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- PDB-7bel: Crystal structure of the receptor binding domain of SARS-CoV-2 Sp... -

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Basic information

Entry
Database: PDB / ID: 7bel
TitleCrystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-88 and COVOX-45 Fabs
Components
  • COVOX-45 heavy chain
  • COVOX-45 light chain
  • COVOX-88 heavy chain
  • COVOX-88 light chain
  • Spike glycoproteinSpike protein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / antibody / germline / V-gene / receptor-binding-domain / spike / neutralisation / protection / glycosylation / valency / VIRAL PROTEIN / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / 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 / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
ACETATE ION / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsZhou, D. / Zhao, Y. / Ren, J. / Stuart, D.
Funding support United Kingdom, China, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 China
CitationJournal: Cell / Year: 2021
Title: The antigenic anatomy of SARS-CoV-2 receptor binding domain.
Authors: Wanwisa Dejnirattisai / Daming Zhou / Helen M Ginn / Helen M E Duyvesteyn / Piyada Supasa / James Brett Case / Yuguang Zhao / Thomas S Walter / Alexander J Mentzer / Chang Liu / Beibei Wang ...Authors: Wanwisa Dejnirattisai / Daming Zhou / Helen M Ginn / Helen M E Duyvesteyn / Piyada Supasa / James Brett Case / Yuguang Zhao / Thomas S Walter / Alexander J Mentzer / Chang Liu / Beibei Wang / Guido C Paesen / Jose Slon-Campos / César López-Camacho / Natasha M Kafai / Adam L Bailey / Rita E Chen / Baoling Ying / Craig Thompson / Jai Bolton / Alex Fyfe / Sunetra Gupta / Tiong Kit Tan / Javier Gilbert-Jaramillo / William James / Michael Knight / Miles W Carroll / Donal Skelly / Christina Dold / Yanchun Peng / Robert Levin / Tao Dong / Andrew J Pollard / Julian C Knight / Paul Klenerman / Nigel Temperton / David R Hall / Mark A Williams / Neil G Paterson / Felicity K R Bertram / C Alistair Siebert / Daniel K Clare / Andrew Howe / Julika Radecke / Yun Song / Alain R Townsend / Kuan-Ying A Huang / Elizabeth E Fry / Juthathip Mongkolsapaya / Michael S Diamond / Jingshan Ren / David I Stuart / Gavin R Screaton /
Abstract: Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and ...Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and focus mainly on 80 that bind the receptor binding domain (RBD). We devise a competition data-driven method to map RBD binding sites. We find that although antibody binding sites are widely dispersed, neutralizing antibody binding is focused, with nearly all highly inhibitory mAbs (IC < 0.1 μg/mL) blocking receptor interaction, except for one that binds a unique epitope in the N-terminal domain. Many of these neutralizing mAbs use public V-genes and are close to germline. We dissect the structural basis of recognition for this large panel of antibodies through X-ray crystallography and cryoelectron microscopy of 19 Fab-antigen structures. We find novel binding modes for some potently inhibitory antibodies and demonstrate that strongly neutralizing mAbs protect, prophylactically or therapeutically, in animal models.
History
DepositionDec 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entity_branch_descriptor / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: Spike glycoprotein
A: COVOX-45 heavy chain
H: COVOX-88 heavy chain
L: COVOX-88 light chain
B: COVOX-45 light chain
X: Spike glycoprotein
C: COVOX-45 heavy chain
E: COVOX-88 heavy chain
F: COVOX-88 light chain
D: COVOX-45 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,14018
Polymers244,28310
Non-polymers2,8588
Water2,648147
1
R: Spike glycoprotein
A: COVOX-45 heavy chain
H: COVOX-88 heavy chain
L: COVOX-88 light chain
B: COVOX-45 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,5879
Polymers122,1415
Non-polymers1,4454
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: Spike glycoprotein
C: COVOX-45 heavy chain
E: COVOX-88 heavy chain
F: COVOX-88 light chain
D: COVOX-45 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,5549
Polymers122,1415
Non-polymers1,4124
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.081, 140.721, 130.976
Angle α, β, γ (deg.)90.000, 124.557, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 186 or resid 188 through 222))
d_2ens_1(chain "C" and (resid 1 through 186 or resid 188 through 222))
d_1ens_2(chain "B" and (resid 1 through 162 or resid 164 through 193 or resid 195 through 213))
d_2ens_2(chain "D" and (resid 1 through 162 or resid 164 through 193 or resid 195 through 213))
d_1ens_3(chain "E" and (resid 1 through 12 or resid 14 through 128 or resid 301 through 306))
d_2ens_3(chain "H" and (resid 1 through 12 or resid 14 through 128 or resid 301 through 306))
d_1ens_4(chain "F" and ((resid 1 and (name N or name...
d_2ens_4(chain "L" and (resid 1 through 17 or resid 19 through 113))
d_1ens_5(chain "R" and (resid 334 through 518 or resid 520 through 527 or resid 601 or resid 801))
d_2ens_5(chain "X" and (resid 334 through 518 or resid 520 through 527 or resid 601 or resid 801))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNLEUE1 - 180
d_12ens_1SERLYSE182 - 216
d_21ens_1GLNLEUS1 - 180
d_22ens_1SERLYSS184 - 218
d_11ens_2ASPSERN1 - 162
d_12ens_2THRALAN166 - 195
d_13ens_2GLUGLUN199 - 217
d_21ens_2ASPSERD1 - 162
d_22ens_2THRALAD166 - 195
d_23ens_2GLUGLUD199 - 217
d_11ens_3GLNVALT1 - 12
d_12ens_3PROALAT14 - 128
d_13ens_3NAGNAGU
d_14ens_3NAGNAGV
d_15ens_3BMABMAW
d_16ens_3MANMANX
d_17ens_3MANMANY
d_18ens_3MANMANZ
d_21ens_3GLNVALF1 - 12
d_22ens_3PROALAF14 - 128
d_23ens_3NAGNAGG
d_24ens_3NAGNAGH
d_25ens_3BMABMAI
d_26ens_3MANMANJ
d_27ens_3MANMANK
d_28ens_3MANMANL
d_11ens_4GLNARGF1 - 17
d_12ens_4THRPROF21 - 115
d_21ens_4GLNARGM1 - 17
d_22ens_4THRPROM21 - 115
d_11ens_5ASNLEUA1 - 185
d_12ens_5ALALYSA187 - 194
d_13ens_5ACTACTB
d_14ens_5NAGNAGD
d_21ens_5ASNLEUO1 - 185
d_22ens_5ALALYSO187 - 194
d_23ens_5ACTACTP
d_24ens_5NAGNAGR

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixVector
1given(-0.996076238276, -0.00951927198744, -0.0879858568298), (-0.0132769476985, 0.999020047063, 0.0422216558924), (0.0874977154048, 0.0432241717944, -0.995226517317)57.386410461, -2.8014614431, 56.0882599852
2given(-0.99610746492, 0.0100886585893, -0.0875679010759), (0.00839047557038, 0.999769955022, 0.0197392237668), (0.0877468988094, 0.0189276518111, -0.995962964043)58.6676791971, -1.5125427417, 54.4639805034
3given(-0.997124841664, -0.00477438609052, 0.0756257586654), (-0.00583343304566, 0.999887909804, -0.0137890857793), (-0.07555144734, -0.0141905977741, -0.997040924807)52.4202729781, 0.414484597472, 57.2354202588
4given(-0.997381365219, -0.0154644246449, 0.0706488774418), (-0.0168375491583, 0.999679934787, -0.0188818675428), (-0.070334267976, -0.0200219767746, -0.997322521151)52.3469405289, 0.728597384498, 57.0920116829
5given(-0.993479769703, -0.0298061763228, -0.110043350747), (-0.0263842843438, 0.999125946228, -0.0324224168389), (0.110913555214, -0.0293076001581, -0.993397829594)57.8433567277, 2.19624840138, 52.1094034521

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Components

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Protein , 1 types, 2 molecules RX

#1: Protein Spike glycoprotein / Spike protein / S glycoprotein / E2 / Peplomer protein


Mass: 23150.891 Da / Num. of mol.: 2
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

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Antibody , 4 types, 8 molecules ACHELFBD

#2: Antibody COVOX-45 heavy chain


Mass: 24187.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody COVOX-88 heavy chain


Mass: 25853.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody COVOX-88 light chain


Mass: 24278.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody COVOX-45 light chain


Mass: 24671.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 2 types, 4 molecules

#6: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#9: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 151 molecules

#7: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.8 Å3/Da / Density % sol: 56.03 % / Description: presence of translational NCS
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.15 M (NH4)2SO4, 0.1 M Tris pH 8.0 and 15% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.53→58.9 Å / Num. obs: 88040 / % possible obs: 97.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 55.7 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.189 / Net I/σ(I): 5.6
Reflection shellResolution: 2.53→2.57 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 3392 / CC1/2: 0.326

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Processing

Software
NameVersionClassification
GDA1.18.1_3865data collection
PHENIX1.18.1_3865refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BEK

7bek


Resolution: 2.53→49.41 Å / SU ML: 0.5174 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.0924
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2856 4193 4.91 %
Rwork0.2494 81143 -
obs0.2512 85336 94.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.91 Å2
Refinement stepCycle: LAST / Resolution: 2.53→49.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13206 0 190 147 13543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002913740
X-RAY DIFFRACTIONf_angle_d0.611918710
X-RAY DIFFRACTIONf_chiral_restr0.04452113
X-RAY DIFFRACTIONf_plane_restr0.00412387
X-RAY DIFFRACTIONf_dihedral_angle_d16.76294932
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CX-RAY DIFFRACTIONTorsion NCS0.549314383232
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.439374797024
ens_3d_2HX-RAY DIFFRACTIONTorsion NCS0.566106583483
ens_4d_2LX-RAY DIFFRACTIONTorsion NCS0.470736578244
ens_5d_2XX-RAY DIFFRACTIONTorsion NCS0.504513472543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.550.4851560.42681398X-RAY DIFFRACTION48.45
2.55-2.580.4554810.42621711X-RAY DIFFRACTION60.03
2.58-2.620.43071050.40971834X-RAY DIFFRACTION65.13
2.62-2.650.44281270.40282365X-RAY DIFFRACTION81.89
2.65-2.680.47291380.39352637X-RAY DIFFRACTION95.36
2.68-2.720.39351590.40072830X-RAY DIFFRACTION98.32
2.72-2.760.40381300.37292833X-RAY DIFFRACTION99.16
2.76-2.80.40071370.37242824X-RAY DIFFRACTION100
2.8-2.850.40761570.35072834X-RAY DIFFRACTION100
2.85-2.890.39461320.32842836X-RAY DIFFRACTION100
2.89-2.940.36871290.31262891X-RAY DIFFRACTION99.97
2.94-2.990.36491320.3092841X-RAY DIFFRACTION99.9
3-3.050.3061350.32847X-RAY DIFFRACTION99.93
3.05-3.110.34021700.29212824X-RAY DIFFRACTION99.93
3.11-3.180.35791330.28012860X-RAY DIFFRACTION99.9
3.18-3.260.29621490.27042866X-RAY DIFFRACTION99.9
3.26-3.340.31421520.2612829X-RAY DIFFRACTION99.93
3.34-3.430.27951470.2632854X-RAY DIFFRACTION99.97
3.43-3.530.30821440.25052846X-RAY DIFFRACTION99.97
3.53-3.640.29131600.24022812X-RAY DIFFRACTION99.97
3.64-3.770.26921390.22212864X-RAY DIFFRACTION99.97
3.77-3.920.25371540.22442874X-RAY DIFFRACTION99.97
3.92-4.10.24361560.212836X-RAY DIFFRACTION99.9
4.1-4.320.23121470.1972836X-RAY DIFFRACTION99.97
4.32-4.590.2051620.18442861X-RAY DIFFRACTION99.97
4.59-4.940.22281410.18822848X-RAY DIFFRACTION99.83
4.94-5.440.23721490.20092885X-RAY DIFFRACTION99.87
5.44-6.230.26391460.22532855X-RAY DIFFRACTION99.9
6.23-7.840.25431630.23722861X-RAY DIFFRACTION99.9
7.84-49.410.28741630.23562851X-RAY DIFFRACTION97.67
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)
12.067382979791.402805432570.3142760306291.51709134110.06308056487572.748230431140.2131700897060.0913802826958-0.866608959628-0.591652758897-0.2741073118150.6536638679610.21132047461-0.750299185408-0.1961707167351.13269352522-0.0147456627177-0.6680426184650.765626682789-0.1827918976191.3926941723117.1919158425-88.5713438738-25.8808632467
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36.16261006-0.752616770765-0.5527783612552.890896394641.750724394054.457491765960.1030593780830.7167358125271.08250704888-0.5534299884010.202866219183-0.122782664538-0.8870865186370.3522050410520.01507244825690.958680478497-0.121821642016-0.08235493420950.5665096940710.1063413145580.46389476846635.609416216915.870709252-10.5598962278
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505.533390679880.7093872277491.412730969564.313977157310.05127248267927.638702836870.637372695387-0.0429619064247-0.6289701702780.0797394122443-0.0666681174351-0.009234563305280.1968042500740.297703463301-0.6327068119350.4698846964660.0207634698729-0.1808223011730.465273702552-0.03690943665460.74121682179230.3720293311-6.5056463444151.837891602
513.31291321150.0569196108036-0.4282570866812.37349379973-0.8751194907178.40215727960.1038047447850.215450213836-0.629427270578-1.22558106122-0.285126794575-0.5300345304840.9646903449240.891894445450.2130883328080.6743749326160.0779590966633-0.05643958049050.614536967713-0.01734932946030.75637399944135.0851427416-2.2502989084142.015778738
520.637051399535-0.189478333410.1168976684421.172003084361.398683657685.040689848720.239043387982-0.459584189278-0.8934701404350.1123636557460.2208153388280.1737660087360.09038777827060.394580858717-0.538418837160.419764605454-0.00778374488864-0.2003397933420.6545189332260.1275727460040.88630309147231.8073790424-2.0113227377561.9674388385
533.805099943852.7423230207-3.378092101722.19297339369-3.555570363729.33224240390.5673402209980.1150072526450.1681029387870.2534219043880.9049231549470.501196567163-0.73896339312-0.382037244932-1.453423194970.6357828084450.174665700902-0.03835610766630.606155332085-0.2661948436591.1379763091938.72662368255.731869054841.8754631319
540.4092116058810.1603301674770.4960511496092.81045619483-0.2069478713870.599321543187-0.1205534598970.173130262520.233606233674-0.0733761548099-0.0868305953830.0653672713844-0.289684820817-0.498917755142-1.314443281550.141054559052-0.04568554810780.5635026932060.738810281605-0.00799993053235-0.55946950277416.3731870058-62.351668612352.4815072554
551.225415939930.644254337181-0.5450697707993.77116810981-0.3867566468381.00040633294-0.112203410832-0.4171458838040.289098899201-0.0767888218357-0.0219093256868-0.318627902440.137956737682-0.0748284595760.1106862383250.456736326057-0.0150713564351-0.1888888514090.5308581335370.03877164304380.76493982005126.3210067497-56.820400498752.1913122733
560.40608140080.847924837609-0.227288166542.09997079867-0.4034151952911.50869013274-0.1573502089360.09918296601370.175529523917-0.4810059258790.1268933628010.3920626906430.0552549110397-0.403042455839-0.06231261583580.37922706851-0.0460929774393-0.1451336067440.4583612539210.01985428475650.58621251001422.8428842508-57.956176703152.8386023039
570.7685461299620.5042995282980.08539507952371.8667692942-0.4523017314270.3950389010090.2038834519560.09410730711880.1301472722520.325997451674-0.4869773446360.209071988775-0.00561521865310.125438501033-0.3214353832310.517114119357-0.236453270730.5037214707850.5696937610890.002586748143410.047246016069916.7575497882-79.927149972554.3423440285
583.666084811-0.1623019622391.02661719672.547096088151.939510176977.453925483010.393651972962-0.995689366837-0.7875289180910.7611784941-0.31721386208-0.04579157316010.650250942960.544194959349-0.1390822943391.14941556824-0.360822833024-0.2756664682110.799891217550.1125159263370.66409085666220.4670395169-90.419168171982.331058195
593.55012046226-0.1299311200610.488127745833.892760622-1.272929248588.317703451180.134713220044-0.3342612371250.1409803419480.455307852523-0.05769703685110.2562513967350.432403319757-0.707804738095-0.140413488260.468357297249-0.0976397066179-0.1002305438090.42640024971-0.06232579270860.41128027712113.1098506548-84.272580772370.2413438065
607.626848960584.15015207912-2.23281950066.3207584974-3.456398042997.96098189160.0285210361805-0.0589337269993-0.3911416073670.4541923718030.4378158861140.0859063211870.184052196868-0.742057089388-0.549314639410.58590941955-0.0693360142822-0.07638369394660.7006448154860.0739319777940.5922747864498.73347049308-81.828848299577.855245155
612.940002235080.7878107573241.24526172482.7277565403-0.5011954745519.16893683560.325641237023-0.677563177616-0.575214265720.611808797675-0.286953509915-0.09815195930270.174640601425-0.654103555445-0.03246960807430.583195885204-0.12666903051-0.1146708454570.637166430746-0.05426477503010.41158108634914.6665474417-85.412338055874.1226795645
624.075615432511.578490874620.4482858743953.598163862070.2628321776768.890099262020.541766859983-0.903830643945-0.4859525024680.8864077123910.0441475608577-0.3559524318051.81842660879-1.37279348323-0.3346321188510.651815157328-0.276321126886-0.07847863438680.58528980756-0.04877092776650.6596435747929.48558372873-93.834618268972.0317777519
636.158969809582.8569673445-1.827011802695.57788509052-0.3496103748223.917739518140.535829158349-0.0861654582703-1.085025949950.664985165007-0.259700686949-0.4096372778850.01211176063810.105752726062-0.447189471250.4159467727890.139770714108-0.2026225640220.4918550433490.007806529335450.66466855860222.827674284-40.738460910913.4723732741
643.541494361061.480116588531.326510788422.48473314834-0.9536619140361.73930338888-0.00109044248378-0.451525707263-0.07775530124980.336357319002-0.0818471370254-0.180553159339-0.107212289747-0.05524831422350.0770404395840.4977988620110.0814270222522-0.04613811660170.4871404722-0.02383774944250.5593725374712.4923525932-34.828744017513.1300106236
650.939558602681.07809901228-1.365176205212.49148123165-0.3810810500072.94394553488-0.007282473529450.116489065693-0.254292311608-0.03943430313660.0614088303332-0.104803009391-0.1103401310630.36163894841-0.02870461983170.3788821423990.0403613054594-0.16620418750.401911356259-0.001059768929810.59372591055826.0068524493-26.92838535492.15849559579
661.56895141627-0.715784261693-1.901329894462.226492788380.1115503371084.287671937560.429314168912-0.4381249815970.1185124471230.0165296797361-0.03694974902530.421362825344-0.4699527777320.271309077102-0.3754171120410.312524099690.0295469888755-0.03490370580360.484812575641-0.0219834778210.49064370747725.0959202399-25.156328314810.842466009
676.10560924731.05545405405-3.133264707233.95523054504-4.88989787186.619120141370.01419032469290.514066075802-0.093300585542-1.191796653920.1061699189721.176007713291.96676993146-1.63728005253-0.3171754685390.756220946777-0.118001248118-0.2297656702750.841405061052-0.1863187542161.113687129256.72056835975-51.73340361798.86831529166
683.98161005552-2.383541264781.85827847486.317643138442.850823530064.17304275218-0.1149547728480.253317080372-1.01938117361-0.422384599102-0.6737440863380.3844767057650.9203276685010.07677372956230.519796989480.4363775377190.00686453670779-0.1957976367590.5190254511490.143295488550.66566964160216.3237409997-56.7342394966-20.8237530567
695.81184576065-3.07388933942-1.798821449564.83132577353.495957850325.204054212470.6244734360320.422034090369-1.01737994071-0.498298303727-0.4558310287390.8493147487160.39867946051-0.301456864852-0.05125829423010.5360522093150.0720996794051-0.2043890361170.3981059657760.02157869694550.69644719542514.6643782492-50.2473109576-12.1894701304
701.44038887078-1.3263575496-0.1935158933053.948616406731.308714573944.03380916698-0.1096682821480.2205965199860.531301683543-0.3220753651690.1469390096010.376965537225-0.27478483094-0.223200582851-0.0653336608550.451772779131-0.0385856847691-0.1594877441290.4242861109870.06130080427880.49039242021220.0652597212-45.9211421798-15.9607535843
710.300473100628-0.8655262332320.06742210476213.137269677731.368032994784.51104212453-0.0549372634029-0.18820578651-0.102166691709-0.1698485666540.110130991922-0.0224648434540.1568012679650.249770833029-0.0926865398470.417189211234-0.0232445967313-0.2184582850750.405500090815-0.09065198834920.65068548050421.9760784377-49.6361950772-12.3115320864
722.64468219843-2.043898654020.2166523656446.809339915981.847496242030.779227857550.4166801391850.495592644951-0.626938896653-0.521967647158-0.4025853815320.7780108049640.190842133068-0.05754712316560.00978233846280.5918357820730.0487214702164-0.2820965569940.579739937714-0.06261185746560.74745562304723.0944691412-75.1542899821-21.9894351763
733.447026439780.699254692665-0.7685296969092.468843716540.3087846790076.195360406330.3874238456920.188432948027-0.8637942802860.379205802394-0.522958919212-0.0100307201758-0.865055446711-0.796188200291-0.1152398645520.6965862168670.182422604629-0.3215002119830.532024739174-0.1563280453290.83892576135922.7913497123-78.7618072682-19.2566720402
743.17298514480.00795535593086-0.3893726234431.137472590061.912122763785.881001962450.518728209215-0.0280837482292-1.661691453140.0828007040835-0.393377699598-0.32579662491.20694722869-0.6067365662840.09315919682311.09834094139-0.0852194013597-0.5468450950890.626478596723-0.003134599778311.1073875741224.5111953749-89.4483407226-16.860891933
752.59757941175-1.30415035505-0.6211843873646.11400787745-0.5062690190184.524764548450.634811882231-0.133949687696-1.13325402629-1.12076329214-0.382399144432.054119497690.681730193551-1.07694401349-0.328016199160.739272085118-0.0673266020656-0.4765274427070.9600645191610.01118104507451.2885648416815.4824778573-84.8008395586-21.4952126989
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 212 through 222 )CS212 - 222208 - 218
22chain 'E' and (resid 1 through 8 )ET1 - 81 - 8
33chain 'E' and (resid 9 through 25 )ET9 - 259 - 25
44chain 'E' and (resid 26 through 41 )ET26 - 4126 - 41
55chain 'E' and (resid 42 through 74 )ET42 - 7442 - 74
66chain 'E' and (resid 75 through 84 )ET75 - 8475 - 84
77chain 'E' and (resid 85 through 101 )ET85 - 10185 - 101
88chain 'E' and (resid 102 through 111 )ET102 - 111102 - 111
99chain 'E' and (resid 112 through 128 )ET112 - 128112 - 128
1010chain 'F' and (resid 1 through 8 )FAA - F1 - 81 - 8
1111chain 'F' and (resid 9 through 16 )FF9 - 169 - 16
1212chain 'F' and (resid 17 through 39 )FF17 - 3917 - 41
1313chain 'F' and (resid 40 through 70 )FF40 - 7042 - 72
1414chain 'F' and (resid 71 through 85 )FF71 - 8573 - 87
1515chain 'F' and (resid 86 through 101 )FF86 - 10188 - 103
1616chain 'F' and (resid 102 through 113 )FF102 - 113104 - 115
1717chain 'D' and (resid 1 through 18 )DD1 - 181 - 18
1818chain 'D' and (resid 19 through 38 )DD19 - 3819 - 38
1919chain 'D' and (resid 39 through 75 )DD39 - 7539 - 75
2020chain 'D' and (resid 76 through 90 )DD76 - 9076 - 90
2121chain 'D' and (resid 91 through 102 )DD91 - 10291 - 102
2222chain 'D' and (resid 103 through 113 )DD103 - 113103 - 113
2323chain 'D' and (resid 114 through 150 )DD114 - 150114 - 150
2424chain 'D' and (resid 151 through 163 )DD151 - 163151 - 165
2525chain 'D' and (resid 164 through 213 )DD164 - 213166 - 217
2626chain 'R' and (resid 334 through 358 )RA334 - 3581 - 25
2727chain 'R' and (resid 359 through 380 )RA359 - 38026 - 47
2828chain 'R' and (resid 381 through 393 )RA381 - 39348 - 60
2929chain 'R' and (resid 394 through 451 )RA394 - 45161 - 118
3030chain 'R' and (resid 452 through 494 )RA452 - 494119 - 161
3131chain 'R' and (resid 495 through 516 )RA495 - 516162 - 183
3232chain 'R' and (resid 517 through 527 )RA517 - 527184 - 194
3333chain 'A' and (resid 1 through 17 )AE1 - 171 - 17
3434chain 'A' and (resid 18 through 83 )AE18 - 8318 - 83
3535chain 'A' and (resid 84 through 98 )AE84 - 9884 - 98
3636chain 'A' and (resid 99 through 153 )AE99 - 15399 - 147
3737chain 'A' and (resid 154 through 183 )AE154 - 183148 - 177
3838chain 'A' and (resid 184 through 211 )AE184 - 211178 - 205
3939chain 'A' and (resid 212 through 222 )AE212 - 222206 - 216
4040chain 'H' and (resid 1 through 8 )HF1 - 81 - 8
4141chain 'H' and (resid 9 through 33 )HF9 - 339 - 33
4242chain 'H' and (resid 34 through 62 )HF34 - 6234 - 62
4343chain 'H' and (resid 63 through 74 )HF63 - 7463 - 74
4444chain 'H' and (resid 75 through 84 )HF75 - 8475 - 84
4545chain 'H' and (resid 85 through 101 )HF85 - 10185 - 101
4646chain 'H' and (resid 102 through 111 )HF102 - 111102 - 111
4747chain 'H' and (resid 112 through 128 )HF112 - 128112 - 128
4848chain 'L' and (resid 1 through 8 )LM1 - 81 - 8
4949chain 'L' and (resid 9 through 23 )LM9 - 239 - 25
5050chain 'L' and (resid 24 through 70 )LM24 - 7026 - 72
5151chain 'L' and (resid 71 through 85 )LM71 - 8573 - 87
5252chain 'L' and (resid 86 through 101 )LM86 - 10188 - 103
5353chain 'L' and (resid 102 through 113 )LM102 - 113104 - 115
5454chain 'B' and (resid 1 through 18 )BN1 - 181 - 18
5555chain 'B' and (resid 19 through 61 )BN19 - 6119 - 61
5656chain 'B' and (resid 62 through 102 )BN62 - 10262 - 102
5757chain 'B' and (resid 103 through 113 )BN103 - 113103 - 113
5858chain 'B' and (resid 114 through 128 )BN114 - 128114 - 128
5959chain 'B' and (resid 129 through 150 )BN129 - 150129 - 150
6060chain 'B' and (resid 151 through 163 )BN151 - 163151 - 165
6161chain 'B' and (resid 164 through 198 )BN164 - 198166 - 202
6262chain 'B' and (resid 199 through 213 )BN199 - 213203 - 217
6363chain 'X' and (resid 334 through 358 )XO334 - 3581 - 25
6464chain 'X' and (resid 359 through 421 )XO359 - 42126 - 88
6565chain 'X' and (resid 422 through 487 )XO422 - 48789 - 154
6666chain 'X' and (resid 488 through 516 )XO488 - 516155 - 183
6767chain 'X' and (resid 517 through 527 )XO517 - 527184 - 194
6868chain 'C' and (resid 1 through 17 )CS1 - 171 - 17
6969chain 'C' and (resid 18 through 40 )CS18 - 4018 - 40
7070chain 'C' and (resid 41 through 83 )CS41 - 8341 - 83
7171chain 'C' and (resid 84 through 108 )CS84 - 10884 - 108
7272chain 'C' and (resid 109 through 153 )CS109 - 153109 - 147
7373chain 'C' and (resid 154 through 183 )CS154 - 183148 - 177
7474chain 'C' and (resid 184 through 198 )CS184 - 198178 - 194
7575chain 'C' and (resid 199 through 211 )CS199 - 211195 - 207

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