[English] 日本語
Yorodumi
- PDB-3m1o: Human Transthyretin (TTR) complexed with 2-((3,5-dichloro-4-hydro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3m1o
TitleHuman Transthyretin (TTR) complexed with 2-((3,5-dichloro-4-hydroxyphenyl)amino)benzoic acid
ComponentsTransthyretin
KeywordsHORMONE / AMYLOID / INHIBITOR / AMYLOIDOSIS / DISEASE MUTATION / GAMMA-CARBOXYGLUTAMIC ACID / GLYCOPROTEIN / NEUROPATHY / SECRETED / THYROID HORMONE / TRANSPORT
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) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / Retinoid metabolism and transport / hormone activity ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / 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
Chem-CJZ / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKolstoe, S.E. / Wood, S.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Trapping of palindromic ligands within native transthyretin prevents amyloid formation.
Authors: Kolstoe, S.E. / Mangione, P.P. / Bellotti, V. / Taylor, G.W. / Tennent, G.A. / Deroo, S. / Morrison, A.J. / Cobb, A.J. / Coyne, A. / McCammon, M.G. / Warner, T.D. / Mitchell, J. / Gill, R. / ...Authors: Kolstoe, S.E. / Mangione, P.P. / Bellotti, V. / Taylor, G.W. / Tennent, G.A. / Deroo, S. / Morrison, A.J. / Cobb, A.J. / Coyne, A. / McCammon, M.G. / Warner, T.D. / Mitchell, J. / Gill, R. / Smith, M.D. / Ley, S.V. / Robinson, C.V. / Wood, S.P. / Pepys, M.B.
History
DepositionMar 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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)28,1514
Polymers27,5552
Non-polymers5962
Water4,486249
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3028
Polymers55,1094
Non-polymers1,1924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)42.525, 85.390, 63.625
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-128-

CJZ

21A-128-

CJZ

31A-128-

CJZ

41A-128-

CJZ

51A-128-

CJZ

61A-128-

CJZ

71B-128-

CJZ

81B-128-

CJZ

91B-128-

CJZ

101B-128-

CJZ

111B-128-

CJZ

121B-128-

CJZ

-
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 / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-CJZ / 2-[(3,5-dichloro-4-hydroxyphenyl)amino]benzoic acid


Mass: 298.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H9Cl2NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 25- 32% V/V PEG550-MONOMETHYL ETHER, 70 MM NAAC BUFFER PH 4-5 AND 100 MM NACL, VAPOR DIFFUSION, HANGING DROP, temperature 298K
PH range: 4-5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.2→38.07 Å / Num. all: 73223 / Num. obs: 73223 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 9.9 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.2
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 3.4 / Num. unique all: 10525 / % possible all: 100

-
Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC& Phenix.refinerefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ROX

2rox


Resolution: 1.2→35.453 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.171 3687 -RANDOM
Rwork0.143 ---
all0.144 73132 --
obs-73078 99.92 %-
Displacement parametersBiso mean: 12.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.4915 Å2-0 Å20 Å2
2---0.887 Å2-0 Å2
3---0.3955 Å2
Refinement stepCycle: LAST / Resolution: 1.2→35.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1753 0 38 249 2040
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONfOND0.021
X-RAY DIFFRACTIONfNGLE1.851
X-RAY DIFFRACTIONfHIRALITY0.108
X-RAY DIFFRACTIONfLANARITY0.012
X-RAY DIFFRACTIONfIHEDRAL17.802
LS refinement shellResolution: 1.2→1.2158 Å
RfactorNum. reflection% reflection
Rfree0.222 124 -
Rwork0.1923 --
obs-2667 100 %

+
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