[English] 日本語
Yorodumi
- PDB-3cn1: Human transthyretin (TTR) in complex with 3,5-Dibromo-4-hydroxyst... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cn1
TitleHuman transthyretin (TTR) in complex with 3,5-Dibromo-4-hydroxystilbene
ComponentsTransthyretin
Keywordshormone / Transport protein / Transthyretin / Tetramer
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / 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 / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / 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/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
2,6-dibromo-4-[(E)-2-phenylethenyl]phenol / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsConnelly, S. / Wilson, I.A.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Toward optimization of the linker substructure common to transthyretin amyloidogenesis inhibitors using biochemical and structural studies.
Authors: Johnson, S.M. / Connelly, S. / Wilson, I.A. / Kelly, J.W.
History
DepositionMar 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)28,2634
Polymers27,5552
Non-polymers7082
Water2,378132
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5268
Polymers55,1094
Non-polymers1,4164
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8750 Å2
ΔGint-47.3 kcal/mol
Surface area18510 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-11.6 kcal/mol
Surface area11380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.739, 85.035, 65.093
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-

LJ2

21B-128-

LJ2

31B-128-

LJ2

-
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) / Plasmid: pmmHA / Production host: Escherichia coli (E. coli) / Strain (production host): Epicurean Gold / References: UniProt: P02766
#2: Chemical ChemComp-LJ2 / 2,6-dibromo-4-[(E)-2-phenylethenyl]phenol / 3,5-Dibromo-4-hydroxystilbene


Mass: 354.037 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H10Br2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.15 Å3/Da / Density % sol: 42.69 %
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 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 24, 2007 / Details: Mirrors
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. all: 34319 / Num. obs: 36190 / % possible obs: 96.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.5 Å2 / Rsym value: 0.058 / Χ2: 0.962 / Net I/σ(I): 15.4
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 4.9 / Num. unique all: 3096 / Rsym value: 0.257 / Χ2: 0.769 / % possible all: 84.5

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→38.19 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.322 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1815 5 %RANDOM
Rwork0.16 ---
obs0.162 36134 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.582 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2---0.69 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.52→38.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 34 132 2046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221980
X-RAY DIFFRACTIONr_bond_other_d0.0030.021309
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.9642722
X-RAY DIFFRACTIONr_angle_other_deg1.0213.0023199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7615263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2624.25387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14715315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.649159
X-RAY DIFFRACTIONr_chiral_restr0.1210.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022246
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02397
X-RAY DIFFRACTIONr_nbd_refined0.2130.2280
X-RAY DIFFRACTIONr_nbd_other0.2050.21247
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2943
X-RAY DIFFRACTIONr_nbtor_other0.090.21098
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3120.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.216
X-RAY DIFFRACTIONr_mcbond_it2.5831.51544
X-RAY DIFFRACTIONr_mcbond_other0.9041.5481
X-RAY DIFFRACTIONr_mcangle_it3.11621973
X-RAY DIFFRACTIONr_scbond_it4.6383933
X-RAY DIFFRACTIONr_scangle_it5.8214.5732
X-RAY DIFFRACTIONr_rigid_bond_restr2.95934104
X-RAY DIFFRACTIONr_sphericity_free9.9773134
X-RAY DIFFRACTIONr_sphericity_bonded4.34733221
LS refinement shellResolution: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 114 -
Rwork0.133 2141 -
all-2255 -
obs--83.18 %

+
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