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- PDB-3aps: Crystal structure of Trx4 domain of ERdj5 -

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Basic information

Entry
Database: PDB / ID: 3aps
TitleCrystal structure of Trx4 domain of ERdj5
ComponentsDnaJ homolog subfamily C member 10
KeywordsOXIDOREDUCTASE / THIOREDOXIN FOLD / CXXC MOTIF / ENDOPLASMIC RETICULUM
Function / homology
Function and homology information


oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / endoplasmic reticulum chaperone complex / protein folding in endoplasmic reticulum / disulfide oxidoreductase activity / misfolded protein binding / positive regulation of ATP-dependent activity / IRE1-mediated unfolded protein response / ATPase activator activity / protein-disulfide reductase activity ...oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / endoplasmic reticulum chaperone complex / protein folding in endoplasmic reticulum / disulfide oxidoreductase activity / misfolded protein binding / positive regulation of ATP-dependent activity / IRE1-mediated unfolded protein response / ATPase activator activity / protein-disulfide reductase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / : / Hsp70 protein binding / response to endoplasmic reticulum stress / negative regulation of protein phosphorylation / ATPase binding / protein-folding chaperone binding / endoplasmic reticulum lumen / endoplasmic reticulum
Similarity search - Function
DnaJ homologue subfamily C member 10 / ERdj5, first thioredoxin domain / ERdj5, C-terminal thioredoxin domain / DnaJ domain / Endoplasmic reticulum targeting sequence. / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Thioredoxin ...DnaJ homologue subfamily C member 10 / ERdj5, first thioredoxin domain / ERdj5, C-terminal thioredoxin domain / DnaJ domain / Endoplasmic reticulum targeting sequence. / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / 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
DnaJ homolog subfamily C member 10
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsInaba, K. / Suzuki, M. / Nagata, K.
CitationJournal: Mol.Cell / Year: 2011
Title: Structural basis of an ERAD pathway mediated by the ER-resident protein disulfide reductase ERdj5.
Authors: Hagiwara, M. / Maegawa, K. / Suzuki, M. / Ushioda, R. / Araki, K. / Matsumoto, Y. / Hoseki, J. / Nagata, K. / Inaba, K.
History
DepositionOct 20, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DnaJ homolog subfamily C member 10
B: DnaJ homolog subfamily C member 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0744
Polymers27,8862
Non-polymers1882
Water1,40578
1
A: DnaJ homolog subfamily C member 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1313
Polymers13,9431
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DnaJ homolog subfamily C member 10


Theoretical massNumber of molelcules
Total (without water)13,9431
Polymers13,9431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.060, 33.419, 68.343
Angle α, β, γ (deg.)90.00, 92.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DnaJ homolog subfamily C member 10 / ER-RESIDENT PROTEIN ERDJ5 / ENDOPLASMIC RETICULUM DNAJ-PDI FUSION PROTEIN 1


Mass: 13943.077 Da / Num. of mol.: 2 / Fragment: TRX4 DOMAIN (UNP RESIDUES 668-789)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: DNAJC10, ERDJ5, JPDI / Plasmid: PCOLD-TF / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI / References: UniProt: Q9DC23
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 17.5 % PEG 3350, 140MM LISO4, 70MM HEPES PH7.5, 70MM GLYCINE, 12% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Oct 8, 2007 / Details: MIRROR
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→34.12 Å / Num. obs: 20060 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 3.7 / % possible all: 94.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXC/D/Emodel building
REFMAC5.5.0085refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXC/D/Ephasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→30.02 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.754 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1021 5.1 %RANDOM
Rwork0.206 ---
obs0.208 19032 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.194 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20.85 Å2
2---1.02 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 11 78 1915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221885
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.9572551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1595226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.50824.63482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.56415332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.699158
X-RAY DIFFRACTIONr_chiral_restr0.110.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211400
X-RAY DIFFRACTIONr_mcbond_it0.9161.51140
X-RAY DIFFRACTIONr_mcangle_it1.67621836
X-RAY DIFFRACTIONr_scbond_it2.6723745
X-RAY DIFFRACTIONr_scangle_it4.4454.5715
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 70 -
Rwork0.281 1330 -
obs--92.9 %
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)
12.18840.25040.48063.24750.012.4243-0.00980.19990.1048-0.27490.0314-0.00080.12030.0856-0.02160.0930.00610.02120.04450.00260.0227-0.2341.76124.385
23.36181.86111.4778.09582.2015.5229-0.10660.3752-0.3830.21750.6622-1.11940.36680.704-0.55560.10210.0458-0.00070.1668-0.1580.2331-17.9340.3130.843
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A669 - 782
2X-RAY DIFFRACTION2B669 - 780

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