[English] 日本語
Yorodumi
- PDB-4gfx: Crystal structure of the N-terminal domain of TXNIP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gfx
TitleCrystal structure of the N-terminal domain of TXNIP
ComponentsThioredoxin-interacting protein
KeywordsPROTEIN BINDING / Arrestin-like fold
Function / homology
Function and homology information


cellular response to tumor cell / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of cell division / enzyme inhibitor activity / Regulation of FOXO transcriptional activity by acetylation / The NLRP3 inflammasome / platelet-derived growth factor receptor signaling pathway / Purinergic signaling in leishmaniasis infection / response to glucose / response to mechanical stimulus ...cellular response to tumor cell / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of cell division / enzyme inhibitor activity / Regulation of FOXO transcriptional activity by acetylation / The NLRP3 inflammasome / platelet-derived growth factor receptor signaling pathway / Purinergic signaling in leishmaniasis infection / response to glucose / response to mechanical stimulus / keratinocyte differentiation / response to progesterone / response to hydrogen peroxide / Cytoprotection by HMOX1 / response to calcium ion / protein import into nucleus / protein transport / response to estradiol / regulation of cell population proliferation / response to oxidative stress / inflammatory response / positive regulation of apoptotic process / response to xenobiotic stimulus / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / cytosol / cytoplasm
Similarity search - Function
: / Immunoglobulin-like - #640 / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / Immunoglobulin E-set / Immunoglobulin-like ...: / Immunoglobulin-like - #640 / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Thioredoxin-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHwang, J. / Kim, M.H.
CitationJournal: Nat Commun / Year: 2014
Title: The structural basis for the negative regulation of thioredoxin by thioredoxin-interacting protein.
Authors: Hwang, J. / Suh, H.W. / Jeon, Y.H. / Hwang, E. / Nguyen, L.T. / Yeom, J. / Lee, S.G. / Lee, C. / Kim, K.J. / Kang, B.S. / Jeong, J.O. / Oh, T.K. / Choi, I. / Lee, J.O. / Kim, M.H.
History
DepositionAug 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Thioredoxin-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1502
Polymers17,0581
Non-polymers921
Water1,802100
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.431, 56.621, 67.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Thioredoxin-interacting protein / TXNIP / Thioredoxin-binding protein 2 / TBP-2 / Vitamin D3 up-regulated protein 1 / VDUP1


Mass: 17057.500 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 4-154) / Mutation: F4V,K5A,K6A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TXNIP, VDUP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H3M7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.75 M sodium/potassium phosphate, 0.1 M HEPES sodium, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 10, 2007
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 18976 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.6→1.66 Å / % possible all: 90.5

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PARTIALLY REFINED STRUCTURE OF MSE-LABELED TXNIP N-TERMINAL DOMAIN

Resolution: 1.6→18.78 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.815 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22711 972 5.1 %RANDOM
Rwork0.17136 ---
obs0.17423 17968 97.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.152 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2--1.57 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.6→18.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1189 0 6 100 1295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221236
X-RAY DIFFRACTIONr_angle_refined_deg1.1291.9731673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4555154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.0612556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96315216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.421156
X-RAY DIFFRACTIONr_chiral_restr0.0750.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02939
X-RAY DIFFRACTIONr_nbd_refined0.1890.2470
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2844
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.280
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.210
X-RAY DIFFRACTIONr_mcbond_it2.6243789
X-RAY DIFFRACTIONr_mcangle_it3.50451233
X-RAY DIFFRACTIONr_scbond_it5.7218520
X-RAY DIFFRACTIONr_scangle_it7.97711440
LS refinement shellResolution: 1.6→1.644 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 66 -
Rwork0.175 1164 -
obs--86.99 %
Refinement TLS params.Method: refined / Origin x: 16.603 Å / Origin y: -1.654 Å / Origin z: 1.97 Å
111213212223313233
T-0.0181 Å20 Å2-0.0027 Å2-0.0051 Å20 Å2---0.0419 Å2
L0.977 °2-0.4797 °20.3257 °2-0.3478 °2-0.1286 °2--0.4541 °2
S-0.0141 Å °-0.0378 Å °-0.025 Å °0.0094 Å °0.0361 Å °-0.0045 Å °0.0003 Å °-0.0356 Å °-0.022 Å °

+
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