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- PDB-6gr7: Crystal Structure Of Human Transthyretin in complex with 2,4,5-tr... -

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Basic information

Entry
Database: PDB / ID: 6gr7
TitleCrystal Structure Of Human Transthyretin in complex with 2,4,5-trichlorophenoxyacetic acid (2,4,5-T)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / transthyretin / thyroxine disrupting chemicals / TDCs / 2 / 4 / 5-trichlorophenoxyacetic acid / 5-T
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, 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
Similarity search - Domain/homology
2-[2,4,5-tris(chloranyl)phenoxy]ethanoic acid / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGrundstrom, C. / Zhang, J. / Olofsson, A. / Andersson, P.L. / Sauer-Eriksson, A.E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Citation
Journal: Environ. Sci. Technol. / Year: 2018
Title: Interspecies Variation between Fish and Human Transthyretins in Their Binding of Thyroid-Disrupting Chemicals.
Authors: Zhang, J. / Grundstrom, C. / Brannstrom, K. / Iakovleva, I. / Lindberg, M. / Olofsson, A. / Andersson, P.L. / Sauer-Eriksson, A.E.
#1: Journal: Environ. Sci. Technol. / Year: 2016
Title: Structure-Based Virtual Screening Protocol for in Silico Identification of Potential Thyroid Disrupting Chemicals Targeting Transthyretin.
Authors: Zhang, J. / Begum, A. / Brannstrom, K. / Grundstrom, C. / Iakovleva, I. / Olofsson, A. / Sauer-Eriksson, A.E. / Andersson, P.L.
History
DepositionJun 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Apr 24, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0664
Polymers27,5552
Non-polymers5112
Water4,288238
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1318
Polymers55,1094
Non-polymers1,0224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area6710 Å2
ΔGint-42 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.878, 85.486, 64.488
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-421-

HOH

21B-400-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13777.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-F52 / 2-[2,4,5-tris(chloranyl)phenoxy]ethanoic acid


Mass: 255.482 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H5Cl3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: The purified human TTR was dialyzed against 10 mM Na-phosphate buffer with 100 mM KCl (pH 7.6) and concentrated to 5 mg/mL The reservoir contained 28% PEG 4K, 0.1M NaAc pH 4.5, 0.2M AmAc. ...Details: The purified human TTR was dialyzed against 10 mM Na-phosphate buffer with 100 mM KCl (pH 7.6) and concentrated to 5 mg/mL The reservoir contained 28% PEG 4K, 0.1M NaAc pH 4.5, 0.2M AmAc. Drop size 3 plus 3 microliter.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.4→42.7 Å / Num. obs: 46647 / % possible obs: 98.5 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 17.3
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4301 / % possible all: 89.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F41

1f41


Resolution: 1.4→42.7 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.81
RfactorNum. reflection% reflection
Rfree0.1877 2231 4.78 %
Rwork0.1687 --
obs0.1696 46647 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 28 238 2058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092092
X-RAY DIFFRACTIONf_angle_d0.9142884
X-RAY DIFFRACTIONf_dihedral_angle_d14.981757
X-RAY DIFFRACTIONf_chiral_restr0.084313
X-RAY DIFFRACTIONf_plane_restr0.009386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.43050.30861440.2692500X-RAY DIFFRACTION90
1.4305-1.46370.32441250.25022674X-RAY DIFFRACTION97
1.4637-1.50030.22011470.22392744X-RAY DIFFRACTION99
1.5003-1.54090.25281320.21172768X-RAY DIFFRACTION99
1.5409-1.58630.22491540.20382750X-RAY DIFFRACTION99
1.5863-1.63750.21931410.19062752X-RAY DIFFRACTION99
1.6375-1.6960.21421380.1862796X-RAY DIFFRACTION99
1.696-1.76390.22361400.1822758X-RAY DIFFRACTION99
1.7639-1.84420.19761550.18252793X-RAY DIFFRACTION100
1.8442-1.94140.17861340.16692828X-RAY DIFFRACTION100
1.9414-2.0630.19781200.15622831X-RAY DIFFRACTION100
2.063-2.22230.18811410.1552808X-RAY DIFFRACTION100
2.2223-2.44590.1731280.15512679X-RAY DIFFRACTION94
2.4459-2.79980.17491290.15932819X-RAY DIFFRACTION98
2.7998-3.52720.16531490.1642900X-RAY DIFFRACTION100
3.5272-42.76290.17561540.15913016X-RAY DIFFRACTION99

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