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- PDB-2riw: The Reactive loop cleaved human Thyroxine Binding Globulin comple... -

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Basic information

Entry
Database: PDB / ID: 2riw
TitleThe Reactive loop cleaved human Thyroxine Binding Globulin complexed with thyroxine
Components(Thyroxine-binding globulin) x 2
KeywordsSIGNALING PROTEIN / Thyroxine binding globulin / thyroxine / complex / serpin / TBG / Disease mutation / Glycoprotein / Secreted
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
3,5,3',5'-TETRAIODO-L-THYRONINE / Thyroxine-binding globulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsZhou, A. / Wei, Z. / Stanley, P.L.D. / Read, R.J. / Stein, P.E. / Carrell, R.W.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Allosteric modulation of hormone release from thyroxine and corticosteroid-binding globulins
Authors: Qi, X. / Loiseau, F. / Chan, W.L. / Yan, Y. / Wei, Z. / Milroy, L.G. / Myers, R.M. / Ley, S.V. / Read, R.J. / Carrell, R.W. / Zhou, A.
History
DepositionOct 12, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,2703
Polymers42,4932
Non-polymers7771
Water5,314295
1
A: Thyroxine-binding globulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6642
Polymers37,8881
Non-polymers7771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thyroxine-binding globulin


Theoretical massNumber of molelcules
Total (without water)4,6051
Polymers4,6051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-35 kcal/mol
Surface area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.594, 42.164, 55.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1449-

HOH

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Components

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


Mass: 37887.547 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 39-375
Source method: isolated from a genetically manipulated source
Details: Purified from the supernatant of the cell lysate / Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA7, TBG / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star (DE3) / References: UniProt: P05543
#2: Protein/peptide Thyroxine-binding globulin / TBG / T4-binding globulin / Serpin A7


Mass: 4605.383 Da / Num. of mol.: 1
Fragment: reactive loop cleaved TBG, C-teemingly domain, UNP residues 376-415
Source method: isolated from a genetically manipulated source
Details: Purified from the supernatant of the cell lysate / Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA7, TBG / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star (DE3) / References: UniProt: P05543
#3: Chemical ChemComp-T44 / 3,5,3',5'-TETRAIODO-L-THYRONINE


Mass: 776.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11I4NO4 / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE REACTIVE LOOP P10-P1' CLEAVED CONFORMATION OF TBG WAS MUTATED TO GAMFLEAIPRS. THE FIRST ...THE REACTIVE LOOP P10-P1' CLEAVED CONFORMATION OF TBG WAS MUTATED TO GAMFLEAIPRS. THE FIRST RESIDUES, GAMFLEAIPR, ARE LOCATED AT C-TERMINAL IN CHAIN A AND THE LAST RESIDUE, S, IS LOCATED AT N-TERMINAL IN CHAIN B.

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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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.4
Details: 20% PEG 3350, 0.2M CaCl2, pH 7.4, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.5419 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 22, 2007 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.04→24.8 Å / Num. all: 25769 / Num. obs: 25486 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 14.1
Reflection shellResolution: 2.04→2.09 Å / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1692 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RIV

2riv


Resolution: 2.04→23.11 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9 / SU B: 6.589 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 4.2 / ESU R: 0.21 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24352 1351 5 %RANDOM
Rwork0.19571 ---
all0.19809 25486 --
obs0.198 25486 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.142 Å2
Baniso -1Baniso -2Baniso -3
1--2.37 Å20 Å20 Å2
2--1.98 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.04→23.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 24 295 3243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223058
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9684152
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9195383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52825.267131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36915548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.074157
X-RAY DIFFRACTIONr_chiral_restr0.0770.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022274
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.21387
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.22098
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5451.51890
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.93323042
X-RAY DIFFRACTIONr_scbond_it1.37231287
X-RAY DIFFRACTIONr_scangle_it2.1784.51103
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.038→2.091 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 94 -
Rwork0.222 1692 -
obs-1692 90.98 %
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)
10.99470.169-0.47610.412-0.05791.2675-0.01740.03390.0183-0.02520.0362-0.0106-0.01130.1787-0.0187-0.0364-0.0037-0.0092-0.0595-0.0097-0.056124.394312.360122.5626
21.38320.2935-0.83260.9393-0.23372.93880.0205-0.0632-0.06220.01470.0240.001-0.07830.0604-0.0445-0.00450.003-0.0096-0.1075-0.0099-0.019116.3510.530534.1044
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA19 - 3552 - 338
2X-RAY DIFFRACTION2BB362 - 3957 - 40

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