[English] 日本語
Yorodumi
- PDB-3imv: Transthyretin in complex with (E)-4-(4-aminostyryl)-2,6-dibromoaniline -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3imv
TitleTransthyretin in complex with (E)-4-(4-aminostyryl)-2,6-dibromoaniline
ComponentsTransthyretin
KeywordsHORMONE / Growth Factor / Amyloid / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Polymorphism / Polyneuropathy / Retinol-binding / Secreted / Thyroid hormone / Transport / Vitamin A
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/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
Chem-IW5 / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsConnelly, S. / Wilson, I.A.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: A substructure combination strategy to create potent and selective transthyretin kinetic stabilizers that prevent amyloidogenesis and cytotoxicity.
Authors: Choi, S. / Reixach, N. / Connelly, S. / Johnson, S.M. / Wilson, I.A. / Kelly, J.W.
History
DepositionAug 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...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_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2914
Polymers27,5552
Non-polymers7362
Water2,018112
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5828
Polymers55,1094
Non-polymers1,4724
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)42.781, 85.169, 64.158
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-128-

IW5

21A-128-

IW5

31A-128-

IW5

41B-128-

IW5

51B-128-

IW5

61B-128-

IW5

71B-128-

IW5

-
Components

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


Mass: 13777.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pmmHA / Production host: Escherichia coli (E. coli) / Strain (production host): Epicuran gold / References: UniProt: P02766
#2: Chemical ChemComp-IW5 / 4-[(E)-2-(4-aminophenyl)ethenyl]-2,6-dibromoaniline


Mass: 368.066 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12Br2N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature using the vapor-diffusion sitting drop method. Crystals were grown from 1. ...Details: The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature using the vapor-diffusion sitting drop method. Crystals were grown from 1.395 M sodium citrate, 3.5% v/v glycerol at pH 5.5. The crystals were frozen using a cryo-protectant solution of 1.395 M sodium citrate, pH 5.5, containing 10% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9797 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
Details: Flat mirror (vertical focusing), single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.47→85.13 Å / Num. obs: 39462 / % possible obs: 97.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 21.7 Å2 / Rsym value: 0.034 / Net I/σ(I): 36.5
Reflection shellResolution: 1.47→1.53 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 3951 / Rsym value: 0.523 / % possible all: 99.4

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2QGB

2qgb


Resolution: 1.47→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.221 / WRfactor Rwork: 0.186 / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.882 / SU B: 2.208 / SU ML: 0.039 / SU R Cruickshank DPI: 0.083 / SU Rfree: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1981 5 %RANDOM
Rwork0.168 ---
obs0.169 39433 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.8 Å2 / Biso mean: 24.48 Å2 / Biso min: 9.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.47→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 36 112 2055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222015
X-RAY DIFFRACTIONr_bond_other_d0.0010.021344
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9652777
X-RAY DIFFRACTIONr_angle_other_deg1.0343.0013291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9375274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53424.09188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42815329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7291510
X-RAY DIFFRACTIONr_chiral_restr0.10.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212298
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02408
X-RAY DIFFRACTIONr_mcbond_it1.8981.51220
X-RAY DIFFRACTIONr_mcbond_other0.9191.5489
X-RAY DIFFRACTIONr_mcangle_it3.00122006
X-RAY DIFFRACTIONr_scbond_it3.8883795
X-RAY DIFFRACTIONr_scangle_it5.9064.5749
X-RAY DIFFRACTIONr_rigid_bond_restr1.93233359
X-RAY DIFFRACTIONr_sphericity_free9.1793114
X-RAY DIFFRACTIONr_sphericity_bonded4.73833285
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 121 -
Rwork0.234 2478 -
all-2599 -
obs--88.49 %

+
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