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- PDB-3nes: V30M mutant human transthyretin (TTR) complexed with GC-1 (V30M:GC-1) -

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Basic information

Entry
Database: PDB / ID: 3nes
TitleV30M mutant human transthyretin (TTR) complexed with GC-1 (V30M:GC-1)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / TTR / TRANSTHYRETIN / AMYLOID / 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 / molecular replacement / Resolution: 1.75 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: Bleicher, L. / Montanari, C.A. / Foguel, D. / Trivella, D.B. / Wiggers, H.J. / Lima, L.M.
History
DepositionJun 9, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)26,4047
Polymers25,4712
Non-polymers9335
Water3,603200
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,80714
Polymers50,9414
Non-polymers1,86610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)43.731, 85.451, 64.215
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-1-

B72

41A-147-

HOH

51B-132-

HOH

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Components

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


Mass: 12735.282 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 30-145 / Mutation: V30M
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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
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: 1.43016 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: 1.43016 Å / Relative weight: 1
ReflectionRedundancy: 4.6 % / Av σ(I) over netI: 4.7 / Number: 141212 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / D res high: 1.6 Å / D res low: 85.451 Å / Num. obs: 30636 / % possible obs: 94.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.0630.0696.210.0570.0574.2
3.585.0698.910.0540.0544.4
2.923.5898.110.0560.0564.6
2.532.9297.110.0650.0654.6
2.262.5396.310.0750.0754.6
2.072.2695.310.0970.0974.6
1.912.0794.410.1250.1254.6
1.791.9193.310.170.174.7
1.691.7992.310.280.284.7
1.61.6991.410.4440.4444.7
ReflectionResolution: 1.6→85.451 Å / Num. all: 30636 / Num. obs: 30636 / % possible obs: 94.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 14.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.694.70.4441.71998342700.44491.4
1.69-1.794.70.282.71893340410.2892.3
1.79-1.914.70.173.71807738840.1793.3
1.91-2.074.60.1252.21701336660.12594.4
2.07-2.264.60.0973.71564634020.09795.3
2.26-2.534.60.0758.21446531290.07596.3
2.53-2.924.60.0658.71296628180.06597.1
2.92-3.584.60.0568.11099424120.05698.1
3.58-5.064.40.0549.5854719250.05498.9
5.06-30.064.20.0578.4458810890.05796.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→27.59 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.182 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.849 / SU B: 2.394 / SU ML: 0.08 / SU R Cruickshank DPI: 0.143 / SU Rfree: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1212 5.1 %RANDOM
Rwork0.182 ---
obs0.184 23735 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 49.36 Å2 / Biso mean: 18.884 Å2 / Biso min: 5.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→27.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 66 200 2053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222312
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.9763204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9245306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28823.29997
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24415353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6631512
X-RAY DIFFRACTIONr_chiral_restr0.1210.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211873
X-RAY DIFFRACTIONr_mcbond_it1.0491.51386
X-RAY DIFFRACTIONr_mcangle_it1.8222305
X-RAY DIFFRACTIONr_scbond_it2.5363926
X-RAY DIFFRACTIONr_scangle_it3.8934.5892
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 75 -
Rwork0.247 1565 -
all-1640 -
obs--92.24 %

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