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- PDB-3nee: Wild type human transthyretin (TTR) complexed with GC-1 (TTRwt:GC-1) -

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Basic information

Entry
Database: PDB / ID: 3nee
TitleWild type human transthyretin (TTR) complexed with GC-1 (TTRwt:GC-1)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / TTR / TRANSTHYRETIN / AMYLOID / ligand / GC-1
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / 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) / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / 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
Chem-B72 / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsTrivella, D.B.B. / Polikarpov, I.
Citation
Journal: J.Struct.Biol. / Year: 2011
Title: The binding of synthetic triiodo l-thyronine analogs to human transthyretin: molecular basis of cooperative and non-cooperative ligand recognition.
Authors: Trivella, D.B. / Sairre, M.I. / Foguel, D. / Lima, L.M. / Polikarpov, I.
#1: Journal: J.STRUCT.BIOL. / Year: 2010
Title: Conformational differences between the wild type and V30M mutant transthyretin modulate its binding to genistein: implications to tetramer stability and ligand-binding.
Authors: Trivella, D.B. / Bleicher, L. / Palmieri, L.C. / Wiggers, H.J. / Montanari, C.A. / Kelly, J.W. / Lima, L.M. / Foguel, D. / Polikarpov, I.
History
DepositionJun 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)26,1555
Polymers25,4062
Non-polymers7493
Water2,846158
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,31110
Polymers50,8134
Non-polymers1,4986
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area7380 Å2
ΔGint-44 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.516, 85.161, 64.044
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-1-

B72

21B-1-

B72

31B-139-

HOH

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Components

#1: Protein Transthyretin / Prealbumin / TBPA / TTR / ATTR


Mass: 12703.217 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 30-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PALB, TTR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02766
#2: Chemical ChemComp-B72 / {4-[4-hydroxy-3-(1-methylethyl)benzyl]-3,5-dimethylphenoxy}acetic acid


Mass: 328.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M CaCl2, 0.1 M HEPES pH 7.5, 28% PEG 400, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 1.55→21.24 Å / Num. obs: 35324 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→21.24 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.187 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.857 / SU B: 3.085 / SU ML: 0.051 / SU R Cruickshank DPI: 0.114 / SU Rfree: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1774 5.1 %RANDOM
Rwork0.183 ---
obs0.185 35064 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 129.84 Å2 / Biso mean: 21.694 Å2 / Biso min: 10.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.55→21.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 54 158 1997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222078
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9712864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.155270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50923.97683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49815308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.643157
X-RAY DIFFRACTIONr_chiral_restr0.0990.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211622
X-RAY DIFFRACTIONr_mcbond_it1.3951.51271
X-RAY DIFFRACTIONr_mcangle_it2.38822088
X-RAY DIFFRACTIONr_scbond_it3.0413807
X-RAY DIFFRACTIONr_scangle_it4.6124.5769
X-RAY DIFFRACTIONr_rigid_bond_restr1.41832078
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 121 -
Rwork0.313 2282 -
all-2403 -
obs--94.16 %

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