[English] 日本語
Yorodumi
- PDB-5nfw: Neutron structure of human transthyretin (TTR) S52P mutant at roo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nfw
TitleNeutron structure of human transthyretin (TTR) S52P mutant at room temperature to 1.8A resolution (quasi-Laue)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / transthyretin / prealbumin / homotetramer
Function / homology
Function and homology information


Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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 / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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 / NEUTRON DIFFRACTION / NUCLEAR REACTOR / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYee, A.W. / Moulin, M. / Blakeley, M.P. / Cooper, J.B. / Haertlein, M. / Mitchell, E.P. / Forsyth, V.T.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/C015452/1 United Kingdom
Engineering and Physical Sciences Research CouncilGR/R99393/01 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: A molecular mechanism for transthyretin amyloidogenesis.
Authors: Yee, A.W. / Aldeghi, M. / Blakeley, M.P. / Ostermann, A. / Mas, P.J. / Moulin, M. / de Sanctis, D. / Bowler, M.W. / Mueller-Dieckmann, C. / Mitchell, E.P. / Haertlein, M. / de Groot, B.L. / ...Authors: Yee, A.W. / Aldeghi, M. / Blakeley, M.P. / Ostermann, A. / Mas, P.J. / Moulin, M. / de Sanctis, D. / Bowler, M.W. / Mueller-Dieckmann, C. / Mitchell, E.P. / Haertlein, M. / de Groot, B.L. / Boeri Erba, E. / Forsyth, V.T.
History
DepositionMar 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 2.0Jan 9, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_struct_assembly ...atom_site / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 3.0Mar 20, 2019Group: Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_database_proc
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _citation.country / _citation.journal_abbrev / _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
Revision 3.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)28,0932
Polymers28,0932
Non-polymers00
Water73941
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)56,1874
Polymers56,1874
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)43.778, 86.299, 65.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 14046.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pET-M11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.9M sodium malonate pD 6.4, 25mg/ml protein

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
NUCLEAR REACTORILL LADI12.90-3.90
SYNCHROTRONESRF ID30B20.9763
Detector
TypeIDDetectorDate
LADI III1IMAGE PLATEJun 14, 2016
DECTRIS PILATUS 6M-F2PIXELJul 28, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
12.91
23.91
30.97631
Reflection

Entry-ID: 5NFW

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
1.8-39.0422333879.55.20.1590.06118.4
1.8-33.541845998.76.50.0480.021233.4
Reflection shell

Resolution: 1.8→1.9 Å

Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allDiffraction-ID% possible all
2.80.2024.918060.112154.3
6.60.0720.533890.029299.5

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
LAUEGENdata reduction
XDSdata reduction
LSCALEdata scaling
SCALAdata scaling
Cootmodel building
REFMACphasing
Refinement

% reflection Rfree: 10.01 % / Cross valid method: NONE / Method to determine structure: MOLECULAR REPLACEMENT / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 5CLX

5clx

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection obs (%)SU MLDiffraction-IDσ(F)Phase error
1.8-39.042X-RAY DIFFRACTION0.21030.17240.176223352333898.410.1521.9919.11
1.8-33.54NEUTRON DIFFRACTION0.26070.21140.216418471845377.820.22124.72
Refinement stepCycle: LAST / Resolution: 1.8→39.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 0 41 1835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154007
X-RAY DIFFRACTIONf_angle_d1.6287160
X-RAY DIFFRACTIONf_dihedral_angle_d13.1881943
X-RAY DIFFRACTIONf_chiral_restr0.074286
X-RAY DIFFRACTIONf_plane_restr0.009774
NEUTRON DIFFRACTIONf_bond_d0.0154007
NEUTRON DIFFRACTIONf_angle_d1.6287160
NEUTRON DIFFRACTIONf_dihedral_angle_d13.1881943
NEUTRON DIFFRACTIONf_chiral_restr0.074286
NEUTRON DIFFRACTIONf_plane_restr0.009774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83680.22831380.17061238X-RAY DIFFRACTION99
1.8368-1.87670.20321350.16141223X-RAY DIFFRACTION100
1.8767-1.92030.20261370.15651232X-RAY DIFFRACTION100
1.9203-1.96840.18591360.15331215X-RAY DIFFRACTION99
1.9684-2.02160.2111350.15491229X-RAY DIFFRACTION99
2.0216-2.08110.20941370.15711228X-RAY DIFFRACTION99
2.0811-2.14820.22061340.15871207X-RAY DIFFRACTION98
2.1482-2.2250.19281320.16441181X-RAY DIFFRACTION96
2.225-2.31410.2271300.15871179X-RAY DIFFRACTION94
2.3141-2.41940.21591370.17931226X-RAY DIFFRACTION99
2.4194-2.54690.25431380.17681246X-RAY DIFFRACTION99
2.5469-2.70650.21661370.18151236X-RAY DIFFRACTION99
2.7065-2.91540.22761390.18061251X-RAY DIFFRACTION99
2.9154-3.20860.20111380.19621244X-RAY DIFFRACTION99
3.2086-3.67260.23081410.17211272X-RAY DIFFRACTION99
3.6726-4.62590.18961380.15611231X-RAY DIFFRACTION95
4.6259-39.0510.19671530.18941365X-RAY DIFFRACTION99
1.8001-1.84870.3238880.3337795NEUTRON DIFFRACTION50
1.8487-1.90310.331030.2937928NEUTRON DIFFRACTION57
1.9031-1.96460.27751180.26251063NEUTRON DIFFRACTION66
1.9646-2.03480.28111300.22981158NEUTRON DIFFRACTION72
2.0348-2.11620.27441350.21981222NEUTRON DIFFRACTION75
2.1162-2.21250.24751440.21211303NEUTRON DIFFRACTION80
2.2125-2.32910.26691450.21231305NEUTRON DIFFRACTION80
2.3291-2.4750.27621470.21681318NEUTRON DIFFRACTION81
2.475-2.6660.27471520.20451359NEUTRON DIFFRACTION83
2.666-2.93420.24851590.20721440NEUTRON DIFFRACTION87
2.9342-3.35840.25191670.21611494NEUTRON DIFFRACTION91
3.3584-4.230.25531720.16921554NEUTRON DIFFRACTION93
4.23-33.54660.22351870.18361667NEUTRON DIFFRACTION94

+
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://pdbjlvh1.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