+Open data
-Basic information
Entry | Database: PDB / ID: 4hiq | ||||||
---|---|---|---|---|---|---|---|
Title | The Structure of V122I Mutant Transthyretin in Complex with AG10 | ||||||
Components | Transthyretin | ||||||
Keywords | HORMONE BINDING PROTEIN/INHIBITOR / THYROID HORMONE TRANSPORT / Thyroxine / Retinol Binding Protein / HORMONE BINDING PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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 / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å | ||||||
Authors | Connelly, S. / Alhamadsheh, M. / Graef, I. / Wilson, I.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: AG10 inhibits amyloidogenesis and cellular toxicity of the familial amyloid cardiomyopathy-associated V122I transthyretin. Authors: Penchala, S.C. / Connelly, S. / Wang, Y. / Park, M.S. / Zhao, L. / Baranczak, A. / Rappley, I. / Vogel, H. / Liedtke, M. / Witteles, R.M. / Powers, E.T. / Reixach, N. / Chan, W.K. / Wilson, ...Authors: Penchala, S.C. / Connelly, S. / Wang, Y. / Park, M.S. / Zhao, L. / Baranczak, A. / Rappley, I. / Vogel, H. / Liedtke, M. / Witteles, R.M. / Powers, E.T. / Reixach, N. / Chan, W.K. / Wilson, I.A. / Kelly, J.W. / Graef, I.A. / Alhamadsheh, M.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4hiq.cif.gz | 119.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4hiq.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 4hiq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hiq_validation.pdf.gz | 971 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4hiq_full_validation.pdf.gz | 975.1 KB | Display | |
Data in XML | 4hiq_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 4hiq_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/4hiq ftp://data.pdbj.org/pub/pdb/validation_reports/hi/4hiq | HTTPS FTP |
-Related structure data
Related structure data | 4hisC 2fbrS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 13791.387 Da / Num. of mol.: 2 / Mutation: V122I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PALB, TTR / Plasmid: PMMHA / Production host: Escherichia coli (E. coli) / Strain (production host): Epicurean Gold / References: UniProt: P02766 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.42 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: THE WT-TTR WAS CONCENTRATED TO 4 MG/ML IN 10 MM NAPI, 100 MM KCL, AT PH 7.6 AND CO-CRYSTALLIZED AT ROOM TEMPERATURE WITH INHIBITORS USING THE VAPOR-DIFFUSION SITTING DROP METHOD, CRYSTALS ...Details: THE WT-TTR WAS CONCENTRATED TO 4 MG/ML IN 10 MM NAPI, 100 MM KCL, AT PH 7.6 AND CO-CRYSTALLIZED AT ROOM TEMPERATURE WITH INHIBITORS USING THE VAPOR-DIFFUSION SITTING DROP METHOD, CRYSTALS WERE GROWN FROM 1.395 M SODIUM CITRATE, 3.5% V/V GLYCEROL AT PH 5.5. THE CRYSTALS WERE FROZEN USING A CRYO-PROTECTANT SOLUTION OF 1.395 M SODIUM CITRATE, PH 5.5, CONTAINING 10% V/V GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9797 Å |
---|---|
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2012 / Details: Rh coated flat mirror |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→63.91 Å / Num. obs: 75242 / % possible obs: 98.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 12.9 Å2 / Rsym value: 0.022 / Net I/σ(I): 34.5 |
Reflection shell | Resolution: 1.18→1.25 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 9986 / Rsym value: 0.332 / % possible all: 91 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FBR Resolution: 1.18→63.91 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.184 / WRfactor Rwork: 0.1575 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.908 / SU B: 0.983 / SU ML: 0.021 / SU R Cruickshank DPI: 0.04 / SU Rfree: 0.0395 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 185.14 Å2 / Biso mean: 19.0955 Å2 / Biso min: 7.66 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.18→63.91 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.184→1.215 Å / Total num. of bins used: 20
|