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- PDB-3apq: Crystal structure of J-Trx1 fragment of ERdj5 -

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Basic information

Entry
Database: PDB / ID: 3apq
TitleCrystal structure of J-Trx1 fragment of ERdj5
ComponentsDnaJ homolog subfamily C member 10
KeywordsOXIDOREDUCTASE / THIOREDOXIN FOLD / DNAJ DOMAIN / 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 / DnaJ domain / Endoplasmic reticulum targeting sequence. / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain ...DnaJ homologue subfamily C member 10 / ERdj5, first thioredoxin domain / ERdj5, C-terminal thioredoxin domain / DnaJ 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 / Helix Hairpins / Thioredoxin-like superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / 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: 1.84 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,2842
Polymers48,2842
Non-polymers00
Water7,314406
1
A: DnaJ homolog subfamily C member 10


Theoretical massNumber of molelcules
Total (without water)24,1421
Polymers24,1421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DnaJ homolog subfamily C member 10


Theoretical massNumber of molelcules
Total (without water)24,1421
Polymers24,1421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.008, 61.179, 62.912
Angle α, β, γ (deg.)90.00, 106.34, 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 / J DOMAIN-CONTAINING ...ER-RESIDENT PROTEIN ERDJ5 / ENDOPLASMIC RETICULUM DNAJ-PDI FUSION PROTEIN 1 / J DOMAIN-CONTAINING PROTEIN DISULFIDE ISOMERASE-LIKE PROTEIN / J DOMAIN-CONTAINING PDI-LIKE PROTEIN / JPDI


Mass: 24142.125 Da / Num. of mol.: 2 / Fragment: J-TRX1 DOMAIN (UNP RESIDUES 34-242)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: DNAJC10, ERDJ5, JPDI / Plasmid: PGEX-5X / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI / References: UniProt: Q9DC23
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DEPOSITORS STATES THAT THIS PROTEIN ACTUALLY CONTAINS ASP91 IN THE NATIVE SEQUENCE. THE FEATURE ...THE DEPOSITORS STATES THAT THIS PROTEIN ACTUALLY CONTAINS ASP91 IN THE NATIVE SEQUENCE. THE FEATURE OF UNIPROT (Q9DC23, DJC10_MOUSE) SHOWS "CONFLICT" AT THIS POSITION: H -> D (in Ref. 1; AAN73273, 2; AAQ14555 and 4; AAH33461) AS THE EXPERIMENTAL INFO

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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: 2.07 Å3/Da / Density % sol: 40.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 13% PEG 4000, 6.5% ISOPROPANOL, 65MM HEPES PH7.5, 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 Å
DetectorType: DIP6040 / Detector: IMAGE PLATE / Date: Jul 17, 2008 / 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: 1.84→39.56 Å / Num. obs: 33995 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 15.3
Reflection shellResolution: 1.84→1.94 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 3.3 / % possible all: 97.8

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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: 1.84→39.56 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1724 5.1 %RANDOM
Rwork0.17 ---
obs0.173 32251 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20.59 Å2
2---0.56 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.84→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3317 0 0 406 3723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223465
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.9474679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6655426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12723.388183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45815609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4571529
X-RAY DIFFRACTIONr_chiral_restr0.120.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212705
X-RAY DIFFRACTIONr_mcbond_it0.9841.52059
X-RAY DIFFRACTIONr_mcangle_it1.73923297
X-RAY DIFFRACTIONr_scbond_it3.05831406
X-RAY DIFFRACTIONr_scangle_it4.7094.51373
LS refinement shellResolution: 1.84→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 120 -
Rwork0.223 2244 -
obs--95.05 %
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)
10.9409-0.7243-0.54821.92960.44580.65180.0543-0.0158-0.0129-0.1677-0.0557-0.0875-0.10480.08010.00130.0352-0.02220.00050.05290.03870.057533.596.6389.707
21.46630.0284-0.10431.8976-0.80671.2074-0.00330.0152-0.0388-0.20450.09370.06120.0908-0.1562-0.09030.0421-0.0225-0.00120.0419-0.0040.02027.767-0.7074.834
31.3046-0.0359-0.22412.0162-0.13232.59770.00290.0455-0.06820.10150.08060.14960.0016-0.1225-0.08340.02280.01630.02690.02020.01980.041113.851-8.22231.225
42.46780.893-1.2521.5791-1.08092.7852-0.1612-0.247-0.30780.0012-0.2157-0.31160.12540.36790.37680.01780.0220.02550.07020.09120.145538.911-15.32127.711
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 120
2X-RAY DIFFRACTION2A121 - 240
3X-RAY DIFFRACTION3B33 - 120
4X-RAY DIFFRACTION4B121 - 235

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