
8383chain 'H' and (resid 147 through 162 )HI147 - 162142 - 157
8484chain 'H' and (resid 163 through 169 )HI163 - 169158 - 164
8585chain 'H' and (resid 170 through 187 )HI170 - 187165 - 182
8686chain 'H' and (resid 188 through 215 )HI188 - 215183 - 210
8787chain 'H' and (resid 216 through 228 )HI216 - 228211 - 223
8888chain 'Y' and (resid 334 through 364 )YJ334 - 3641 - 31
8989chain 'Y' and (resid 365 through 375 )YJ365 - 37532 - 42
9090chain 'Y' and (resid 376 through 442 )YJ376 - 44243 - 109
9191chain 'Y' and (resid 443 through 459 )YJ443 - 459110 - 126
9292chain 'Y' and (resid 460 through 479 )YJ460 - 479127 - 146
9393chain 'Y' and (resid 480 through 527 )YJ480 - 527147 - 194
9494chain 'D' and (resid 1 through 18 )DK1 - 181 - 18
9595chain 'D' and (resid 19 through 48 )DK19 - 4819 - 48
9696chain 'D' and (resid 49 through 83 )DK49 - 8349 - 83
9797chain 'D' and (resid 84 through 101 )DK84 - 10184 - 101
9898chain 'D' and (resid 102 through 113 )DK102 - 113102 - 113
9999chain 'D' and (resid 114 through 143 )DK114 - 143114 - 143
100100chain 'D' and (resid 144 through 155 )DK144 - 155144 - 155
101101chain 'D' and (resid 156 through 174 )DK156 - 174156 - 174
102102chain 'D' and (resid 175 through 213 )DK175 - 213175 - 213
103103chain 'C' and (resid 2 through 33 )CL2 - 331 - 32
104104chain 'C' and (resid 34 through 123 )CL34 - 12333 - 122
105105chain 'C' and (resid 124 through 146 )CL124 - 146123 - 141
106106chain 'C' and (resid 147 through 187 )CL147 - 187142 - 182
107107chain 'C' and (resid 188 through 228 )CL188 - 228183 - 223
108108chain 'X' and (resid 334 through 364 )XM334 - 3641 - 31
109109chain 'X' and (resid 365 through 375 )XM365 - 37532 - 42
110110chain 'X' and (resid 376 through 442 )XM376 - 44243 - 109
111111chain 'X' and (resid 443 through 459 )XM443 - 459110 - 126
112112chain 'X' and (resid 460 through 479 )XM460 - 479127 - 146
113113chain 'X' and (resid 480 through 527 )XM480 - 527147 - 194
114114chain 'B' and (resid 1 through 18 )BN1 - 181 - 18
115115chain 'B' and (resid 19 through 48 )BN19 - 4819 - 48
116116chain 'B' and (resid 49 through 83 )BN49 - 8349 - 83
117117chain 'B' and (resid 84 through 128 )BN84 - 12884 - 128
118118chain 'B' and (resid 129 through 163 )BN129 - 163129 - 163
119119chain 'B' and (resid 164 through 174 )BN164 - 174164 - 174
120120chain 'B' and (resid 175 through 188 )BN175 - 188175 - 188
121121chain 'B' and (resid 189 through 198 )BN189 - 198189 - 198
122122chain 'B' and (resid 199 through 213 )BN199 - 213199 - 213
123123chain 'A' and (resid 2 through 33 )AO2 - 331 - 32
124124chain 'A' and (resid 34 through 123 )AO34 - 12333 - 122
125125chain 'A' and (resid 124 through 228 )AO124 - 228123 - 223

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