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- PDB-8ve1: Human transthyretin covalently modified with A2-derived stilbene ... -

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Basic information

Entry
Database: PDB / ID: 8ve1
TitleHuman transthyretin covalently modified with A2-derived stilbene in the canonical conformation
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Amyloidosis
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, 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-1WZ / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsBasanta, B. / Nugroho, K. / Yan, N. / Kline, G.M. / Tsai, F.J. / Wu, M. / Kelly, J.W. / Lander, G.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM142196 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AG067594 United States
CitationJournal: To Be Published
Title: The conformational landscape of human transthyretin revealed by cryo-EM
Authors: Basanta, B. / Nugroho, K. / Yan, N. / Kline, G.M. / Powers, E.T. / Tsai, F.J. / Wu, M. / Hansel-Harris, A. / Chen, J. / Forli, S. / Kelly, J.W. / Lander, G.C.
History
DepositionDec 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2576
Polymers55,6344
Non-polymers6232
Water48627
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13908.557 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-1WZ / 3-(dimethylamino)-5-[(E)-2-(4-hydroxy-3,5-dimethylphenyl)ethenyl]benzoic acid / (E)-3-(dimethylamino)-5-(4-hydroxy-3,5-dimethylstyryl)benzoic acid


Mass: 311.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C19H21NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Transthyretin / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.056136 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.6
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMPotassium ChlorideKCl1
28.66 mMPotassium PhosphateK2HPO41
31.34 mMPotassium PhosphateKH2PO41
41 mMEDTAC10H16N2O81
50.01 % w/vbeta-octyl glucoside (BOG)C14H28O61
61.25 % v/vDMSOC2H6OS1
SpecimenConc.: 0.41 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Graphene grids were treated with UV/ozone using the UVOCS T10xT10 system. A 10-minute warmup run was performed immediately prior to inserting and treating the grids for 4 minutes.
Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 279 K
Details: 3 uL of sample were applied onto the graphene side of the grid after it was mounted on the plunger (always at the same height), and immediately blotted for 6 seconds by holding a 1 x 6 cm ...Details: 3 uL of sample were applied onto the graphene side of the grid after it was mounted on the plunger (always at the same height), and immediately blotted for 6 seconds by holding a 1 x 6 cm piece of Whatman 1 filter paper parallel to the grid, in full contact. Timing was kept with the help of a metronome. The blotting countdown was started after the blotted liquid spot on the filter paper stopped spreading and the grid was plunged in liquid ethane at the same time the blotting paper was pulled back, in a single motion.

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 73000 X / Calibrated magnification: 88968 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 85 K / Temperature (min): 78 K
Image recordingAverage exposure time: 6.8 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4536
Image scansSampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 50

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Processing

EM software
IDNameVersionCategory
2PHENIX1.19.2_4158:model refinement
3Leginon3.6image acquisition
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 289981 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033728
ELECTRON MICROSCOPYf_angle_d0.4745094
ELECTRON MICROSCOPYf_dihedral_angle_d4.103500
ELECTRON MICROSCOPYf_chiral_restr0.046573
ELECTRON MICROSCOPYf_plane_restr0.003648

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