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- PDB-2ceo: thyroxine-binding globulin complex with thyroxine -

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Basic information

Entry
Database: PDB / ID: 2ceo
Titlethyroxine-binding globulin complex with thyroxine
ComponentsTHYROXINE-BINDING GLOBULIN
KeywordsTRANSPORT / THYROXINE-BINDING GLOBULIN / SERPIN / HORMONE TRANSPORT / THYROXINE / DISEASE MUTATION / GLYCOPROTEIN
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: 2.8 Å
AuthorsZhou, A. / Wei, Z. / Read, R.J. / Carrell, R.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Structural Mechanism for the Carriage and Release of Thyroxine in the Blood.
Authors: Zhou, A. / Wei, Z. / Read, R.J. / Carrell, R.W.
History
DepositionFeb 8, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)86,7846
Polymers85,0462
Non-polymers1,7384
Water46826
1
A: THYROXINE-BINDING GLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3923
Polymers42,5231
Non-polymers8692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: THYROXINE-BINDING GLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3923
Polymers42,5231
Non-polymers8692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.404, 88.022, 124.118
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111TYRTYRILEILE1AA20 - 1694 - 153
211TYRTYRILEILE1BB20 - 1694 - 153
121LEULEUGLUGLU1AA172 - 349156 - 333
221LEULEUGLUGLU1BB172 - 349156 - 333
131PROPROGLUGLU1AA363 - 394347 - 378
231PROPROGLUGLU1BB363 - 394347 - 378
141GLNGLNASPASP5AA170 - 171154 - 155
241GLNGLNASPASP5BB170 - 171154 - 155
151ASNASNHISHIS5AA358 - 362342 - 346
251ASNASNHISHIS5BB358 - 362342 - 346
112T44T44T44T441AC1395
212T44T44T44T441BE1395

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.99881, -0.04783, -0.00945), (-0.04807, 0.99846, 0.02773), (0.0081, 0.02816, -0.99957)
Vector: -0.27787, 2.18242, -99.26411)

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Components

#1: Protein THYROXINE-BINDING GLOBULIN / T4-BINDING GLOBULIN


Mass: 42522.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Production host: Escherichia coli BL21(DE3) / Strain (production host): STAR / References: UniProt: P05543
#2: Chemical ChemComp-T44 / 3,5,3',5'-TETRAIODO-L-THYRONINE


Mass: 776.870 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H11I4NO4 / Comment: hormone*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMAJOR THYROID HORMONE TRANSPORT PROTEIN IN SERUM
Sequence detailsFIRST 18 RESIDUES OF MATURE SEQUENCE REPLACED BY HIS-TAG AND THROMBIN CLEAVAGE SITE. GLY-SER LEFT ...FIRST 18 RESIDUES OF MATURE SEQUENCE REPLACED BY HIS-TAG AND THROMBIN CLEAVAGE SITE. GLY-SER LEFT AT N-TERMINUS AFTER CLEAVAGE.

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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: 2.27 Å3/Da / Density % sol: 46 %
Crystal growpH: 7.4
Details: 10MM TRIS-HCL, 50MM NACL, 1MM EDTA PH 7.4, 20% PEG 3350, 0.2M NAF, 5% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 25, 2005 / Details: MIRRORS
RadiationMonochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→30.14 Å / Num. obs: 19138 / % possible obs: 93.6 % / Observed criterion σ(I): -5 / Redundancy: 13.8 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 9.65
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.24 / % possible all: 64.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YXA

1yxa


Resolution: 2.8→30.14 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.879 / SU B: 41.661 / SU ML: 0.375 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.469 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 17-19, 350-357 AND 395 OF BOTH CHAINS A AND B ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.283 972 5.1 %RANDOM
Rwork0.235 ---
obs0.237 18166 93.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.19 Å2
Baniso -1Baniso -2Baniso -3
1--3.34 Å20 Å20 Å2
2--5.53 Å20 Å2
3----2.19 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5798 0 60 26 5884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225980
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0111.9698092
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.785730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.11425.433254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.015151070
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0591512
X-RAY DIFFRACTIONr_chiral_restr0.0680.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024398
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1840.22428
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.24077
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2155
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.44153679
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.372105940
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.42952510
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.168102152
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2838tight positional0.020.05
21A24tight positional0.010.05
22B24tight positional0.010.05
11A28medium positional0.490.5
11A33loose positional0.865
11A2838tight thermal0.382
21A24tight thermal0.592
22B24tight thermal0.592
11A28medium thermal0.312
11A33loose thermal1.1610
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.495 48
Rwork0.364 879
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)
12.2135-0.2687-1.02671.45580.99197.7413-0.0458-0.20160.09130.1175-0.0915-0.04310.3047-0.06740.13730.2505-0.0177-0.03790.1215-0.04130.062413.57-4.389-34.084
21.73030.2885-0.61341.3988-0.28795.312-0.04560.07380.1758-0.006-0.0815-0.08150.0990.04420.12710.2235-0.0233-0.020.15370.04240.0552-13.268-3.773-65.241
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 349
2X-RAY DIFFRACTION1A358 - 394
3X-RAY DIFFRACTION1A1395
4X-RAY DIFFRACTION2B20 - 349
5X-RAY DIFFRACTION2B358 - 394
6X-RAY DIFFRACTION2B1395

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