[English] 日本語
Yorodumi
- PDB-1e5a: Structure of human transthyretin complexed with bromophenols: a n... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1e5a
TitleStructure of human transthyretin complexed with bromophenols: a new mode of binding
ComponentsTRANSTHYRETIN
KeywordsPROTEIN TRANSPORT / TRANSPORT(THYROXINE) / ENVIRONMENTAL POLLUTANTS
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
2,4,6-TRIBROMOPHENOL / Transthyretin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGhosh, M. / Meerts, I.A.T.M. / Cook, A. / Bergman, A. / Brouwer, A. / Johnson, L.N.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Structure of Human Transthyretin Complexed with Bromophenols : A New Mode of Binding
Authors: Ghosh, M. / Meerts, I.A.T.M. / Cook, A. / Bergman, A. / Brouwer, A. / Johnson, L.N.
#1: Journal: J.Mol.Biol. / Year: 1978
Title: Structure of Prealbumin: Secondary,Tertiary and Quaternary Interactions Determined by Fourier Refinment at 1.8A.
Authors: Blake, C.C.F. / Geisow, M.J. / Oatley, S.J. / Rerat, C. / Rerat, B.
#2: Journal: Nature / Year: 1977
Title: Protein-DNA and Protein-Hormone Interactions in Prealbumin : A Model of the Thyroid Hormone Nuclear Receptor ?
Authors: Blake, C.C.F. / Oatley, S.J.
History
DepositionJul 20, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2000Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 13, 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)28,2164
Polymers27,5552
Non-polymers6622
Water2,648147
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules

A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4338
Polymers55,1094
Non-polymers1,3234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area8280 Å2
ΔGint-33.6 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.800, 84.900, 64.400
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-999-

TBP

21A-999-

TBP

31B-999-

TBP

41A-2081-

HOH

51B-2024-

HOH

61B-2058-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9913, -0.1309, 0.0143), (-0.131, 0.9914, -0.0038), (-0.0136, -0.0057, -0.9999)
Vector: 84.667, 5.445, 32.652)
DetailsTHIS COORDINATE SET COMPRISES TWO CHAINS REPRESENTING TWO CHEMICALLY EQUIVALENT, BUT CRYSTALLOGRAPHICALLY DISTINCT, ENTITIES. THE OTHER HALF OF THE COMPLETE TETRAMER MAY BEGENERATED FROM THIS DIMER BY THE APPLICATION OF THE CRYSTALLOGRAPHIC TWO-FOLD AXIS PARALLEL TO Z THROUGH THE ORIGIN OF THIS COORDINATE SYSTEM.

-
Components

#1: Protein TRANSTHYRETIN / PREALBUMIN / ATTR / TBPA


Mass: 13777.360 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Organ: PLASMA / References: UniProt: P02766
#2: Chemical ChemComp-TBP / 2,4,6-TRIBROMOPHENOL


Mass: 330.799 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H3Br3O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: THYROID HORMONE-BINDING PROTEIN. PROBABLY TRANSPORTS THYROXINE FROM THE BLOODSTREAM TO ...FUNCTION: THYROID HORMONE-BINDING PROTEIN. PROBABLY TRANSPORTS THYROXINE FROM THE BLOODSTREAM TO THE BRAIN. TISSUE SPECIFICITY: MOST ABUNDANT IN THE CHOROID PLEXUS. ALSO PRESENT IN THE LIVER. DISEASE: FAMILIAL AMYLOIDOTIC POLYNEUROPATHY (FAP) IS A LATE-ONSET DISEASE WITH A DOMINANT MODE OF INHERITANCE. PROTEIN FIBRILS FORM IN MANY TISSUES, AND DEPOSITION AROUND NERVES CAUSES PERIPHERAL AND AUTONOMIC NEUROPATHY. SYMPTOMS INCLUDE PARALYSIS, CHRONIC DIARRHEA, AND CARDIOMYOPATHY. MANY SEQUENCE VARIANTS HAVE BEEN IDENTIFIED IN AMYLOID FIBRILS FROM PATIENTS WITH FAP. SOME FORMS OF AMYLOID DEPOSITION ARE THE CAUSE OF FAMILIAL AMYLOIDOTIC CARDIOMYOPATHY (FAC). SOME FORM OF FAP ARE ASSOCIATED WITH CARPAL TUNNEL SYNDROME (CTS). DISEASE: IN SENILE SYSTEMIC AMYLOIDOSIS (SSA) MECHANISMS OTHER THAN VARIATIONS IN THE PRIMARY STRUCTURE OF TTR ARE IMPORTANT FOR THE FIBRIL FORMATION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growpH: 5.5 / Details: pH 5.50
Crystal grow
*PLUS
Temperature: 295 K / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.37 mMTTR1drop
214.6 mMTBP1drop
3100 mMTris1drop
4100 mM1dropNaCl
51 mMEDTA1drop
650-55 %ammonium sulfate1reservoir
7100 mMsodium citrate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998 / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 20818 / % possible obs: 92.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 29.4
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.345 / % possible all: 92.8
Reflection
*PLUS
Num. measured all: 249678
Reflection shell
*PLUS
% possible obs: 92.8 % / Num. unique obs: 2543

-
Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TTA

1tta


Resolution: 1.8→20 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE TRIBROMOPHENOL MOLECULE IS LOCATED NEAR THE THYROXINE BINDING SITE BUT NOT SYMMETRICALLY ON THE CRYSTALLOGRAPHIC Z AXIS AS IS THE CASE FOR A SIMILAR COMPOUND PENTABROMOPHENOL. THERE ARE ...Details: THE TRIBROMOPHENOL MOLECULE IS LOCATED NEAR THE THYROXINE BINDING SITE BUT NOT SYMMETRICALLY ON THE CRYSTALLOGRAPHIC Z AXIS AS IS THE CASE FOR A SIMILAR COMPOUND PENTABROMOPHENOL. THERE ARE TWO SYMMETRY EQUIVALENT POSITIONS ABOUT THE TWO FOLD AXIS, EACH WITH AN OCCUPANCY .5 AT EACH OF THE BINDING SITES. WATER MOLECULES W91, W306, W336 LOCATED ON THE SAME SYMMETRY AXIS WERE KEPT FIXED IN POSITION DURING THE REFINEMENT. RESIDUES 1-9 AND 126-127 OF BOTH THE CHAINS WERE NOT OBSERVED IN THE ELECTRON DENSITY MAP.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1065 5 %RANDOM
Rwork0.214 ---
obs0.214 20764 99.9 %-
Displacement parametersBiso mean: 18.2 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 20 147 1959
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.8→1.94 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.286 226 5 %
Rwork0.256 3690 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3246.PAR246.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

+
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