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- PDB-5jid: Crystal Structure of Human Transthyretin in Complex with Perfluor... -

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Basic information

Entry
Database: PDB / ID: 5jid
TitleCrystal Structure of Human Transthyretin in Complex with Perfluorooctanoic acid (PFOA)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / thyroxine binding / Perfluorooctanoic acid(PFOA)complex
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 / Non-integrin membrane-ECM interactions / molecular sequestering activity / 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 / Non-integrin membrane-ECM interactions / molecular sequestering activity / 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
pentadecafluorooctanoic acid / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsBegum, A. / Zhang, J. / Olofsson, A. / Andersson, P. / Sauer-Eriksson, A.E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Citation
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.
#1: Journal: Plos One / Year: 2016
Title: Tetrabromobisphenol A is an efficient stabilizer of the transthyretin tetramer
Authors: Iakovleva, I. / Begum, A. / Brannstrom, K. / Wijesekera, A. / Nilsson, L. / Zhang, J. / Andersson, P. / Sauer-Eriksson, A.E. / Olofsson, A.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)28,4065
Polymers27,5552
Non-polymers8513
Water3,783210
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,81210
Polymers55,1094
Non-polymers1,7026
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)42.653, 85.674, 63.420
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-301-

8PF

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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-8PF / pentadecafluorooctanoic acid


Mass: 414.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8HF15O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Purified TTRwt was dialyzed against 10 mM sodiumphosphate buffer with 100 mM KCl pH 7.6 and concentrated to 5 mg per ml. PFOA was added at 5 x molar excess to the protein. The reservoir ...Details: Purified TTRwt was dialyzed against 10 mM sodiumphosphate buffer with 100 mM KCl pH 7.6 and concentrated to 5 mg per ml. PFOA was added at 5 x molar excess to the protein. The reservoir contained 1.3 to 1.6 M sodium citrate and 3.5 percent glycerol at pH 5.5. Drop size 3 plus 3 microliter.
PH range: 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.913 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.913 Å / Relative weight: 1
ReflectionResolution: 1.2→40 Å / Num. obs: 71054 / % possible obs: 96.6 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.26
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 1.79 / % possible all: 75.14

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F41

1f41


Resolution: 1.2→38.183 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.22
RfactorNum. reflection% reflection
Rfree0.1632 3582 5.04 %
Rwork0.1424 --
obs0.1435 71049 96.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.2→38.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 51 210 2053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082088
X-RAY DIFFRACTIONf_angle_d1.3282904
X-RAY DIFFRACTIONf_dihedral_angle_d14.346754
X-RAY DIFFRACTIONf_chiral_restr0.079309
X-RAY DIFFRACTIONf_plane_restr0.008380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1992-1.2150.2532890.2411793X-RAY DIFFRACTION68
1.215-1.23170.2466970.21722087X-RAY DIFFRACTION78
1.2317-1.24930.21271130.20462249X-RAY DIFFRACTION85
1.2493-1.26790.20841430.18092432X-RAY DIFFRACTION93
1.2679-1.28770.18681470.16572561X-RAY DIFFRACTION97
1.2877-1.30880.22721340.15952612X-RAY DIFFRACTION99
1.3088-1.33140.18561230.15272664X-RAY DIFFRACTION99
1.3314-1.35560.17821220.14762630X-RAY DIFFRACTION99
1.3556-1.38170.19161320.1322682X-RAY DIFFRACTION99
1.3817-1.40990.15671340.13242639X-RAY DIFFRACTION99
1.4099-1.44050.17181350.13062648X-RAY DIFFRACTION99
1.4405-1.47410.1891270.12772675X-RAY DIFFRACTION99
1.4741-1.51090.15261690.11792592X-RAY DIFFRACTION99
1.5109-1.55180.16051410.11532668X-RAY DIFFRACTION100
1.5518-1.59740.11661740.11412612X-RAY DIFFRACTION100
1.5974-1.6490.141440.11342679X-RAY DIFFRACTION100
1.649-1.70790.13971510.11932671X-RAY DIFFRACTION100
1.7079-1.77630.15131710.12712647X-RAY DIFFRACTION100
1.7763-1.85720.15621270.12372690X-RAY DIFFRACTION100
1.8572-1.95510.14491340.11812700X-RAY DIFFRACTION100
1.9551-2.07760.13531360.12242693X-RAY DIFFRACTION100
2.0776-2.23790.131400.12572723X-RAY DIFFRACTION100
2.2379-2.46310.16671290.13912727X-RAY DIFFRACTION100
2.4631-2.81940.17341420.15712747X-RAY DIFFRACTION100
2.8194-3.55180.19221450.1552780X-RAY DIFFRACTION100
3.5518-38.20210.16191830.15582866X-RAY DIFFRACTION100

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