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- PDB-1tyr: TRANSTHYRETIN COMPLEX WITH RETINOIC ACID -

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Basic information

Entry
Database: PDB / ID: 1tyr
TitleTRANSTHYRETIN COMPLEX WITH RETINOIC ACID
ComponentsTRANSTHYRETIN
KeywordsRETINOL-BINDING / RETINOL-BINDING PROTEIN
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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
(9cis)-retinoic acid / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsZanotti, G. / D'Acunto, M.R. / Malpeli, G. / Folli, C. / Berni, R.
Citation
Journal: Eur.J.Biochem. / Year: 1995
Title: Crystal structure of the transthyretin--retinoic-acid complex
Authors: Zanotti, G. / D'Acunto, M.R. / Malpeli, G. / Folli, C. / Berni, R.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Crystallographic Studies on Complexes between Retinoids and Plasma Retinol-Binding Protein
Authors: Zanotti, G. / Marcello, M. / Malpeli, G. / Folli, C. / Sartori, G. / Berni, R.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Crystal Structure Determination at 2.3 Angstroms of Human Transthyretin-3',5'-Dibromo-2',4,4', 6-Tetra-Hydroxyaurone Complex
Authors: Ciszak, E. / Cody, V. / Luft, J.R.
#3: 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. / Cody, V.
#4: Journal: Nature / Year: 1977
Title: Protein-DNA and Protein-Hormone Interactions in Prealbumin: A Model of the Thyroid Hormone Nuclear Receptor?
Authors: Blake, C.C.F. / Oatley, S.J.
#5: Journal: J.Mol.Biol. / Year: 1974
Title: Structure of Human Plasma Prealbumin at 2.5 Angstroms Resolution, a Preliminary Report on the Polypeptide Chain Conformation, Quaternary Structure and Thyroxine Binding
Authors: Blake, C.C.F. / Geisow, M.J. / Swan, I.D.A. / Rerat, C. / Rerat, B.
History
DepositionMay 12, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 9, 2016Group: Non-polymer description
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1564
Polymers27,5552
Non-polymers6012
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-12 kcal/mol
Surface area12390 Å2
MethodPISA
2
A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules

A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3118
Polymers55,1094
Non-polymers1,2024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area9270 Å2
ΔGint-35 kcal/mol
Surface area20380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.800, 86.220, 65.780
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-131-

9CR

DetailsTHE ENTIRE PROTEIN IS A TETRAMER, BUT THE ASYMMETRIC UNIT CONTAINS A DIMER. THE TWO DIMERS ARE RELATED BY A TWO FODL AXIS, WHILST THE TWO INDEPENDENT MONOMERS IN THE DIMER ARE RELATED BY A PSEUDO TWO-FOLD AXIS. THE LIGAND IS BOUND IN THE INTERNAL CHANNEL, MADE UP BY THE TWO INDEPENDENT MONOMERS. A CRYSTALLOGRAPHIC TWO-FOLD AXIS RUNS THROUGH THE CHANNEL, MAKING IT SYMMETRIC. MOREOVER, PERPENDICULAR TO THE PREVIOUS ONE, THERE IS THE PSEUDO TWO-FOLD, WHICH MAKES THE TWO HALFS OF THE CHANNEL NEARLY IDENTICAL. AS A RESULT OF ALL THAT, TWO INDEPENDENT BINDING SITES ARE PRESENT PER TERAMER, BUT, SINCE THE LIGAND IN THIS CASE DOES NOT PRESENT ANY SYMMETRY, EACH LIGAND IN THE CRYSTAL APPEARS TO BE SUPERIMPOSED TO ITS SYMMETRY-RELATED. IN CONCLUSION, FOUR RETINOIC ACID BOUND MOLECULES ARE SEEN, EACH PAIRS SUPERIMPOSED. IN ADDITION, SOLUTION DATA STRONGLY SUGGEST THAT ONLY ONE LIGAND MOLECULE IS BOUND TO A TTR TETRAMER. IN CONCLUSION, THE COORDINATES OF TWO 9CR MOLECULES ARE GIVEN, WHICH APPLYING THE CRYSTALLOGRAPHIC SYMMETRY, BECOMES FOUR, BUT ONLY ONE MUST BE CONSIDERED STATISTICALLY PRESENT IN THE TETRAMER.

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Components

#1: Protein TRANSTHYRETIN / / PREALBUMIN


Mass: 13777.360 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02766
#2: Chemical ChemComp-9CR / (9cis)-retinoic acid / Alitretinoin


Mass: 300.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O2 / Comment: anticancer, antineoplastic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Mammonium sulfate1reservoir
20.2 Msodium citrate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Nov 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 3 % / Rmerge(I) obs: 0.07

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Processing

Software
NameClassification
TNTrefinement
SAINTdata reduction
RefinementResolution: 1.8→9 Å / σ(F): 0
Details: THE ENTRY CONTAINS RETINOIC ACID MOLECULES IN BOTH BINDING SITES. THE OCCUPANCIES OF SITES WERE NOT REFINED, SINCE THE ELECTRON DENSITY REFLECTS THE PRESENCE OF THE CRYSTALLOGRAPHIC TWO-FOLD ...Details: THE ENTRY CONTAINS RETINOIC ACID MOLECULES IN BOTH BINDING SITES. THE OCCUPANCIES OF SITES WERE NOT REFINED, SINCE THE ELECTRON DENSITY REFLECTS THE PRESENCE OF THE CRYSTALLOGRAPHIC TWO-FOLD AXIS. IN THE FUNCTIONAL TETRAMER THE RETINOIC ACID MOLECULES ARE DISORDERED DUE TO THE CRYSTALLOGRAPHIC TWO-FOLD RUNNING THROUGH THE BINDING SITE. RESIDUES 1 - 9 OF BOTH CHAINS, AS WELL AS 126 - 127 OF CHAIN B, ARE ILL-DEFINED IN THE ELECTRON DENSITY. THEY HAVE BEEN INCLUDED, BUT THE TEMPERATURE FACTORS ARE VERY HIGH.
RfactorNum. reflection% reflection
obs0.196 20172 85 %
Refinement stepCycle: LAST / Resolution: 1.8→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 44 97 2085
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg3.8
X-RAY DIFFRACTIONt_dihedral_angle_d19.6
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.001
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg3.5
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg19.6
X-RAY DIFFRACTIONt_planar_d0.007

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