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- PDB-7q9n: Transthyretin complexed with (E)-4-(2-(naphthalen-2-yl)vinyl)benz... -

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Basic information

Entry
Database: PDB / ID: 7q9n
TitleTransthyretin complexed with (E)-4-(2-(naphthalen-2-yl)vinyl)benzene-1,2-diol
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Transthyretin / hormone-binding protein / thyroxine / transport / fluorescence / amyloid
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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) / Non-integrin membrane-ECM interactions / purine nucleobase 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
Chem-9PS / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsDerbyshire, D.J. / Hammarstrom, P. / von Castelmur, E. / Begum, A.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2019-04405 Sweden
CitationJournal: Acs Chem Neurosci / Year: 2023
Title: Transthyretin Binding Mode Dichotomy of Fluorescent trans -Stilbene Ligands.
Authors: Begum, A. / Zhang, J. / Derbyshire, D. / Wu, X. / Konradsson, P. / Hammarstrom, P. / von Castelmur, E.
History
DepositionNov 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 1, 2024Group: 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.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)26,7064
Polymers26,1812
Non-polymers5252
Water2,594144
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4128
Polymers52,3634
Non-polymers1,0494
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
MethodPISA
Unit cell
Length a, b, c (Å)42.545, 63.876, 85.137
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-201-

9PS

21A-201-

9PS

31A-201-

9PS

41B-201-

9PS

51B-201-

9PS

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 11 - 123 / Label seq-ID: 3 - 115

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 13090.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Evidence for alternative conformation for loop A:100-103 at crystal packing interface. Density not convincing enough to model; set occupancy to 50%.
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-9PS / 4-[(~{E})-2-naphthalen-2-ylethenyl]benzene-1,2-diol


Mass: 262.303 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H14O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: TTR:SB14 complex at 5.2mg/ml in 10mM sodium phosphate pH7.6 and 100mM potassium chloride was mixed 1:1 with 1.3-1.6M sodium citrate and 3.5% glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97993 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97993 Å / Relative weight: 1
ReflectionResolution: 1.45→42.55 Å / Num. obs: 41908 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 20.923 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.016 / Rrim(I) all: 0.057 / Χ2: 1.02 / Net I/σ(I): 19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.4713.31.57520270.7750.4411.6361.09100
7.94-42.559.50.0432820.9980.0150.0460.9691.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.23 Å38.06 Å
Translation3.23 Å38.06 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model

Resolution: 1.45→38.09 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.413 / SU ML: 0.04 / SU R Cruickshank DPI: 0.0606 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1708 2073 5 %RANDOM
Rwork0.1458 ---
obs0.1471 39765 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 79.4 Å2 / Biso mean: 26.665 Å2 / Biso min: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2--1.03 Å2-0 Å2
3----1.75 Å2
Refinement stepCycle: final / Resolution: 1.45→38.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1712 0 40 144 1896
Biso mean--29.51 42.18 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131810
X-RAY DIFFRACTIONr_bond_other_d0.0360.0151629
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.6772479
X-RAY DIFFRACTIONr_angle_other_deg2.5261.5823737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1815229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.8521.88469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.8815246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.98156
X-RAY DIFFRACTIONr_chiral_restr0.0770.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022040
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02416
X-RAY DIFFRACTIONr_rigid_bond_restr9.60533439
Refine LS restraints NCS

Ens-ID: 1 / Number: 3072 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 156 -
Rwork0.224 2895 -
all-3051 -
obs--99.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.01530.0032-0.0130.00490.00080.0142-0.00110.00030.0005-0.00040.0013-0.00050.00060.0008-0.00020.00060.0003-00.00440.00040.007924.38146.378112.3931
20.02680.01470.01090.0216-0.00540.0258-0.0010.0005-0.0042-0.00180.0006-0.00080.0004-0.0020.00040.000200.00010.0042-0.00050.007421.195225.84112.8486
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 124
2X-RAY DIFFRACTION2B11 - 125

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