[English] 日本語
Yorodumi
- PDB-4pvn: Neutron structure of human transthyretin (TTR) at room temperatur... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pvn
TitleNeutron structure of human transthyretin (TTR) at room temperature to 2.3A resolution (monochromatic)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / BETA SANDWICH / SERUM
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/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
DEUTERATED WATER / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFisher, S.J. / Blakeley, M.P. / Haupt, M. / Mason, S.A. / Cooper, J.B. / Mitchell, E.P. / Forsyth, V.T.
CitationJournal: IUCrJ / Year: 2014
Title: Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein
Authors: Haupt, M. / Blakeley, M.P. / Fisher, S.J. / Mason, S.A. / Cooper, J.B. / Mitchell, E.P. / Forsyth, V.T.
History
DepositionMar 18, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)28,0732
Polymers28,0732
Non-polymers00
Water1,51384
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)56,1474
Polymers56,1474
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)43.680, 86.260, 65.720
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-216-

DOD

21A-223-

DOD

31A-235-

DOD

41B-217-

DOD

51B-217-

DOD

61B-227-

DOD

71B-229-

DOD

-
Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 14036.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PALB, TTR / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02766
#2: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: D2O

-
Experimental details

-
Experiment

Experiment
MethodNumber of used crystals
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION1

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 2.15M SODIUM MALONATE, 23MG/ML PROTEIN, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
NUCLEAR REACTOROTHER12.42
SYNCHROTRONESRF ID23-120.9791
Detector
TypeIDDetectorDate
HE3 POSITION SENSITIVE DETECTOR1AREA DETECTORJun 23, 2010
ADSC QUANTUM 315r2CCDFeb 12, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Graphite (002)SINGLE WAVELENGTHMneutron1
2SI(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
12.421
20.97911
Reflection

Entry-ID: 4PVN

Resolution (Å)Num. allNum. obs% possible obs (%)Observed criterion σ(F)Observed criterion σ(I)Redundancy (%)Biso Wilson estimate (Å2)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2.3-52.276114381139599.31.31.33.514.90.15217.7
1.85-43.132171899.423.519.80.09327.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.3-2.422.60.6451.61613198.7
1.85-1.953.490.422.67297.9

-
Processing

Software
NameVersionClassification
MADSYSphasing
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_914)refinement
RETREATdata reduction
SCALAdata scaling
PHENIXphasing
Refinement

Baniso 13: 0 Å2 / Baniso 23: -0 Å2 / Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Method to determine structureResolution (Å)Refine-IDBaniso 11 (Å2)Baniso 12 (Å2)Baniso 22 (Å2)Baniso 33 (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)Bsol (Å2)ksol (e/Å3)Biso max (Å2)Biso mean (Å2)Biso min (Å2)Num. reflection RworkFOM work R setSU MLPhase error
2.3-52.276NEUTRON DIFFRACTION-1.80402.1028-0.29880.2620.20930.2118571113955.0198.6211.3527.2890.6
MOLECULAR REPLACEMENT1.95-43.13X-RAY DIFFRACTION-0.2524-0-0.10380.35620.18510.1560.157493318655599.4421.3434.7120.39197.6429.5611.15177220.82150.1817.27
Refinement stepCycle: LAST / Resolution: 2.3→52.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1801 0 0 84 1885
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0123800
NEUTRON DIFFRACTIONf_angle_d1.3096774
NEUTRON DIFFRACTIONf_chiral_restr0.084289
NEUTRON DIFFRACTIONf_plane_restr0.007644
NEUTRON DIFFRACTIONf_dihedral_angle_d15.6271029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection allTotal num. of bins used% reflection obs (%)
2.3001-2.53150.32181390.25822630NEUTRON DIFFRACTION2769498
2.5315-2.89780.31331400.23932660NEUTRON DIFFRACTION2800499
2.8978-3.65080.24661440.19952734NEUTRON DIFFRACTION28784100
3.6508-52.28980.22081480.17982800NEUTRON DIFFRACTION2948498
1.95-2.05280.22591290.18532512X-RAY DIFFRACTION26417100
2.0528-2.18140.21021340.15552482X-RAY DIFFRACTION26167100
2.1814-2.34980.17941300.1492499X-RAY DIFFRACTION26297100
2.3498-2.58630.19391330.15422507X-RAY DIFFRACTION26407100
2.5863-2.96050.18651340.15912530X-RAY DIFFRACTION26647100
2.9605-3.72950.17331330.15072554X-RAY DIFFRACTION2687799
3.7295-43.14050.17611400.15472638X-RAY DIFFRACTION2778798

+
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