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- PDB-2cfy: Crystal structure of human thioredoxin reductase 1 -

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Basic information

Entry
Database: PDB / ID: 2cfy
TitleCrystal structure of human thioredoxin reductase 1
ComponentsTHIOREDOXIN REDUCTASE 1
KeywordsOXIDOREDUCTASE / PHOSPHORYLATION / REDOX-ACTIVE CENTER / NADP
Function / homology
Function and homology information


Metabolism of ingested MeSeO2H into MeSeH / NADPH peroxidase / NADPH peroxidase activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / Uptake and function of diphtheria toxin ...Metabolism of ingested MeSeO2H into MeSeH / NADPH peroxidase / NADPH peroxidase activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / Uptake and function of diphtheria toxin / mesoderm formation / FAD binding / cell redox homeostasis / TP53 Regulates Metabolic Genes / PPARA activates gene expression / fibrillar center / cell population proliferation / signal transduction / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain ...Thioredoxin/glutathione reductase selenoprotein / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin reductase 1, cytoplasmic
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDebreczeni, J.E. / Johansson, C. / Kavanagh, K. / Savitsky, P. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / von Delft, F. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Thioredoxin Reductase 1
Authors: Debreczeni, J.E. / Johansson, C. / Kavanagh, K. / Savitsky, P. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / von Delft, F. / Oppermann, U.
History
DepositionFeb 26, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THIOREDOXIN REDUCTASE 1
B: THIOREDOXIN REDUCTASE 1
C: THIOREDOXIN REDUCTASE 1
D: THIOREDOXIN REDUCTASE 1
E: THIOREDOXIN REDUCTASE 1
F: THIOREDOXIN REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,41212
Polymers343,6996
Non-polymers4,7136
Water4,107228
1
A: THIOREDOXIN REDUCTASE 1
B: THIOREDOXIN REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,1374
Polymers114,5662
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: THIOREDOXIN REDUCTASE 1
D: THIOREDOXIN REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,1374
Polymers114,5662
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: THIOREDOXIN REDUCTASE 1
F: THIOREDOXIN REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,1374
Polymers114,5662
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)89.756, 149.651, 146.789
Angle α, β, γ (deg.)90.00, 91.96, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11C-2034-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A10 - 495
2113B10 - 495
3113C10 - 495
4113D10 - 495
5113E10 - 495
6113F10 - 495

NCS oper:
IDCodeMatrixVector
1given(0.0593, 0.67412, 0.73624), (0.67878, -0.56802, 0.46542), (0.73194, 0.47214, -0.49126)29.58975, -61.99845, 14.58618
2given(-0.05296, -0.67313, 0.73763), (-0.67657, 0.56748, 0.46928), (-0.73447, -0.4742, -0.48547)62.43633, -28.46729, 95.97807
3given(-0.99999, -0.00041, 0.00344), (0.00041, -1, 0.00057), (0.00344, 0.00057, 0.99999)84.46125, 41.59736, -0.11094
4given(-0.14172, -0.72885, -0.66984), (-0.66199, 0.57289, -0.4833), (0.736, 0.37493, -0.56368)151.53459, -42.2028, 22.45863
5given(0.08368, 0.62147, -0.77895), (0.62793, -0.63986, -0.44305), (-0.77376, -0.45205, -0.44378)26.39412, 74.69446, 94.94545

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Components

#1: Protein
THIOREDOXIN REDUCTASE 1 / HUMAN THIOREDOXIN REDUCTASE / TR / TR1


Mass: 57283.168 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3
References: UniProt: Q16881, thioredoxin-disulfide reductase (NADPH)
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.1 Å3/Da / Density % sol: 61 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 150 UL SITTING DROPS, 20% PEG3350, 0.1 M TRIS PH 7, ADDITIVE: NSDB-221

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 24, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→47 Å / Num. obs: 100946 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 3.25 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H6V

1h6v


Resolution: 2.7→149.07 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.902 / SU B: 24.607 / SU ML: 0.24 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.099 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 5025 5 %RANDOM
Rwork0.203 ---
obs0.205 95921 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å2-0.35 Å2
2--1.56 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.7→149.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21968 0 272 228 22468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02222721
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214868
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.97330925
X-RAY DIFFRACTIONr_angle_other_deg0.916336431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.452900
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32624.51918
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.772153644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1615102
X-RAY DIFFRACTIONr_chiral_restr0.0780.23508
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0225401
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024406
X-RAY DIFFRACTIONr_nbd_refined0.2170.24493
X-RAY DIFFRACTIONr_nbd_other0.1870.214965
X-RAY DIFFRACTIONr_nbtor_refined0.1830.211209
X-RAY DIFFRACTIONr_nbtor_other0.0850.211964
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2377
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4641.514728
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.785223044
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.14839504
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9424.57880
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2833tight positional0.030.05
2B2833tight positional0.030.05
3C2833tight positional0.030.05
4D2833tight positional0.030.05
5E2833tight positional0.020.05
6F2833tight positional0.020.05
1A2983loose positional0.285
2B2983loose positional0.345
3C2983loose positional0.345
4D2983loose positional0.35
5E2983loose positional0.45
6F2983loose positional0.355
1A2833tight thermal8.3930
2B2833tight thermal8.930
3C2833tight thermal9.2930
4D2833tight thermal9.5130
5E2833tight thermal18.0930
6F2833tight thermal17.6830
1A2983loose thermal8.4130
2B2983loose thermal8.8830
3C2983loose thermal9.2530
4D2983loose thermal9.4130
5E2983loose thermal17.9130
6F2983loose thermal17.5930
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.359 350
Rwork0.312 6950
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)
10.5259-0.01720.08190.5937-0.15890.7564-0.0090.0591-0.05030.1785-0.0290.1170.1233-0.10060.038-0.0238-0.03670.0979-0.1003-0.0581-0.072360.1264-11.902155.3794
20.74750.12670.11361.0666-0.25790.4437-0.02610.26170.0807-0.0886-0.05590.01020.09550.03990.082-0.17230.00810.0180.0864-0.0048-0.1265.615811.494725.8087
30.62010.0411-0.05450.96850.27080.4914-0.05170.2076-0.0683-0.0956-0.03790.058-0.07470.0010.0896-0.1612-0.0054-0.03420.06160.0008-0.10418.838930.111125.7679
40.60010.0182-0.13250.6380.28890.8651-0.0010.03930.04380.1076-0.0115-0.0281-0.10920.10310.0124-0.0714-0.027-0.0617-0.08060.0522-0.085324.445953.561655.3492
51.1546-0.10820.08081.3546-0.10711.2852-0.045-0.15110.1811-0.0652-0.0762-0.3928-0.17290.39450.12120.3205-0.0563-0.0518-0.1301-0.0207-0.060816.679996.367327.9541
61.292-0.0208-0.23570.83610.23681.7123-0.1216-0.0634-0.1533-0.1244-0.14090.36550.0337-0.27170.26240.3114-0.031-0.0418-0.2681-0.17810.0125-20.779793.990129.6456
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 493
2X-RAY DIFFRACTION2B10 - 493
3X-RAY DIFFRACTION3C10 - 493
4X-RAY DIFFRACTION4D10 - 493
5X-RAY DIFFRACTION5E10 - 493
6X-RAY DIFFRACTION6F10 - 493

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