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- PDB-4mrb: Wild Type Human Transthyretin pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 4mrb
TitleWild Type Human Transthyretin pH 7.5
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Hormone Transporter / Thyroxine T4
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/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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsChen, W.J. / Wood, S.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Proteolytic cleavage of Ser52Pro variant transthyretin triggers its amyloid fibrillogenesis.
Authors: Mangione, P.P. / Porcari, R. / Gillmore, J.D. / Pucci, P. / Monti, M. / Porcari, M. / Giorgetti, S. / Marchese, L. / Raimondi, S. / Serpell, L.C. / Chen, W. / Relini, A. / Marcoux, J. / ...Authors: Mangione, P.P. / Porcari, R. / Gillmore, J.D. / Pucci, P. / Monti, M. / Porcari, M. / Giorgetti, S. / Marchese, L. / Raimondi, S. / Serpell, L.C. / Chen, W. / Relini, A. / Marcoux, J. / Clatworthy, I.R. / Taylor, G.W. / Tennent, G.A. / Robinson, C.V. / Hawkins, P.N. / Stoppini, M. / Wood, S.P. / Pepys, M.B. / Bellotti, V.
History
DepositionSep 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)27,6354
Polymers27,5552
Non-polymers802
Water1,47782
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2708
Polymers55,1094
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6480 Å2
ΔGint-75 kcal/mol
Surface area17580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.210, 41.320, 63.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-346-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13777.360 Da / Num. of mol.: 2 / Fragment: UNP residues 21-147 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02766
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 1.99 Å3/Da / Density % sol: 38.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 100mM HEPES, 200mM CaCl2, 28% PEG400 v/v, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 15, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.27→42.1 Å / Num. all: 58650 / Num. obs: 58474 / % possible obs: 99.7 %
Reflection shellResolution: 1.27→1.3 Å / Rmerge(I) obs: 0.626

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→35.01 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.155 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20897 2962 5.1 %RANDOM
Rwork0.16609 ---
obs0.16824 55633 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.394 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0 Å20 Å2
2--0.44 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.27→35.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1631 0 2 82 1715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0191734
X-RAY DIFFRACTIONr_bond_other_d0.0020.021561
X-RAY DIFFRACTIONr_angle_refined_deg2.7981.9292388
X-RAY DIFFRACTIONr_angle_other_deg1.1933589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2535234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34623.33360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55515232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.124153
X-RAY DIFFRACTIONr_chiral_restr0.1920.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211968
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02391
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_it3.7381.805906
X-RAY DIFFRACTIONr_mcbond_other3.7341.803905
X-RAY DIFFRACTIONr_mcangle_it4.0932.711129
X-RAY DIFFRACTIONr_mcangle_other4.0942.7121130
X-RAY DIFFRACTIONr_scbond_it4.5162.12828
X-RAY DIFFRACTIONr_scbond_other4.512.119828
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0363.0791252
X-RAY DIFFRACTIONr_long_range_B_refined4.84415.2731804
X-RAY DIFFRACTIONr_long_range_B_other4.78215.081772
X-RAY DIFFRACTIONr_rigid_bond_restr9.24133295
X-RAY DIFFRACTIONr_sphericity_free25.723517
X-RAY DIFFRACTIONr_sphericity_bonded17.13953309
LS refinement shellResolution: 1.27→1.303 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 218 -
Rwork0.196 4042 -
obs--99.6 %

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