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- PDB-2xwt: CRYSTAL STRUCTURE OF THE TSH RECEPTOR IN COMPLEX WITH A BLOCKING ... -

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Basic information

Entry
Database: PDB / ID: 2xwt
TitleCRYSTAL STRUCTURE OF THE TSH RECEPTOR IN COMPLEX WITH A BLOCKING TYPE TSHR AUTOANTIBODY
Components
  • (THYROID BLOCKING HUMAN AUTOANTIBODY K1-70 ...) x 2
  • THYROTROPIN RECEPTOR
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / SIGNALING PROTEIN-IMMUNE SYSTEM COMPLEX / GPCR / GRAVES' DISEASE / AUTOIMMUNITY / RECEPTOR-AUTOANTIBODY COMPLEX
Function / homology
Function and homology information


thyroid-stimulating hormone signaling pathway / cellular response to glycoprotein / cellular response to thyrotropin-releasing hormone / thyroid-stimulating hormone receptor activity / Hormone ligand-binding receptors / G protein-coupled peptide receptor activity / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / hormone-mediated signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell-cell signaling ...thyroid-stimulating hormone signaling pathway / cellular response to glycoprotein / cellular response to thyrotropin-releasing hormone / thyroid-stimulating hormone receptor activity / Hormone ligand-binding receptors / G protein-coupled peptide receptor activity / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / hormone-mediated signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell-cell signaling / signaling receptor activity / positive regulation of cold-induced thermogenesis / G alpha (s) signalling events / basolateral plasma membrane / cell surface receptor signaling pathway / receptor complex / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / protein-containing complex binding / cell surface / plasma membrane
Similarity search - Function
Thyrotropin receptor / Glycoprotein hormone receptor family / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Thyrotropin receptor / Glycoprotein hormone receptor family / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Thyrotropin receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSanders, J. / Sanders, P. / Young, S. / Kabelis, K. / Baker, S. / Sullivan, A. / Evans, M. / Clark, J. / Wilmot, J. / Hu, X. ...Sanders, J. / Sanders, P. / Young, S. / Kabelis, K. / Baker, S. / Sullivan, A. / Evans, M. / Clark, J. / Wilmot, J. / Hu, X. / Roberts, E. / Powell, M. / Nunez Miguel, R. / Furmaniak, J. / Rees Smith, B.
Citation
Journal: J.Mol.Endocrinol. / Year: 2011
Title: Crystal Structure of the Tsh Receptor (Tshr) Bound to a Blocking-Type Tshr Autoantibody.
Authors: Sanders, P. / Young, S. / Sanders, J. / Kabelis, K. / Baker, S. / Sullivan, A. / Evans, M. / Clark, J. / Wilmot, J. / Hu, X. / Roberts, E. / Powell, M. / Nunez Miguel, R. / Furmaniak, J. / Rees Smith, B.
#1: Journal: Thyroid / Year: 2007
Title: Crystal Structure of the Tsh Receptor in Complex with a Thyroid-Stimulating Autoantibody
Authors: Sanders, J. / Chirgadze, D.Y. / Sanders, P. / Baker, S. / Sullivan, A. / Bhardwaja, A. / Bolton, J. / Reeve, M. / Nakatake, N. / Evans, M. / Richards, T. / Powell, M. / Miguel, R.N. / ...Authors: Sanders, J. / Chirgadze, D.Y. / Sanders, P. / Baker, S. / Sullivan, A. / Bhardwaja, A. / Bolton, J. / Reeve, M. / Nakatake, N. / Evans, M. / Richards, T. / Powell, M. / Miguel, R.N. / Blundell, T.L. / Furmaniak, J. / Smith, B.R.
#2: Journal: Clinical Endocrinol. / Year: 2010
Title: Monoclonal Autoantibodies to the Tsh Receptor, One with Stimulating Activity and One with Blocking Activity, Obtained from the Same Blood Sample.
Authors: Evans, M. / Sanders, J. / Tagami, T. / Sanders, P. / Young, S. / Roberts, E. / Wilmot, J. / Hu, X. / Kabelis, K. / Clark, J. / Holl, S. / Richards, T. / Collyer, A. / Furmaniak, J. / Smith, B.R.
#3: Journal: Horm.Metab.Res. / Year: 2009
Title: Tsh Receptor - Autoantibody Interactions.
Authors: Rees Smith, B. / Sanders, J. / Evans, M. / Tagami, T. / Furmaniak, J.
#4: Journal: Lancet / Year: 2003
Title: Human Monoclonal Thyroid Stimulating Autoantibody
Authors: Sanders, J. / Evans, M. / Premawardhana, L.D.K.E. / Depraetere, H. / Jeffreys, J. / Richards, T. / Furmaniak, J. / Smith, B.R.
#5: Journal: Thyroid / Year: 2004
Title: Characteristics of a Human Monoclonal Autoantibody to the Thyrotropin Receptor: Sequence Structure and Function
Authors: Sanders, J. / Jeffreys, J. / Depraetere, H. / Evans, M. / Richards, T. / Kiddie, A. / Brereton, K. / Premawardhana, L.D.K.E. / Chirgadze, D.Y. / Miguel, R.N. / Blundell, T.L. / Furmaniak, J. / Smith, B.R.
#6: Journal: J.Mol.Endocrinol. / Year: 2009
Title: Thyroid Stimulating Autoantibody M22 Mimics Tsh Binding to the Tsh Receptor Leucine Rich Domain: A Comparative Structural Study of Protein-Protein Interactions.
Authors: Nunez Miguel, R. / Sanders, J. / Chirgadze, D.Y. / Furmaniak, J. / Rees Smith, B.
#7: Journal: Thyroid / Year: 2006
Title: Effects of Tsh Receptor Mutations on Binding and Biological Activity of Monoclonal Antibodies and Tsh
Authors: Sanders, J. / Bolton, J. / Sanders, P. / Jeffreys, J. / Nakatake, N. / Richards, T. / Evans, M. / Kiddie, A. / Summerhayes, S. / Roberts, E. / Miguel, R.N. / Furmaniak, J. / Smith, B.R.
#8: Journal: Thyroid / Year: 2007
Title: Molecular Interactions between the Tsh Receptor and a Thyroid-Stimulating Monoclonal Autoantibody
Authors: Sanders, J. / Miguel, R.N. / Bolton, J. / Bhardwaja, A. / Sanders, P. / Nakatake, N. / Evans, M. / Furmaniak, J. / Smith, B.R.
#9: Journal: J.Mol.Endocrinol. / Year: 2008
Title: Fsh and Tsh Binding to Their Respective Receptors: Similarities, Differences and Implication for Glycoprotein Hormone Specificity
Authors: Miguel, R.N. / Sanders, J. / Chirgadze, D.Y. / Blundell, T.L. / Furmaniak, J. / Rees Smith, B.
History
DepositionNov 5, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THYROID BLOCKING HUMAN AUTOANTIBODY K1-70 HEAVY CHAIN
B: THYROID BLOCKING HUMAN AUTOANTIBODY K1-70 LIGHT CHAIN
C: THYROTROPIN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7957
Polymers73,1793
Non-polymers1,6154
Water14,376798
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-29.3 kcal/mol
Surface area35920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.020, 89.300, 101.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules AB

#1: Antibody THYROID BLOCKING HUMAN AUTOANTIBODY K1-70 HEAVY CHAIN


Mass: 23637.561 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT HEAVY CHAIN, RESIDUES 1-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Production host: MOUSE-HUMAN HETEROHYBRIDOMA CELL LINE (others)
#2: Antibody THYROID BLOCKING HUMAN AUTOANTIBODY K1-70 LIGHT CHAIN


Mass: 22598.064 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT LIGHT CHAIN, RESIDUES 1-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Production host: MOUSE-HUMAN HETEROHYBRIDOMA CELL LINE (others)

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Protein / Non-polymers , 2 types, 799 molecules C

#3: Protein THYROTROPIN RECEPTOR / / THYROID-STIMULATING HORMONE RECEPTOR / TSH-R


Mass: 26943.828 Da / Num. of mol.: 1 / Fragment: LEUCINE RICH REPEAT DOMAIN, RESIDUES 22-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P16473
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 798 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 3 types, 4 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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: isolated from a genetically manipulated source
Formula: C8H15NO6
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 5 / Details: 16% PEG 3350, 0.2 M SODIUM MALONATE PH 5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 17, 2009 / Details: COLLIMATOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 56573 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.7
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.5 / % possible all: 64.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G04

3g04


Resolution: 1.9→66.98 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.911 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.22674 2861 5.1 %RANDOM
Rwork0.17691 ---
obs0.17943 53657 94.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.891 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20 Å20 Å2
2---0.7 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.9→66.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5028 0 106 798 5932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225303
X-RAY DIFFRACTIONr_bond_other_d0.0010.023469
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9857261
X-RAY DIFFRACTIONr_angle_other_deg0.84538529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4785666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40924.822197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28815814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9451514
X-RAY DIFFRACTIONr_chiral_restr0.080.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215804
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02983
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6861.53315
X-RAY DIFFRACTIONr_mcbond_other0.1661.51328
X-RAY DIFFRACTIONr_mcangle_it1.25925393
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.96531988
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2114.51864
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 138 -
Rwork0.262 2692 -
obs--64.8 %

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