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- PDB-3g04: Crystal structure of the TSH receptor in complex with a thyroid-s... -

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Entry
Database: PDB / ID: 3g04
TitleCrystal structure of the TSH receptor in complex with a thyroid-stimulating autoantibody
Components
  • (HUMAN THYROID STIMULATING AUTOANTIBODY M22 ...) x 2
  • Thyrotropin receptor
KeywordsIMMUNE SYSTEM / TSH RECEPTOR / GPCR / THYROID / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSanders, J. / Chirgadze, D.Y. / Sanders, P. / Baker, S. / Sullivan, A. / Bhardwaja, A. / Bolton, J. / Reeve, M. / Nakatake, N. / Evans, M. ...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.
Citation
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.
#1: 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.
#2: 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.
#3: Journal: Thyroid / Year: 2004
Title: Analysis of the thyrotropin receptor-thyrotropin interaction by comparative modeling
Authors: Miguel, R.N. / Sanders, J. / Jeffreys, J. / Depraetere, H. / Evans, M. / Richards, T. / Blundell, T.L. / Rees Smith, B. / Furmaniak, J.
#4: Journal: Thyroid / Year: 2005
Title: Comparative Modelling of the Thyrotropin Receptor
Authors: Miguel, R.N. / Sanders, J. / Blundell, T.L. / Smith, B.R. / Furmaniak, J.
#5: 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.
#6: 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.
#7: 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.
#8: Journal: To be Published / Year: 2009
Title: Thyroid stimulating autoantibody M22 mimics TSH in its binding to the TSH receptor: a comparative structural study of protein-protein interactions
Authors: Miguel, R.N. / Sanders, J. / Chirgadze, D.Y. / Furmaniak, J. / Smith, B.R.
History
DepositionJan 27, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
A: HUMAN THYROID STIMULATING AUTOANTIBODY M22 LIGHT CHAIN
B: HUMAN THYROID STIMULATING AUTOANTIBODY M22 HEAVY CHAIN
C: Thyrotropin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,12914
Polymers74,4753
Non-polymers1,65411
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-79 kcal/mol
Surface area28610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.888, 175.784, 205.806
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-245-

HOH

21B-235-

HOH

31B-255-

HOH

41C-294-

HOH

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Components

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Antibody , 2 types, 2 molecules AB

#1: Antibody HUMAN THYROID STIMULATING AUTOANTIBODY M22 LIGHT CHAIN


Mass: 23043.408 Da / Num. of mol.: 1 / Fragment: FAB fragment light chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: mouse-human heterohybridoma cell line (others)
#2: Antibody HUMAN THYROID STIMULATING AUTOANTIBODY M22 HEAVY CHAIN


Mass: 24487.438 Da / Num. of mol.: 1 / Fragment: FAB fragment heavy chain
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 / Sugars , 2 types, 7 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 (SEGMENT 22-260)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSHR / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): HIGH FIVE / References: UniProt: P16473
#4: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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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Non-polymers , 2 types, 294 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 8% PEG 8000, 0.1M MES, 0.25M ZINC ACETATE, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 2006
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. all: 26775 / Num. obs: 25731 / % possible obs: 96.1 % / Observed criterion σ(I): 2.5 / Redundancy: 4.6 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 10.5
Reflection shellResolution: 2.55→2.61 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.361 / Rsym value: 0.361 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PXGENdata collection
AMoREphasing
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XWD
Resolution: 2.55→26.72 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.904 / SU B: 17.888 / SU ML: 0.208 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.665 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1301 5.1 %RANDOM
Rwork0.181 ---
obs0.184 24426 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.55→26.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5036 0 89 289 5414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225255
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9817173
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5285651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.59924.604202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.20715834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9341518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2831
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023901
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.22170
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23515
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2322
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1770.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0460.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.77553363
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.67365320
X-RAY DIFFRACTIONr_scbond_it2.26152175
X-RAY DIFFRACTIONr_scangle_it3.3927.51853
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 95 -
Rwork0.224 1803 -
obs-1898 97.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.1583-0.20310.01191.71880.82031.4269-0.03240.05790.0065-0.0352-0.0012-0.0419-0.079-0.04570.0336-0.0992-0.01020.0096-0.0050.0087-0.07966.82274.08616.829
20.68760.2497-0.3280.2971-0.22163.03670.02250.0778-0.01430.0199-0.0828-0.00210.2942-0.24160.0603-0.0899-0.06330.033-0.002-0.0539-0.0185-5.70560.60938.709
33.38680.8695-1.48423.63961.28534.7819-0.1155-0.25180.46320.1353-0.02250.2909-0.3013-0.39290.138-0.11060.062-0.01540.0031-0.04340.0174-16.45162.81673.889
40.33220.17260.26091.14520.74241.96060.00790.0186-0.0030.1340.0002-0.04810.04470.0818-0.0081-0.11180.01250.0205-0.01110.0152-0.003712.25571.28145.001
50.82011.1967-0.02493.2481-0.48841.0542-0.0206-0.1103-0.01050.09960.00510.0388-0.0492-0.01880.0154-0.0636-0.03120.0285-0.0159-0.0223-0.0933-1.04658.47579.463
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C30 - 257
2X-RAY DIFFRACTION2B1 - 114
3X-RAY DIFFRACTION3B115 - 213
4X-RAY DIFFRACTION4A1 - 108
5X-RAY DIFFRACTION5A109 - 208

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