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- PDB-1thc: CRYSTAL STRUCTURE DETERMINATION AT 2.3A OF HUMAN TRANSTHYRETIN-3'... -

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Basic information

Entry
Database: PDB / ID: 1thc
TitleCRYSTAL STRUCTURE DETERMINATION AT 2.3A OF HUMAN TRANSTHYRETIN-3',5'-DIBROMO-2',4,4',6-TETRA-HYDROXYAURONE COMPLEX
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT (THYROXINE / RETINOL) IN SERUM
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / 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'-DIBROMO-2',4,4',6'-TETRAHYDROXY AURONE / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsCiszak, E. / Cody, V. / Luft, J.R.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Crystal structure determination at 2.3-A resolution of human transthyretin-3',5'-dibromo-2',4,4',6-tetrahydroxyaurone complex.
Authors: Ciszak, E. / Cody, V. / Luft, J.R.
#1: 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.
#2: Journal: Nature / Year: 1977
Title: Protein-DNA and Protein-Hormone Interactions in Prealbumin, a Model of the Thyroid Hormone Nuclear Receptor (Query)
Authors: Blake, C.C.F. / Oatley, S.J.
#3: 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.
#4: Journal: J.Mol.Biol. / Year: 1971
Title: An X-Ray Study of the Subunit Structure of Prealbumin
Authors: Blake, C.C.F. / Swan, I.D.A. / Rerat, C. / Berthou, J. / Laurent, A. / Rerat, B.
History
DepositionApr 20, 1992Processing site: BNL
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE FIRST STRAND OF THE *EXTERNAL* SHEET IN EACH SUBUNIT IS DISCONTINUOUS. TO ACCOMMODATE ...SHEET THE FIRST STRAND OF THE *EXTERNAL* SHEET IN EACH SUBUNIT IS DISCONTINUOUS. TO ACCOMMODATE THESE DISCONTINUITIES EACH *EXTERNAL* SHEET IS REPRESENTED HERE TWICE, WITH A DIFFERENT STRAND 1 IN EACH CASE. STRANDS 2,3,4 OF *X1A* ARE IDENTICAL TO STRANDS 2,3,4 OF *X2A*. SIMILARLY STRANDS 2,3,4 OF *X1B* ARE IDENTICAL TO STRANDS 2,3,4 OF *X2B*. THIS DESCRIPTION IS CONSISTENT WITH THAT USED BY BLAKE AND COWORKERS FOR THE NATIVE TRANSTHYRETIN (PROTEIN DATA BANK ENTRY 2PAB).

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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)29,3296
Polymers27,5532
Non-polymers1,7764
Water1,71195
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules

A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,65812
Polymers55,1064
Non-polymers3,5528
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area10360 Å2
ΔGint-42 kcal/mol
Surface area18130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.402, 85.837, 65.784
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-130-

FL9

21A-131-

FL9

31A-131-

FL9

41A-131-

FL9

51A-131-

FL9

61B-130-

FL9

71B-130-

FL9

81B-131-

FL9

91B-131-

FL9

101B-131-

FL9

111B-131-

FL9

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Components

#1: Protein TRANSTHYRETIN


Mass: 13776.376 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P02766
#2: Chemical
ChemComp-FL9 / 3',5'-DIBROMO-2',4,4',6'-TETRAHYDROXY AURONE


Mass: 444.028 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H8Br2O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE STRUCTURE CONTAINS THE 3',5'-DIBROMO-2',4,4',6-TETRAHYDROXY AURONE MOLECULES THAT BIND IN TWO ...THE STRUCTURE CONTAINS THE 3',5'-DIBROMO-2',4,4',6-TETRAHYDROXY AURONE MOLECULES THAT BIND IN TWO OVERLAPPING BINDING MODES IN EACH OF TWO INDEPENDENT BINDING SITES OF THE TETRAMER. SINCE THE BROMOAURONE BINDING IS ALONG 2-FOLD CRYSTALLOGRAPHIC AXIS, OCCUPANCY OF 25% CORRESPONDS TO SATURATION OF EACH OF THE BINDING SITES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal grow
*PLUS
pH: 6.9 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 %satammonium sulfate11
20.1 Msodium phosphate11

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Data collection

Reflection
*PLUS
Num. obs: 11830 / Num. measured all: 18899 / Rmerge(I) obs: 0.05

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.179 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 68 95 1954
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_deg3.9
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 10 Å / Num. reflection obs: 8442 / σ(F): 2 / Rfactor all: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg0.04
X-RAY DIFFRACTIONp_planar_d0.050.063
X-RAY DIFFRACTIONp_plane_restr0.020.016
X-RAY DIFFRACTIONp_chiral_restr0.150.197

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