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- PDB-4ll4: The structure of the TRX and TXNIP complex -

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Basic information

Entry
Database: PDB / ID: 4ll4
TitleThe structure of the TRX and TXNIP complex
Components
  • Thioredoxin-interacting protein
  • Thioredoxin
KeywordsANTITUMOR PROTEIN/PROTEIN BINDING / Arrestin-like domain / ANTITUMOR PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


Protein repair / cellular response to tumor cell / cellular detoxification of hydrogen peroxide / cellular response to oxidised low-density lipoprotein particle stimulus / positive regulation of peptidyl-cysteine S-nitrosylation / negative regulation of cell division / protein-disulfide reductase (NAD(P)H) activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / negative regulation of protein export from nucleus ...Protein repair / cellular response to tumor cell / cellular detoxification of hydrogen peroxide / cellular response to oxidised low-density lipoprotein particle stimulus / positive regulation of peptidyl-cysteine S-nitrosylation / negative regulation of cell division / protein-disulfide reductase (NAD(P)H) activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / negative regulation of protein export from nucleus / enzyme inhibitor activity / Regulation of FOXO transcriptional activity by acetylation / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide / Detoxification of Reactive Oxygen Species / The NLRP3 inflammasome / platelet-derived growth factor receptor signaling pathway / protein-disulfide reductase activity / positive regulation of DNA binding / response to glucose / Purinergic signaling in leishmaniasis infection / response to mechanical stimulus / keratinocyte differentiation / activation of protein kinase B activity / cell redox homeostasis / response to progesterone / TP53 Regulates Metabolic Genes / response to radiation / response to hydrogen peroxide / Cytoprotection by HMOX1 / response to calcium ion / protein import into nucleus / protein transport / response to estradiol / positive regulation of peptidyl-serine phosphorylation / regulation of cell population proliferation / Oxidative Stress Induced Senescence / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to xenobiotic stimulus / cell cycle / inflammatory response / positive regulation of apoptotic process / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / 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 / Thioredoxin / Thioredoxin / Thioredoxin, conserved site ...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 / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Immunoglobulin E-set / Thioredoxin-like superfamily / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Thioredoxin / Thioredoxin-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
DepositionJul 9, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin-interacting protein
B: Thioredoxin
C: Thioredoxin-interacting protein
D: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)93,5124
Polymers93,5124
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.826, 64.990, 88.416
Angle α, β, γ (deg.)90.00, 90.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35037.496 Da / Num. of mol.: 2 / Fragment: UNP residues 3-317 / Mutation: C170S, C205S, C267S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TXNIP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H3M7
#2: Protein Thioredoxin / / Trx / ATL-derived factor / ADF / Surface-associated sulphydryl protein / SASP


Mass: 11718.413 Da / Num. of mol.: 2 / Mutation: C35A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRX / Production host: Escherichia coli (E. coli) / References: UniProt: P10599
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.16M tri-sodium citrate, 16% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294.15K

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Data collection

DiffractionMean temperature: 173.15 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.1 Å
DetectorDetector: CCD / Date: Jul 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 24910 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.7→2.8 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 4LL1

4ll1


Resolution: 2.7→40 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.905 / SU B: 28.731 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26401 1942 7.8 %RANDOM
Rwork0.19589 ---
obs0.2013 22957 99.49 %-
all-24910 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.593 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å2-1.91 Å2
2--3.94 Å20 Å2
3----2.37 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6011 0 0 59 6070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0226125
X-RAY DIFFRACTIONr_angle_refined_deg2.1481.9678250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4265760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83824.44259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.704151135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3591534
X-RAY DIFFRACTIONr_chiral_restr0.1340.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024504
X-RAY DIFFRACTIONr_nbd_refined0.2680.22664
X-RAY DIFFRACTIONr_nbtor_refined0.3310.24090
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2243
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.28
X-RAY DIFFRACTIONr_mcbond_it1.2521.53896
X-RAY DIFFRACTIONr_mcangle_it1.86526168
X-RAY DIFFRACTIONr_scbond_it2.86632498
X-RAY DIFFRACTIONr_scangle_it4.3754.52082
LS refinement shellResolution: 2.704→2.774 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 139 -
Rwork0.253 1568 -
obs--93.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3745-0.39321.49670.197-0.45121.6361-0.1291-0.13930.00510.04860.0761-0.0456-0.1728-0.07070.0530.03550.07660.03530.0077-0.0359-0.019610.8635-3.825441.4633
23.86540.14271.88561.57440.0413.46050.282-0.0791-0.54090.0235-0.030.60270.2906-0.6732-0.252-0.14670.0086-0.02240.05880.0007-0.0493-27.8363-1.69826.4891
31.1742-0.02031.1790.3796-0.02451.69910.00590.0639-0.0837-0.00270.00250.04180.0416-0.0839-0.0084-0.1103-0.01750.0258-0.0627-0.0014-0.048241.51191.993739.1443
43.64960.3087-0.27253.6691-0.02213.1340.12660.1999-0.23590.1508-0.087-0.29310.13970.325-0.0397-0.13130.0102-0.1147-0.19750.0346-0.138979.49236.312274.6094
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 298
2X-RAY DIFFRACTION2B1 - 105
3X-RAY DIFFRACTION3C8 - 299
4X-RAY DIFFRACTION4D1 - 105

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