[English] 日本語
Yorodumi
- PDB-9h7i: Human Transthyretin in Complex with 4-(1H-pyrazol-4-yl)quinoline -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9h7i
TitleHuman Transthyretin in Complex with 4-(1H-pyrazol-4-yl)quinoline
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Amyloidosis / Retinol / Thyroxine / RBP
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) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsChen, W.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
University of College LondonBXTX United Kingdom
Other privateHN9A
Citation
Journal: Plos One / Year: 2025
Title: Fragment-based drug discovery for transthyretin kinetic stabilisers using a novel capillary zone electrophoresis method.
Authors: Chen, W.
#1: Journal: Biorxiv / Year: 2025
Title: Fragment-Based Drug Discovery for Transthyretin Kinetic Stabilisers Using a Novel Capillary Zone Electrophoresis Method
Authors: Chen, W.
History
DepositionOct 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation / citation_author

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9855
Polymers27,5552
Non-polymers4313
Water1,910106
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,97010
Polymers55,1094
Non-polymers8616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area8210 Å2
ΔGint-66 kcal/mol
Surface area18010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.060, 42.300, 64.770
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-202-

A1ISS

21A-202-

A1ISS

31A-202-

A1ISS

41B-201-

A1ISS

51B-201-

A1ISS

61B-201-

A1ISS

71A-302-

HOH

81B-321-

HOH

-
Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13777.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Blood / Gene: TTR, PALB / Production host: Homo sapiens (human) / References: UniProt: P02766
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-A1ISS / 4-(1H-pyrazol-4-yl)quinoline


Mass: 195.220 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM HEPES, 200 mM CaCl2, 28% v/v PEG400, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.21→35.55 Å / Num. obs: 70465 / % possible obs: 98.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.019 / Net I/σ(I): 19.2
Reflection shellResolution: 1.21→1.25 Å / Rmerge(I) obs: 0.61 / Num. unique obs: 4875 / Rpim(I) all: 0.291

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→35.55 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.081 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18339 3553 5 %RANDOM
Rwork0.15366 ---
obs0.15513 66868 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.173 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å20 Å2
2--0.15 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.21→35.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1694 0 31 106 1831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191809
X-RAY DIFFRACTIONr_bond_other_d0.0020.021633
X-RAY DIFFRACTIONr_angle_refined_deg2.1751.962486
X-RAY DIFFRACTIONr_angle_other_deg0.95733759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4065238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.34223.560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08615250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.18153
X-RAY DIFFRACTIONr_chiral_restr0.1370.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212036
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02407
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_it2.9041.454924
X-RAY DIFFRACTIONr_mcbond_other2.9021.454925
X-RAY DIFFRACTIONr_mcangle_it3.6242.1881153
X-RAY DIFFRACTIONr_mcangle_other3.6752.1921154
X-RAY DIFFRACTIONr_scbond_it4.0421.749885
X-RAY DIFFRACTIONr_scbond_other4.0411.749886
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6252.5131328
X-RAY DIFFRACTIONr_long_range_B_refined4.66312.9771958
X-RAY DIFFRACTIONr_long_range_B_other4.66212.9791959
X-RAY DIFFRACTIONr_rigid_bond_restr8.42333441
X-RAY DIFFRACTIONr_sphericity_free15.494524
X-RAY DIFFRACTIONr_sphericity_bonded10.81453467
LS refinement shellResolution: 1.214→1.246 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 251 -
Rwork0.228 4616 -
obs--93.2 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more