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- PDB-4yia: Structural mechanism of hormone release in thyroxine binding globulin -

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Basic information

Entry
Database: PDB / ID: 4yia
TitleStructural mechanism of hormone release in thyroxine binding globulin
Components(Thyroxine-binding ...) x 2
KeywordsSIGNALING PROTEIN / Thyroxine Binding globulin / Thyroxine / Serpin / hormone release / cation Pi interaction
Function / homology
Function and homology information


thyroid hormone transport / serine-type endopeptidase inhibitor activity / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
INDOMETHACIN / Thyroxine-binding globulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsZheng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: To Be Published
Title: Structural mechanism of hormone release in thyroxine Binding globulin
Authors: Zheng, Y.
History
DepositionMar 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_struct_special_symmetry / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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 / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thyroxine-binding globulin
B: Thyroxine-binding globulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2639
Polymers45,7082
Non-polymers5557
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-105 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.980, 56.070, 173.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

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Components

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Thyroxine-binding ... , 2 types, 2 molecules AB

#1: Protein Thyroxine-binding globulin / / Serpin A7 / T4-binding globulin


Mass: 41794.129 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-382
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA7, TBG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05543
#2: Protein/peptide Thyroxine-binding globulin / / Serpin A7 / T4-binding globulin


Mass: 3913.653 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 382-415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA7, TBG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05543

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Non-polymers , 5 types, 204 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-IMN / INDOMETHACIN / Indometacin


Mass: 357.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16ClNO4 / Comment: medication, antiinflammatory*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsreactive loop (366-382) mutated to GAMFLEAIPR

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 290 K / Method: evaporation / Details: PEG 4000 / PH range: pH6-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.58→26.57 Å / Num. obs: 52812 / % possible obs: 97.98 % / Redundancy: 3.2 % / Net I/σ(I): 3.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→26.57 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.969 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22924 2820 5.1 %RANDOM
Rwork0.20466 ---
obs0.20592 52812 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.006 Å2
Baniso -1Baniso -2Baniso -3
1-3.04 Å2-0 Å20 Å2
2---1.16 Å20 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 1.58→26.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2922 0 31 197 3150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0193019
X-RAY DIFFRACTIONr_bond_other_d0.0010.022921
X-RAY DIFFRACTIONr_angle_refined_deg2.1991.9714089
X-RAY DIFFRACTIONr_angle_other_deg0.97836739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3015372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36625.276127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5715544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.143157
X-RAY DIFFRACTIONr_chiral_restr0.150.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023367
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02674
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_it1.3030.9371483
X-RAY DIFFRACTIONr_mcbond_other1.2980.9361481
X-RAY DIFFRACTIONr_mcangle_it1.981.4021850
X-RAY DIFFRACTIONr_mcangle_other1.9811.4031851
X-RAY DIFFRACTIONr_scbond_it2.21.2381536
X-RAY DIFFRACTIONr_scbond_other2.21.2381537
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3871.7452238
X-RAY DIFFRACTIONr_long_range_B_refined5.2138.7373400
X-RAY DIFFRACTIONr_long_range_B_other5.218.7193399
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.584→1.625 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 198 -
Rwork0.229 3834 -
obs--97.11 %
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)
10.10570.0065-0.07510.29320.17780.21920.01480.02920.02060.0398-0.016-0.010.0083-0.00810.00120.0080.0001-0.0040.0566-0.00420.0612-12.2712-22.610624.5267
20.0481-0.0360.11190.59070.0490.4725-0.00680.0460.00120.0573-0.0305-0.0023-0.00510.03640.03730.0064-0.0020.00470.07610.00110.0613-10.2209-34.076815.8002
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 355
2X-RAY DIFFRACTION2B362 - 394

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