[English] 日本語
Yorodumi
- PDB-9rsp: Cryogenic crystal structure of the perdeuterated TTR mutant V30M ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9rsp
TitleCryogenic crystal structure of the perdeuterated TTR mutant V30M at pH5.
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Transthyretin Amyloidosis V30M mutation Familial amyloidotic polyneuropathy
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, 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: 1.61 Å
AuthorsSagot, J. / Fisher, S.Z. / Forsyth, T.V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryogenic crystal structure of the perdeuterated TTR mutant V30M at pH5.
Authors: Sagot, J. / Fisher, S.Z. / Forsyth, T.V.
History
DepositionJul 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)25,2762
Polymers25,2762
Non-polymers00
Water3,135174
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)50,5534
Polymers50,5534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6280 Å2
ΔGint-45 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.276, 64.258, 85.586
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-235-

HOH

21A-270-

HOH

31B-237-

HOH

41B-304-

HOH

-
Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12638.168 Da / Num. of mol.: 2 / Mutation: V30M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.8 % / Description: cubic crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 1.7 M Sodium Malonate pH 5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.7293 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 1.61→43.29 Å / Num. obs: 31442 / % possible obs: 99.6 % / Redundancy: 13.5 % / Biso Wilson estimate: 18.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.051 / Net I/σ(I): 33.7
Reflection shellResolution: 1.61→1.67 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.359 / Num. unique obs: 3047 / CC1/2: 0.971 / Rrim(I) all: 0.374 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
PHENIX1.21refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→21.33 Å / SU ML: 0.1424 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.9162
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2006 1523 4.85 %
Rwork0.1722 29872 -
obs0.1736 31395 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.94 Å2
Refinement stepCycle: LAST / Resolution: 1.61→21.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 0 174 1952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561978
X-RAY DIFFRACTIONf_angle_d0.82552724
X-RAY DIFFRACTIONf_chiral_restr0.0579301
X-RAY DIFFRACTIONf_plane_restr0.0083359
X-RAY DIFFRACTIONf_dihedral_angle_d13.9459725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.660.26511450.20762632X-RAY DIFFRACTION98.76
1.66-1.720.20541290.19082694X-RAY DIFFRACTION99.47
1.72-1.790.231440.18492639X-RAY DIFFRACTION99.57
1.79-1.870.22311390.17892674X-RAY DIFFRACTION99.75
1.87-1.970.1721410.16812688X-RAY DIFFRACTION99.79
1.97-2.10.20431350.16792707X-RAY DIFFRACTION99.79
2.1-2.260.19781150.16462726X-RAY DIFFRACTION99.86
2.26-2.490.21041500.1822705X-RAY DIFFRACTION100
2.49-2.840.23421410.1812741X-RAY DIFFRACTION100
2.84-3.580.18681490.17012779X-RAY DIFFRACTION100

+
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