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- PDB-3w8j: Crystal structure of P5 a0 in a complex with Prx4 c-term -

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Basic information

Entry
Database: PDB / ID: 3w8j
TitleCrystal structure of P5 a0 in a complex with Prx4 c-term
Components
  • C-terminal peptide from Peroxiredoxin-4
  • Protein disulfide-isomerase A6
KeywordsOXIDOREDUCTASE/ISOMERASE / PDI family member / thioredoxin fold / protein disulfide isomerase / OXIDOREDUCTASE-ISOMERASE complex
Function / homology
Function and homology information


protein disulfide-isomerase / negative regulation of male germ cell proliferation / endoplasmic reticulum chaperone complex / XBP1(S) activates chaperone genes / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / molecular sequestering activity / protein maturation by protein folding / protein disulfide isomerase activity / endoplasmic reticulum-Golgi intermediate compartment ...protein disulfide-isomerase / negative regulation of male germ cell proliferation / endoplasmic reticulum chaperone complex / XBP1(S) activates chaperone genes / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / molecular sequestering activity / protein maturation by protein folding / protein disulfide isomerase activity / endoplasmic reticulum-Golgi intermediate compartment / protein-disulfide reductase activity / smooth endoplasmic reticulum / Neutrophil degranulation / response to endoplasmic reticulum stress / extracellular matrix organization / cell redox homeostasis / reactive oxygen species metabolic process / hydrogen peroxide catabolic process / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / male gonad development / melanosome / protein folding / spermatogenesis / response to oxidative stress / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / extracellular space / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Disulphide isomerase / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. ...Disulphide isomerase / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Peroxiredoxin-4 / Protein disulfide-isomerase A6
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsInaba, K. / Suzuki, M. / Kojima, R.
CitationJournal: Sci Rep / Year: 2013
Title: Synergistic cooperation of PDI family members in peroxiredoxin 4-driven oxidative protein folding
Authors: Sato, Y. / Kojima, R. / Okumura, M. / Hagiwara, M. / Masui, S. / Maegawa, K. / Saiki, M. / Horibe, T. / Suzuki, M. / Inaba, K.
History
DepositionMar 13, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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_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_auth_seq_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_seq_id / _struct_conn.ptnr2_label_asym_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: Protein disulfide-isomerase A6
B: Protein disulfide-isomerase A6
C: C-terminal peptide from Peroxiredoxin-4
D: C-terminal peptide from Peroxiredoxin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,98212
Polymers35,4584
Non-polymers5258
Water1,11762
1
A: Protein disulfide-isomerase A6
C: C-terminal peptide from Peroxiredoxin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8074
Polymers17,7292
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-4 kcal/mol
Surface area7030 Å2
MethodPISA
2
B: Protein disulfide-isomerase A6
D: C-terminal peptide from Peroxiredoxin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1758
Polymers17,7292
Non-polymers4476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-6 kcal/mol
Surface area7180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.045, 53.375, 133.353
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein disulfide-isomerase A6 / Endoplasmic reticulum protein 5 / ER protein 5 / ERp5 / Protein disulfide isomerase P5 / ...Endoplasmic reticulum protein 5 / ER protein 5 / ERp5 / Protein disulfide isomerase P5 / Thioredoxin domain-containing protein 7


Mass: 15636.499 Da / Num. of mol.: 2 / Fragment: P5 a0, UNP residues 20-140 / Mutation: C58A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDIA6, ERP5, P5, TXNDC7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15084, protein disulfide-isomerase
#2: Protein/peptide C-terminal peptide from Peroxiredoxin-4 / Antioxidant enzyme AOE372 / Peroxiredoxin IV / Prx-IV / Thioredoxin peroxidase AO372 / Thioredoxin- ...Antioxidant enzyme AOE372 / Peroxiredoxin IV / Prx-IV / Thioredoxin peroxidase AO372 / Thioredoxin-dependent peroxide reductase A0372


Mass: 2092.330 Da / Num. of mol.: 2 / Fragment: UNP residues 244-263 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: O08807, peroxiredoxin
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.96 Å3/Da / Density % sol: 37.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 22% PEG 2000 MME, 0.1M potassium thiocyanate, 0.1M Tris-HCl (pH 7.3), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2013
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→41.67 Å / Num. obs: 16851 / % possible obs: 98.9 % / Redundancy: 6.7 %
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.7 % / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→41.669 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7874 / SU ML: 0.22 / σ(F): 1.36 / Phase error: 26.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2451 709 5.05 %
Rwork0.1823 --
obs0.1854 14047 82.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.66 Å2 / Biso mean: 42.5837 Å2 / Biso min: 16.89 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 28 62 2052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072028
X-RAY DIFFRACTIONf_angle_d1.0362739
X-RAY DIFFRACTIONf_dihedral_angle_d14.108731
X-RAY DIFFRACTIONf_chiral_restr0.067296
X-RAY DIFFRACTIONf_plane_restr0.004355
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1002-2.26230.2643780.2085156649
2.2623-2.490.3061250.2242223671
2.49-2.85020.26871600.2133294893
2.8502-3.59070.25971890.18663204100
3.5907-41.67670.2111570.1609338499
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)
10.04640.11560.05190.31370.14720.0660.17290.2175-0.4203-0.47840.27070.08150.8466-0.53420.010.6611-0.072-0.17020.37730.07090.370319.8243.739.836
20.17210.16190.22420.16070.2140.2876-0.10370.1195-0.10140.0218-0.07320.21940.0372-0.4249-0.4708-0.1088-0.0132-0.01781.38790.23350.391616.82749.81318.272
30.02110.064-0.01480.7743-0.2150.19240.1998-0.0259-0.1849-0.6590.33360.44110.0576-0.43030.01780.33850.0102-0.05670.33350.00680.260922.57852.224-0.866
40.12910.03540.07020.07780.0010.0339-0.07370.05190.103-0.18890.1482-0.1648-0.35690.0463-0.00010.35240.0971-0.00670.2416-0.00740.242131.36750.4187.25
50.73490.43920.40820.50850.02350.44950.11220.2489-0.2772-0.13130.1099-0.20780.2567-0.49710.27890.1942-0.1237-0.12770.63560.07790.142118.657549.38378.0666
60.08520.28480.07370.95810.26140.0958-0.0107-0.44520.0305-0.02030.30140.3786-0.3011-0.495-0.03340.33830.1991-0.00550.5663-0.00680.287718.001457.84925.4482
70.19440.3496-0.01171.93580.67820.3748-0.3305-0.56750.4556-0.21660.17970.0728-0.5791-0.6134-0.03360.26170.2284-0.0890.69530.05560.378322.65260.79311.565
80.0789-0.0031-0.04170.12330.07730.255-0.0162-0.14540.1912-0.23490.0360.0471-0.46630.0210.0010.29670.0742-0.05260.2975-0.0460.31326.854360.166322.14
90.8497-0.5382-0.930.40030.74691.4882-0.0409-0.3852-0.13950.19910.19010.34140.4836-0.10840.15930.3023-0.14320.07940.21380.03490.277227.331743.77142.5431
100.08310.00450.05870.0103-0.01060.0434-0.00580.16590.0875-0.1961-0.0811-0.17060.2241-0.304-0.00010.30880.01980.01280.2004-0.05430.228635.41343.01731.579
110.32840.0853-0.00950.3227-0.03520.08440.1396-0.09230.04640.1317-0.22610.12160.1005-0.2008-0.00010.30220.0280.05510.2478-0.06430.249329.496952.928342.6862
120.1486-0.01710.09810.02740.00850.0563-0.0239-0.31840.02660.50280.11530.340.4094-0.31740.01020.4748-0.02660.04370.2226-0.00120.19436.8542.9648.577
130.14630.15970.07690.16670.12490.12570.11770-0.05840.12640.0692-0.34010.02620.21660.00010.22280.01540.02630.2381-0.03570.253342.542548.192840.2881
14-0.0018-0.0019-0.03130.2926-0.09730.35380.02680.2291-0.023-0.222-0.3248-0.38020.08630.244-0.01540.34850.08220.13240.023-0.11490.200834.01161.74640.285
150.12540.02950.12840.19450.21170.3162-0.0231-0.08140.1671-0.20970.14920.0293-0.41670.3398-0.00180.28620.06620.00210.1342-0.01410.17835.232656.726.0782
160.0642-0.00290.02330.00420.00510.0117-0.1017-0.06320.20270.1699-0.2826-0.1982-0.20870.173-0.00010.47790.0677-0.060.4163-0.01260.322721.12959.4222-4.9052
170.03140.019700.0104-0.00070.0098-0.2341-0.1330.027-0.0417-0.1571-0.16960.10330.0168-0.0010.4270.00390.01650.3698-0.05680.360240.580755.436453.2685
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 22:36)A22 - 36
2X-RAY DIFFRACTION2chain 'A' and (resseq 37:47)A37 - 47
3X-RAY DIFFRACTION3chain 'A' and (resseq 48:57)A48 - 57
4X-RAY DIFFRACTION4chain 'A' and (resseq 58:73)A58 - 73
5X-RAY DIFFRACTION5chain 'A' and (resseq 74:94)A74 - 94
6X-RAY DIFFRACTION6chain 'A' and (resseq 95:106)A95 - 106
7X-RAY DIFFRACTION7chain 'A' and (resseq 107:121)A107 - 121
8X-RAY DIFFRACTION8chain 'A' and (resseq 122:140)A122 - 140
9X-RAY DIFFRACTION9chain 'B' and (resseq 21:36)B21 - 36
10X-RAY DIFFRACTION10chain 'B' and (resseq 37:47)B37 - 47
11X-RAY DIFFRACTION11chain 'B' and (resseq 48:78)B48 - 78
12X-RAY DIFFRACTION12chain 'B' and (resseq 79:88)B79 - 88
13X-RAY DIFFRACTION13chain 'B' and (resseq 89:113)B89 - 113
14X-RAY DIFFRACTION14chain 'B' and (resseq 114:121)B114 - 121
15X-RAY DIFFRACTION15chain 'B' and (resseq 122:140)B122 - 140
16X-RAY DIFFRACTION16chain 'C' and (resseq 0:5)C0 - 5
17X-RAY DIFFRACTION17chain 'D' and (resseq 0:5)D0 - 5

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