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- PDB-3do4: Crystal structure of transthyretin variant T60A at acidic pH -

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Basic information

Entry
Database: PDB / ID: 3do4
TitleCrystal structure of transthyretin variant T60A at acidic pH
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / TTR / AMYLOID FIBRILS / POINT MUTATION / RETINOL-BINDING / THYROID HORMONE / Amyloid / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Hormone / Polymorphism / Polyneuropathy / Secreted / Vitamin A
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
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
ACETATE ION / Transthyretin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCendron, L. / Zanotti, G. / Folli, C. / Berni, R.
Citation
Journal: To be Published
Title: Amyloidogenic potential of transthyretin variants: Insights from structural and computational analyses
Authors: Cendron, L. / Trovato, A. / Seno, F. / Folli, C. / Alfieri, B. / Zanotti, G. / Berni, R.
#1: Journal: J.Mol.Biol. / Year: 2007
Title: Acidic Ph-Induced Conformational Changes in Amyloidogenic Mutant Transthyretin.
Authors: Pasquato, N. / Berni, R. / Folli, C. / Alfieri, B. / Cendron, L. / Zanotti, G.
#2: Journal: J.Mol.Biol. / Year: 2000
Title: A Comparative Analysis of 23 Structures of the Amyloidogenic Protein Transthyretin.
Authors: Eneqvist, T. / Olofsson, A. / Lundgren, E. / Sauer-Eriksson, A.E.
History
DepositionJul 3, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
C: Transthyretin
D: Transthyretin
E: Transthyretin
F: Transthyretin
G: Transthyretin
H: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,27413
Polymers109,9798
Non-polymers2955
Water2,360131
1
D: Transthyretin
F: Transthyretin
G: Transthyretin
H: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1076
Polymers54,9894
Non-polymers1182
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-45 kcal/mol
Surface area19470 Å2
MethodPISA
2
A: Transthyretin
B: Transthyretin
C: Transthyretin
E: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1667
Polymers54,9894
Non-polymers1773
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-42 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.586, 75.907, 107.267
Angle α, β, γ (deg.)90.00, 93.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31D
41E
51F
61G
71H
81B
91A
101C
111D
121E
131F
141G
151H
161B
171A
181C
191D
201E
211F
221G
231H
241B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSLEULEUAA10 - 5510 - 55
21CYSCYSLEULEUCC10 - 5510 - 55
31CYSCYSLEULEUDD10 - 5510 - 55
41CYSCYSLEULEUEE10 - 5510 - 55
51CYSCYSLEULEUFF10 - 5510 - 55
61CYSCYSLEULEUGG10 - 5510 - 55
71CYSCYSLEULEUHH10 - 5510 - 55
81CYSCYSLEULEUBB10 - 5510 - 55
92VALVALASPASPAA65 - 9965 - 99
102VALVALASPASPCC65 - 9965 - 99
112VALVALASPASPDD65 - 9965 - 99
122VALVALASPASPEE65 - 9965 - 99
132VALVALASPASPFF65 - 9965 - 99
142VALVALASPASPGG65 - 9965 - 99
152VALVALASPASPHH65 - 9965 - 99
162VALVALASPASPBB65 - 9965 - 99
173ARGARGPROPROAA103 - 125103 - 125
183ARGARGPROPROCC103 - 125103 - 125
193ARGARGPROPRODD103 - 125103 - 125
203ARGARGPROPROEE103 - 125103 - 125
213ARGARGPROPROFF103 - 125103 - 125
223ARGARGPROPROGG103 - 125103 - 125
233ARGARGPROPROHH103 - 125103 - 125
243ARGARGPROPROBB103 - 125103 - 125

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Components

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


Mass: 13747.334 Da / Num. of mol.: 8 / Mutation: T60A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P02766
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.6
Details: 15% PEG 4000, 0.05M NaAcetate, 0.1M AmmoniumAcetate , pH 4.6, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9729 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9729 Å / Relative weight: 1
ReflectionResolution: 2.4→107.2 Å / Num. all: 38055 / Num. obs: 38055 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.3
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.9 / Num. unique all: 5558 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F41

1f41


Resolution: 2.4→107.2 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.914 / SU B: 9.698 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.509 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26743 1900 5 %RANDOM
Rwork0.20191 ---
obs0.20517 36139 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.332 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å2-2.4 Å2
2---2.37 Å20 Å2
3---2.47 Å2
Refinement stepCycle: LAST / Resolution: 2.4→107.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7152 0 20 131 7303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0227367
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2151.94910055
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4255920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.84223.684304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.527151112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6281532
X-RAY DIFFRACTIONr_chiral_restr0.1380.21136
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025644
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2670.33074
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3330.54809
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.5535
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.350.364
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4720.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.28724730
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.79437520
X-RAY DIFFRACTIONr_scbond_it2.25423022
X-RAY DIFFRACTIONr_scangle_it3.20632535
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A416medium positional0.20.5
2C416medium positional0.190.5
3D416medium positional0.220.5
4E416medium positional0.20.5
5F416medium positional0.20.5
6G416medium positional0.220.5
7H416medium positional0.220.5
8B416medium positional0.160.5
1A390loose positional0.585
2C390loose positional0.525
3D390loose positional0.515
4E390loose positional0.685
5F390loose positional0.635
6G390loose positional0.585
7H390loose positional0.545
8B390loose positional0.525
1A416medium thermal6.152
2C416medium thermal2.652
3D416medium thermal2.582
4E416medium thermal2.432
5F416medium thermal3.142
6G416medium thermal3.122
7H416medium thermal4.52
8B416medium thermal2.922
1A390loose thermal9.4610
2C390loose thermal4.0910
3D390loose thermal5.410
4E390loose thermal4.8310
5F390loose thermal5.2210
6G390loose thermal5.0410
7H390loose thermal7.0410
8B390loose thermal5.7110
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 139 -
Rwork0.274 2658 -
obs--99.68 %

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