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- PDB-5n7c: Human TTR altered conformation from soaking in CuCl2. -

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Basic information

Entry
Database: PDB / ID: 5n7c
TitleHuman TTR altered conformation from soaking in CuCl2.
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Copper TTR complex / metal binding / Alzheimer beta-amyloid scavenging
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
ACETATE ION / COPPER (II) ION / DI(HYDROXYETHYL)ETHER / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsCiccone, L. / Savko, M. / Shepard, W. / Stura, E.A.
CitationJournal: Sci Rep / Year: 2018
Title: Copper mediated amyloid-beta binding to Transthyretin.
Authors: Ciccone, L. / Fruchart-Gaillard, C. / Mourier, G. / Savko, M. / Nencetti, S. / Orlandini, E. / Servent, D. / Stura, E.A. / Shepard, W.
History
DepositionFeb 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 2.0May 23, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Polymer sequence / Source and taxonomy / Structure summary
Category: entity / entity_poly ...entity / entity_poly / entity_poly_seq / entity_src_nat / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq
Item: _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code ..._entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_end_seq_num / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 2.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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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)26,3418
Polymers25,9232
Non-polymers4186
Water3,153175
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,68216
Polymers51,8464
Non-polymers83612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area7150 Å2
ΔGint-67 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.990, 82.540, 67.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12961.511 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02766

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Non-polymers , 5 types, 181 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: protein: 10 mg/ml Dialysed in 100 milli-M NaCl, 50 milli-M sodium acetate, pH 5.5 Precipitant: 21 % PEG4K, .14 M imidazole malate, pH 6.0, 3.6% MPEG 5K, 0.03 M sodium acetate, pH 5.5 ...Details: protein: 10 mg/ml Dialysed in 100 milli-M NaCl, 50 milli-M sodium acetate, pH 5.5 Precipitant: 21 % PEG4K, .14 M imidazole malate, pH 6.0, 3.6% MPEG 5K, 0.03 M sodium acetate, pH 5.5 cryosoak: 40% CM1 (12.5 % di-ethylene glycol + 12.5 % MPD + 37.5 % 1,2-propanediol + 12.5 % DMSO ), 25 % MPEG 5K,0.1 M CHC (citric acid, HEPES, CHES) 90 % acid at pH 4.0 / 10 % basic at pH 10.0), 30 min soak.
PH range: 5.5-6.0 / Temp details: cooled incubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980035 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 23, 2016 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980035 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 17252 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.02 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rsym value: 0.09 / Net I/σ(I): 12.59
Reflection shellResolution: 2.44→2.59 Å / Redundancy: 6.84 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 3.29 / Num. unique obs: 2726 / CC1/2: 0.912 / Rsym value: 0.621 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K1J

5k1j


Resolution: 2.45→41.27 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.055 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.698 / ESU R Free: 0.303 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25386 467 5 %RANDOM
Rwork0.16853 ---
obs0.17261 8868 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.362 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å2-0 Å2-0 Å2
2---0.69 Å20 Å2
3---2.05 Å2
Refinement stepCycle: 1 / Resolution: 2.45→41.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 18 175 1985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191904
X-RAY DIFFRACTIONr_bond_other_d0.0020.021750
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.952603
X-RAY DIFFRACTIONr_angle_other_deg0.9734046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1325242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39523.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.70115287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.432159
X-RAY DIFFRACTIONr_chiral_restr0.0950.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212164
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02421
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0714.253957
X-RAY DIFFRACTIONr_mcbond_other4.0514.247955
X-RAY DIFFRACTIONr_mcangle_it6.3236.3361202
X-RAY DIFFRACTIONr_mcangle_other6.3266.341203
X-RAY DIFFRACTIONr_scbond_it5.084.972947
X-RAY DIFFRACTIONr_scbond_other5.0784.972947
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1687.1841402
X-RAY DIFFRACTIONr_long_range_B_refined12.17551.9292021
X-RAY DIFFRACTIONr_long_range_B_other12.17251.9562022
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 33 -
Rwork0.203 639 -
obs--100 %

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