[English] 日本語
Yorodumi
- PDB-6fwd: Crystal structure of human transthyretin double mutant R34G/T119M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fwd
TitleCrystal structure of human transthyretin double mutant R34G/T119M at pH 5.5
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Amyloid / Gatekeeper / Aggregation / Stability
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, 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: 1.576 Å
AuthorsEsperante, S. / Ventura, S. / Reverter, D. / Varejao, N.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Disease-associated mutations impacting BC-loop flexibility trigger long-range transthyretin tetramer destabilization and aggregation.
Authors: Esperante, S.A. / Varejao, N. / Pinheiro, F. / Sant'Anna, R. / Luque-Ortega, J.R. / Alfonso, C. / Sora, V. / Papaleo, E. / Rivas, G. / Reverter, D. / Ventura, S.
History
DepositionMar 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)27,4152
Polymers27,4152
Non-polymers00
Water3,855214
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)54,8294
Polymers54,8294
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area6410 Å2
ΔGint-50 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.127, 63.958, 85.978
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11B-298-

HOH

-
Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13707.311 Da / Num. of mol.: 2 / Mutation: R34G, T119M
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 41.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 7% glycerol, 1.3 M sodium citrate, pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.576→63.958 Å / Num. obs: 31271 / % possible obs: 93 % / Redundancy: 7.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.047 / Rrim(I) all: 0.122 / Net I/σ(I): 15.7 / Num. measured all: 232010
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.576-1.5817.71.33126353420.6830.5261.4332.798.3
7.31-63.9586.20.04725184090.9970.0210.05236.6100

-
Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASER1.7.3-928phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F41

1f41


Resolution: 1.576→51.317 Å / FOM work R set: 0.8465 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 1555 4.99 %
Rwork0.1972 29615 -
obs0.1987 31170 92.7 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.231 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso max: 74.58 Å2 / Biso mean: 23.28 Å2 / Biso min: 10.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.2332 Å20 Å2-0 Å2
2--5.6517 Å2-0 Å2
3----4.4185 Å2
Refinement stepCycle: final / Resolution: 1.576→51.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 0 214 1983
Biso mean---34.32 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161828
X-RAY DIFFRACTIONf_angle_d1.6812495
X-RAY DIFFRACTIONf_chiral_restr0.124283
X-RAY DIFFRACTIONf_plane_restr0.011318
X-RAY DIFFRACTIONf_dihedral_angle_d15.356641
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5757-1.62660.34191600.29242830299099
1.6266-1.68470.34261620.279728242986100
1.6847-1.75220.31651510.253828723023100
1.7522-1.8320.22951480.218828362984100
1.832-1.92850.25321050.19922507261286
1.9285-2.04940.22741100.18972193230376
2.0494-2.20760.21191440.188728703014100
2.2076-2.42980.21251340.1882465259985
2.4298-2.78130.23351220.19362330245280
2.7813-3.50410.211440.18612819296395
3.5041-51.34380.21221750.1843069324499
Refinement TLS params.Method: refined / Origin x: -22.5871 Å / Origin y: -15.8698 Å / Origin z: -12.9178 Å
111213212223313233
T0.1189 Å2-0.0027 Å2-0.0026 Å2-0.1482 Å2-0.0001 Å2--0.122 Å2
L0.5615 °20.0964 °20.0778 °2-0.8627 °2-0.0164 °2--0.8793 °2
S-0.0137 Å °0.0887 Å °-0.0158 Å °-0.0311 Å °0.0364 Å °-0.0248 Å °0.0455 Å °-0.016 Å °-0.0215 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 125
2X-RAY DIFFRACTION1allB10 - 125
3X-RAY DIFFRACTION1allS1 - 214

+
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