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- PDB-4gej: N-terminal domain of VDUP-1 -

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Basic information

Entry
Database: PDB / ID: 4gej
TitleN-terminal domain of VDUP-1
ComponentsThioredoxin-interacting protein
KeywordsPROTEIN BINDING / alpha-arrestin / oxidative stress / metabolism / thioredoxin
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 / Regulation of FOXO transcriptional activity by acetylation / platelet-derived growth factor receptor signaling pathway / The NLRP3 inflammasome / response to mechanical stimulus / response to glucose / Purinergic signaling in leishmaniasis infection / keratinocyte differentiation ...cellular response to tumor cell / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of cell division / Regulation of FOXO transcriptional activity by acetylation / platelet-derived growth factor receptor signaling pathway / The NLRP3 inflammasome / response to mechanical stimulus / response to glucose / Purinergic signaling in leishmaniasis infection / keratinocyte differentiation / response to progesterone / enzyme inhibitor activity / response to hydrogen peroxide / Cytoprotection by HMOX1 / response to calcium ion / protein import into nucleus / response to estradiol / regulation of cell population proliferation / protein transport / response to oxidative stress / positive regulation of apoptotic process / response to xenobiotic stimulus / inflammatory response / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / cytoplasm / cytosol
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: 2.9 Å
AuthorsPolekhina, G. / Kok, S.F. / Ascher, D.B. / Waltham, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of the N-terminal domain of human thioredoxin-interacting protein.
Authors: Polekhina, G. / Ascher, D.B. / Kok, S.F. / Beckham, S. / Wilce, M. / Waltham, M.
History
DepositionAug 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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-interacting protein
C: Thioredoxin-interacting protein
D: Thioredoxin-interacting protein
E: Thioredoxin-interacting protein
F: Thioredoxin-interacting protein
G: Thioredoxin-interacting protein
H: Thioredoxin-interacting protein
I: Thioredoxin-interacting protein
J: Thioredoxin-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,26615
Polymers171,06510
Non-polymers2005
Water00
1
A: Thioredoxin-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1472
Polymers17,1071
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin-interacting protein


Theoretical massNumber of molelcules
Total (without water)17,1071
Polymers17,1071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thioredoxin-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1472
Polymers17,1071
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Thioredoxin-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1472
Polymers17,1071
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Thioredoxin-interacting protein


Theoretical massNumber of molelcules
Total (without water)17,1071
Polymers17,1071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Thioredoxin-interacting protein


Theoretical massNumber of molelcules
Total (without water)17,1071
Polymers17,1071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Thioredoxin-interacting protein


Theoretical massNumber of molelcules
Total (without water)17,1071
Polymers17,1071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Thioredoxin-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1472
Polymers17,1071
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Thioredoxin-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1472
Polymers17,1071
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Thioredoxin-interacting protein


Theoretical massNumber of molelcules
Total (without water)17,1071
Polymers17,1071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.740, 178.810, 81.890
Angle α, β, γ (deg.)90.00, 113.32, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.998099, -0.021487, 0.057772), (-0.02675, -0.995406, 0.091927), (0.055531, -0.093298, -0.994088)-1.59737, -4.40958, 74.29827
3given(-0.073441, -0.087606, -0.993444), (0.024884, -0.995985, 0.08599), (-0.996989, -0.018406, 0.075326)61.21162, -23.95721, 58.37457
4given(-0.01918, -0.079169, -0.996677), (0.116942, 0.98984, -0.080876), (0.992954, -0.118104, -0.009727)65.42342, 17.38117, 11.03321
5given(-0.092952, 0.104987, 0.99012), (-0.001632, 0.994408, -0.105595), (-0.995669, -0.011431, -0.092261)-12.89307, -14.56666, 65.39248
6given(-0.106896, 0.057708, 0.992594), (0.088918, -0.993759, 0.067351), (0.990286, 0.09546, 0.101098)-8.85381, 12.41897, 7.38716
7given(-0.771677, -0.006499, -0.635982), (0.02385, 0.998949, -0.039147), (0.635567, -0.045377, -0.770711)67.55037, -35.33961, 50.0869
8given(-0.971142, 0.025786, -0.237105), (-0.065104, -0.985045, 0.159527), (-0.229446, 0.17036, 0.958297)56.74283, 30.89916, 2.20666
9given(-0.728889, 0.042621, 0.683304), (-0.006833, -0.998464, 0.05499), (0.684598, 0.035413, 0.72806)15.56883, -38.29673, -5.45101
10given(-0.979911, -0.021547, 0.19827), (-0.056468, 0.983441, -0.172205), (-0.191277, -0.179942, -0.964901)41.23509, 44.10386, 72.19287

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Components

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


Mass: 17106.529 Da / Num. of mol.: 10 / Fragment: N-terminal domain, UNP residues 2-149 / Mutation: C36S, C49S, C120S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TXNIP, VDUP1 / Plasmid: modified pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): EC538 / References: UniProt: Q9H3M7
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY
Sequence detailsK26R SEQUENCE CONFLICT IN UNP ENTRY Q9H3M7

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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: 3.13 Å3/Da / Density % sol: 60.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes, 0.2 M Calcium Acetate, 10-12% PEG monomethyl ether 5000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 11, 2011 / Details: mirrows
RadiationMonochromator: silicon double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.9→46.71 Å / Num. all: 46358 / Num. obs: 46358 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 97 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 18.5
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2.9 / Num. unique all: 6708 / Rsym value: 0.665 / % possible all: 98.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→46 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.874 / SU B: 40.651 / SU ML: 0.348 / Isotropic thermal model: isotropic with TLS refinement / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 4.27 / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2936 2320 5 %RANDOM
Rwork0.212 ---
all0.224 46358 --
obs0.224 44007 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 89.105 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å20 Å20.2 Å2
2---3.57 Å20 Å2
3---1.37 Å2
Refine analyzeLuzzati coordinate error obs: 0.487 Å
Refinement stepCycle: LAST / Resolution: 2.9→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10933 0 5 0 10938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211157
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.97115051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.53351341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.66424.34523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.804152016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0691570
X-RAY DIFFRACTIONr_chiral_restr0.1070.21625
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218414
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 181 -
Rwork0.324 3156 -
obs--98.52 %
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)
11.0561-0.16921.82712.31190.98556.97610.19450.3019-0.0472-0.2034-0.65090.63910.2756-1.29740.45640.31950.102-0.26030.9568-0.29360.43525.6367-3.747219.4165
22.275-0.2334-1.17332.3311-0.12532.6055-0.0493-0.24980.2045-0.0699-0.09620.3906-0.0901-0.38080.14560.1472-0.02550.06210.2068-0.17630.23254.00734.386255.2729
35.2931-1.153.4284.8108-1.36596.07010.237-0.69650.44150.4869-0.0636-0.92970.13660.3197-0.17350.099-0.0331-0.13040.2736-0.16440.359743.6177-14.387954.3951
44.0026-2.0693-2.87323.99163.23593.5175-0.4235-0.5584-0.40231.10740.0670.41570.8705-0.04460.35650.7145-0.05140.14480.34280.12480.27976.2912-16.692662.0001
53.69110.2203-3.58741.7225-0.24046.217-0.1591-0.0835-0.44870.14310.0638-0.2860.45510.57120.09520.09750.06190.03050.0933-0.06640.258844.730113.764720.6898
62.1261.35192.96933.752.81610.83680.06240.25750.2629-1.2097-0.46930.2062-1.9693-1.62820.40691.14950.872-0.22260.7666-0.13210.26878.580118.044714.435
70.369-1.0604-0.07683.36710.70165.186-0.1571-0.0963-0.00950.13630.2342-0.0740.17490.3689-0.07710.45850.0109-0.00020.37720.0110.211229.040433.213362.2744
85.6561-0.2711-1.65653.31090.30652.44770.0820.41630.50910.14030.3035-0.3493-0.28220.4237-0.38560.1609-0.04910.11780.2052-0.05650.200949.075734.743322.5502
90.48160.1456-1.17562.62962.13875.33880.03820.1561-0.0274-0.43480.18-0.3784-0.4761-0.1806-0.21820.50590.05540.06080.3775-0.07850.211524.0218-34.759312.3468
108.22142.68931.86745.58561.33441.32540.1681-0.9663-0.53930.2928-0.0027-1.05250.3840.1451-0.16540.27990.0728-0.27680.27670.12660.670948.7881-36.088252.5814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 149
2X-RAY DIFFRACTION2B8 - 149
3X-RAY DIFFRACTION3C8 - 149
4X-RAY DIFFRACTION4D8 - 149
5X-RAY DIFFRACTION5E8 - 149
6X-RAY DIFFRACTION6F8 - 149
7X-RAY DIFFRACTION7G8 - 149
8X-RAY DIFFRACTION8H8 - 149
9X-RAY DIFFRACTION9I8 - 149
10X-RAY DIFFRACTION10J8 - 149

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