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- PDB-1ict: MONOCLINIC FORM OF HUMAN TRANSTHYRETIN COMPLEXED WITH THYROXINE (T4) -

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Basic information

Entry
Database: PDB / ID: 1ict
TitleMONOCLINIC FORM OF HUMAN TRANSTHYRETIN COMPLEXED WITH THYROXINE (T4)
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT PROTEIN / ALBUMIN / TRANSPORT / AMYLOID / THYROID HORMONE / LIVER / PLASMA / POLYNEUROPATHY / THYROXINE / PREALBUMIN / GREEK KEY BETA BARREL
Function / homology
Function and homology information


Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family ...Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
3,5,3',5'-TETRAIODO-L-THYRONINE / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWojtczak, A. / Neumann, P. / Cody, V.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of a new polymorphic monoclinic form of human transthyretin at 3 A resolution reveals a mixed complex between unliganded and T4-bound tetramers of TTR.
Authors: Wojtczak, A. / Neumann, P. / Cody, V.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: STRUCTURAL ASPECTS OF INOTROPIC BIPYRIDINE BINDING. CRYSTAL STRUCTURE DETERMINATION TO 1.9 A OF THE HUMAN SERUM TRANSTHYRETIN-MILRINONE COMPLEX
Authors: WOJTCZAK, A. / LUFT, J.R. / CODY, V.
#2: Journal: J.Biol.Chem. / Year: 1992
Title: MECHANISM OF MOLECULAR RECOGNITION. STRUCTURAL ASPECTS OF 3,3'-DIIODO-L-THYRONINE BINDING TO HUMAN SERUM TRANSTHYRETIN
Authors: WOJTCZAK, A. / LUFT, J.R. / CODY, V.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: STRUCTURES OF HUMAN TRANSTHYRETIN COMPLEXED WITH THYROXINE AT 2.0 A RESOLUTION AND 3',5'-DINITRO-N-ACETYL-L-THYRONINE AT 2.2 A RESOLUTION
Authors: WOJTCZAK, A. / CODY, V. / LUFT, J.R. / PANGBORN, W.
History
DepositionApr 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

Downloads & links

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Assembly

Deposited unit
A: TRANSTHYRETIN
B: TRANSTHYRETIN
C: TRANSTHYRETIN
D: TRANSTHYRETIN
E: TRANSTHYRETIN
F: TRANSTHYRETIN
G: TRANSTHYRETIN
H: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,77310
Polymers110,2198
Non-polymers1,5542
Water00
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN
C: TRANSTHYRETIN
D: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6636
Polymers55,1094
Non-polymers1,5542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-40 kcal/mol
Surface area18860 Å2
MethodPISA
2
E: TRANSTHYRETIN
F: TRANSTHYRETIN
G: TRANSTHYRETIN
H: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)55,1094
Polymers55,1094
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-43 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.690, 96.660, 81.740
Angle α, β, γ (deg.)90.00, 106.84, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.15401, -0.92334, -0.35175), (0.9134, -0.00272, 0.40706), (-0.37681, -0.38398, 0.84295)
Vector: -33.73061, -71.70456, 30.62044)
DetailsTHIS ENTRY CONTAINS TWO COMPLETE HUMAN TETRAMERS (TTR) IN THE ASSYMETRIC UNIT OF THE CELL. THEY ARE RELATED BY NCS MATRIX ( 0.15401 -0.92334 -0.35175 ) ( 0.91340 -0.00272 0.40706 ) ( -0.37681 -0.38398 0.84295 ); T= ( -33.73061 -71.70456 30.62044 );

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Components

#1: Protein
TRANSTHYRETIN / PREALBUMIN / TTR / TBPA / ATTR


Mass: 13777.360 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: PLASMA / References: UniProt: P02766
#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

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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: 2.64 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 293 K / Method: hangman hanging drop crystallization method / pH: 4.9
Details: 55% AMMONIUM SULFATE; 0.1 M PHOSPHATE BUFFER, pH 4.9, HANGMAN HANGING DROP CRYSTALLIZATION METHOD, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
155 %ammonium sulfate1reservoir
20.1 Mphosphate1reservoirpH4.9

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→96.66 Å / Num. all: 14537 / Num. obs: 23667 / % possible obs: 61.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.62 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 38.6 / Net I/σ(I): 10.12
Reflection shellResolution: 3→3.1 Å / Redundancy: 1.69 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1267 / % possible all: 59.6
Reflection
*PLUS
Lowest resolution: 58.5 Å / Num. obs: 14537 / Num. measured all: 23667 / Rmerge(I) obs: 0.0982
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.2 Å / % possible obs: 59 % / Mean I/σ(I) obs: 4.7

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TETRAMER GENERATED FROM PDB ENTRY 2ROX WITH ONLY PROTEIN ATOMS FROM RESIDUES 10-125 INCLUDED

2rox


Resolution: 3→15 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 184941.17 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: THIS COORDINATE SET COMPRISES TWO DEFFERENT HUMAN TTR TETRAMERS AN APO ONE (CHAINS E-H) AND A T4-BOUND ONE (CHAINS A-D). THERE ARE NO WATER MOLECULES INCLUDED IN THE MODEL. RESIDUES 1-9 AND ...Details: THIS COORDINATE SET COMPRISES TWO DEFFERENT HUMAN TTR TETRAMERS AN APO ONE (CHAINS E-H) AND A T4-BOUND ONE (CHAINS A-D). THERE ARE NO WATER MOLECULES INCLUDED IN THE MODEL. RESIDUES 1-9 AND 126-127 OF ALL A-H CHAINS ARE ILL-DEFINED IN THE ELECTRON DENSITY MAPS AND HAVE BEEN OMITTED. GROUPED B FACTOR HAVE BEEN REFINED (FOR MAIN AND SIDRCHAIN ATOMS) B RMSD FOR BONDED MAINCHAIN ATOMS = 8.628 B RMSD FOR BONDED SIDECHAIN ATOMS = 11.213 B RMSD FOR ANGLE MAINCHAIN ATOMS = 13.280 B RMSD FOR ANGLE SIDECHAIN ATOMS == 16.102 NCS RESTRAINTS. DETAILS INFORMATIONS: MAIN CHAIN ATOMS SELECTED EFFECTIVE FORCE CONSTANT FOR NCS POSITIONAL RESTRAINTS = 10.00 Kcal/mol-A**2 TARGET DEVIATION OF NCS RELATED B FACTORS FROM AVERAGE = 2.500 A**2 SIDE CHAIN ATOMS SELECTED EFFECTIVE FORCE CONSTANT FOR NCS POSITIONAL RESTRAINTS = 5.00 Kcal/mol-A**2 TARGET DEVIATION OF NCS RELATED B FACTORS FROM AVERAGE = 2.00 A**2
RfactorNum. reflection% reflectionSelection details
Rfree0.289 899 6.3 %SHELLS
Rwork0.229 ---
obs0.229 14405 63.1 %-
all-22820 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.253 e/Å3
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.74 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7168 0 48 0 7216
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d1.14
Refine LS restraints NCSNCS model details: CONSTRAINED / Rms dev position: 0.48 Å / Weight position: 10
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
3-3.160.44841355.80.3737350.077194659.1
3.16-3.350.3181930.28272031
3.35-3.610.34271320.25132101
3.61-3.960.25551350.21382100
3.96-4.520.22691350.16932031
4.52-5.650.25551340.17912092
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2LIG.PARAMLIG.TOP
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.14
LS refinement shell
*PLUS
Rfactor Rfree: 0.4484 / Rfactor Rwork: 0.373

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