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- PDB-3apo: Crystal structure of full-length ERdj5 -

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Basic information

Entry
Database: PDB / ID: 3apo
TitleCrystal structure of full-length ERdj5
ComponentsDnaJ homolog subfamily C member 10
KeywordsOXIDOREDUCTASE / PDI FAMILY / THIOREDOXIN / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 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


Theoretical massNumber of molelcules
Total (without water)88,9981
Polymers88,9981
Non-polymers00
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.100, 53.400, 92.300
Angle α, β, γ (deg.)90.00, 113.40, 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: 88998.133 Da / Num. of mol.: 1
Mutation: H91D, C158S, C161S, G399V, C419S, C480S, C483S, C588S, C591S, C700S, C703S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: DNAJC10, ERDJ5, JPDI / Plasmid: PET15B / 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.: 221 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DEPOSITORS STATES THAT THIS PROTEIN ACTUALLY CONTAINS GLY617 AND THAT UNIPROT IS INCORRECT AT ...THE DEPOSITORS STATES THAT THIS PROTEIN ACTUALLY CONTAINS GLY617 AND THAT UNIPROT IS INCORRECT AT THIS POSITION.

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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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG 8000, 100MM HEPES PH7.5, 8MM CYSTINE, 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: Jun 6, 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: 2.4→45.83 Å / Num. obs: 32121 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 11.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 3 / % possible all: 98.7

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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: MOLECULAR REPLACEMENT / Resolution: 2.4→45.83 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU B: 16.031 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1627 5.1 %RANDOM
Rwork0.197 ---
obs0.199 30477 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.482 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20.61 Å2
2---1.55 Å20 Å2
3---2.25 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5547 0 0 221 5768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225699
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9437723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1225682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41623.804276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.09615953
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6811533
X-RAY DIFFRACTIONr_chiral_restr0.0940.2820
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214362
X-RAY DIFFRACTIONr_mcbond_it0.5121.53427
X-RAY DIFFRACTIONr_mcangle_it0.97925522
X-RAY DIFFRACTIONr_scbond_it1.52432272
X-RAY DIFFRACTIONr_scangle_it2.4384.52201
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 119 -
Rwork0.235 2186 -
obs--97.88 %
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)
13.91421.1922-0.58573.4859-0.95711.52370.05680.3995-0.2264-0.39510.19640.8190.7108-0.6371-0.25310.331-0.0228-0.08890.32-0.10520.3371-10.1441-34.656358.1804
24.97053.01491.28976.04190.98783.8116-0.69611.17150.2999-0.99680.82730.4557-0.0136-0.4695-0.13120.3013-0.2435-0.1510.54960.21080.1509-1.7218-13.217748.3578
31.89380.60110.2284.1508-0.18111.8014-0.14070.0948-0.0311-0.21070.0697-0.3722-0.11920.05290.07090.1294-0.01810.06770.0797-0.01570.063528.4705-3.6956.6066
42.71180.92160.09312.3913-0.64291.90280.08890.14830.1023-0.1212-0.0485-0.09390.00520.0796-0.04040.0280.00010.02890.04550.01120.0397.891-14.742377.0941
53.7723-2.87050.45756.47950.1130.5799-0.1097-0.1237-0.20760.10170.19680.57750.0363-0.1936-0.08710.0189-0.02590.01580.1330.03460.1092-13.9742-22.12979.216
62.60570.1240.75835.56540.38452.9899-0.017-0.225-0.00310.6525-0.1136-0.53110.008-0.21840.13070.0787-0.0186-0.06210.09230.010.1595-45.6418-21.375285.8183
71.2806-0.14160.81563.8214-0.21372.87070.06910.0894-0.0306-0.48880.0299-0.22710.111-0.0216-0.0990.1534-0.00290.06670.0704-0.0330.0527-54.3601-26.795755.3049
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 99
2X-RAY DIFFRACTION2A117 - 233
3X-RAY DIFFRACTION3A234 - 347
4X-RAY DIFFRACTION4A348 - 453
5X-RAY DIFFRACTION5A454 - 555
6X-RAY DIFFRACTION6A556 - 668
7X-RAY DIFFRACTION7A669 - 781

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