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- PDB-5u4f: Wild-type Transthyretin in complex with 1,1'-(1E)-(1,2-Ethenediyl... -

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Basic information

Entry
Database: PDB / ID: 5u4f
TitleWild-type Transthyretin in complex with 1,1'-(1E)-(1,2-Ethenediyl)bis[2-chloro-4-boronic acid]benzene
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Boronic acids / Medicinal chemistry / stilbene / covalent ligand
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) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / Retinoid metabolism and transport / hormone activity ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid 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, 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
Chem-IWW / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWindsor, I.W. / Smith, T.P. / Raines, R.T. / Forest, K.T.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008349 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM044783 United States
National Science Foundation (NSF, United States)MCB 1518160 United States
CitationJournal: J. Med. Chem. / Year: 2017
Title: Stilbene Boronic Acids Form a Covalent Bond with Human Transthyretin and Inhibit Its Aggregation.
Authors: Smith, T.P. / Windsor, I.W. / Forest, K.T. / Raines, R.T.
History
DepositionDec 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)28,4914
Polymers27,8172
Non-polymers6742
Water2,216123
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9818
Polymers55,6344
Non-polymers1,3474
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)42.920, 85.223, 63.942
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-200-

IWW

21B-200-

IWW

31B-200-

IWW

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13908.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pET32b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P02766
#2: Chemical ChemComp-IWW / [(E)-ethene-1,2-diylbis(3-chloro-4,1-phenylene)]diboronic acid


Mass: 336.771 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12B2Cl2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 41.48 % / Mosaicity: 0.486 ° / Mosaicity esd: 0.004 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.3 M Sodium Citrate, 3.0% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.239801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.239801 Å / Relative weight: 1
ReflectionResolution: 1.5→38.5 Å / Num. obs: 38097 / % possible obs: 99.5 % / Redundancy: 6 % / Biso Wilson estimate: 22.21 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.5-1.536.10.42718770.923199.6
1.53-1.556.10.3570.928199.7
1.55-1.586.10.3040.949199.6
1.58-1.626.10.2580.969199.5
1.62-1.6560.2230.972199.5
1.65-1.695.90.1970.974199.5
1.69-1.735.90.1670.982199.5
1.73-1.785.60.140.985199.5
1.78-1.834.80.1170.986198.8
1.83-1.895.10.0970.991199.2
1.89-1.966.50.0810.995199.9
1.96-2.046.50.0740.9961100
2.04-2.136.50.0670.997199.6
2.13-2.246.40.0620.997199.7
2.24-2.386.30.0570.997199.6
2.38-2.566.40.0580.997199.9
2.56-2.825.80.0570.996199.8
2.82-3.234.70.0510.995197.6
3.23-4.076.50.0570.991199.8
4.07-506.50.1190.971198.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXphenix.refine: 1.9_1692refinement
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QGB

2qgb


Resolution: 1.5→38.5 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.31
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2000 5.26 %Random 5%
Rwork0.193 ---
obs0.194 38056 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.99 Å2 / Biso mean: 26.9 Å2 / Biso min: 13.67 Å2
Refinement stepCycle: final / Resolution: 1.5→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 42 123 1950
Biso mean--29.35 35.02 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071912
X-RAY DIFFRACTIONf_angle_d1.122621
X-RAY DIFFRACTIONf_chiral_restr0.047292
X-RAY DIFFRACTIONf_plane_restr0.007337
X-RAY DIFFRACTIONf_dihedral_angle_d14.478673
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5002-1.53770.29931380.24672485262397
1.5377-1.57930.23541410.220125382679100
1.5793-1.62580.25151400.20462523266399
1.6258-1.67830.22771410.200425592700100
1.6783-1.73830.23721420.20732541268399
1.7383-1.80790.25641410.20452545268699
1.8079-1.89010.22491420.19812561270399
1.8901-1.98980.24151410.183425602701100
1.9898-2.11440.21311430.184825722715100
2.1144-2.27770.1851440.176125962740100
2.2777-2.50690.21561430.186325872730100
2.5069-2.86950.21581460.203326252771100
2.8695-3.61480.21091440.18192601274598
3.6148-38.34560.22571540.19712763291799

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