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- PDB-5ayl: Crystal structure of ERdj5 form II -

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Basic information

Entry
Database: PDB / ID: 5ayl
TitleCrystal structure of ERdj5 form II
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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / DnaJ homolog subfamily C member 10
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWatanabe, S. / Maegawa, K. / Inaba, K.
CitationJournal: To Be Published
Title: Highly dynamic nature of ERdj5 is essential for enhancement of the ER associated degradation
Authors: Maegawa, K. / Watanabe, S. / Okumura, M. / Noi, K. / Inoue, M. / Ushioda, R. / Ogura, T. / Nagata, K. / Inaba, K.
History
DepositionAug 22, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5192
Polymers89,3181
Non-polymers2011
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint4 kcal/mol
Surface area36360 Å2
Unit cell
Length a, b, c (Å)75.981, 75.564, 79.237
Angle α, β, γ (deg.)90.00, 99.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DnaJ homolog subfamily C member 10 / Endoplasmic reticulum DNA J domain-containing protein 5 / ERdj5 / Endoplasmic reticulum DnaJ-PDI ...Endoplasmic reticulum DNA J domain-containing protein 5 / ERdj5 / Endoplasmic reticulum DnaJ-PDI fusion protein 1 / J domain-containing protein disulfide isomerase-like protein / JPDI


Mass: 89317.570 Da / Num. of mol.: 1 / Fragment: UNP residues 32-793
Mutation: C148S, C151S, G389V, C409S, C470S, C473S, C578S, C581S, C690S, C693S
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, Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor
#2: Chemical ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.04 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG8000, cystin / PH range: 7.5 or 8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 68376 / % possible obs: 98 % / Redundancy: 3.2 % / Rsym value: 0.126 / Net I/σ(I): 9.1
Reflection shellResolution: 2.4→2.46 Å / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 1.2 / % possible all: 82.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3APO

3apo


Resolution: 2.4→39.085 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.34 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2302 3294 4.94 %
Rwork0.1896 --
obs0.1916 66683 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→39.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5856 0 13 200 6069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036063
X-RAY DIFFRACTIONf_angle_d0.7448233
X-RAY DIFFRACTIONf_dihedral_angle_d15.5252157
X-RAY DIFFRACTIONf_chiral_restr0.029882
X-RAY DIFFRACTIONf_plane_restr0.0041065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.43430.3673820.29992245X-RAY DIFFRACTION82
2.4343-2.47070.36961140.27072379X-RAY DIFFRACTION88
2.4707-2.50930.34031060.26772540X-RAY DIFFRACTION93
2.5093-2.55040.32021450.24592576X-RAY DIFFRACTION96
2.5504-2.59440.2671490.23172622X-RAY DIFFRACTION98
2.5944-2.64150.32151530.2412667X-RAY DIFFRACTION99
2.6415-2.69230.30931220.24292716X-RAY DIFFRACTION100
2.6923-2.74730.2861360.23422697X-RAY DIFFRACTION100
2.7473-2.8070.29711110.23712704X-RAY DIFFRACTION100
2.807-2.87220.32111670.23412632X-RAY DIFFRACTION100
2.8722-2.94410.30041490.21652661X-RAY DIFFRACTION100
2.9441-3.02360.27351710.21022678X-RAY DIFFRACTION100
3.0236-3.11260.2511400.20842661X-RAY DIFFRACTION100
3.1126-3.2130.23461360.19512706X-RAY DIFFRACTION100
3.213-3.32780.25541510.19262699X-RAY DIFFRACTION100
3.3278-3.46090.23431340.17832730X-RAY DIFFRACTION100
3.4609-3.61830.21531160.17372684X-RAY DIFFRACTION100
3.6183-3.80890.20591410.1712710X-RAY DIFFRACTION100
3.8089-4.04740.19641360.16182663X-RAY DIFFRACTION100
4.0474-4.35950.16861440.14442694X-RAY DIFFRACTION100
4.3595-4.79750.16551440.14232700X-RAY DIFFRACTION100
4.7975-5.49010.1841380.16412706X-RAY DIFFRACTION100
5.4901-6.91070.28621540.19822667X-RAY DIFFRACTION100
6.9107-39.09050.14281550.16322652X-RAY DIFFRACTION99
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)
10.99480.0071-0.37280.67810.49660.28910.13460.5859-0.0529-0.03780.0872-0.009-0.4837-0.23990.01230.2580.0606-0.05460.3690.09860.22610.553511.731625.0496
21.665-0.74090.02591.4204-0.20191.8002-0.06060.117-0.0975-0.048-0.03870.31880.0966-0.0839-0.0010.174-0.0014-0.0410.15840.00530.23358.4907-6.580142.5166
30.7661-0.33320.11451.4090.22741.33520.0822-0.10810.02370.0144-0.01310.1459-0.0557-0.1699-00.19770.01820.00580.24290.05590.25927.911-5.923277.4203
41.12150.1255-0.08991.7816-0.70851.6541-0.012-0.1453-0.0738-0.0415-0.0332-0.0824-0.05930.25280.00010.1518-0.0076-0.00840.23070.02550.156627.92859.622358.9873
50.3754-0.0693-0.35850.9119-0.19820.7939-0.07250.0075-0.0487-0.18590.0347-0.22470.0296-0.004-00.25220.01110.02330.1695-0.00360.207837.98929.547737.5491
61.57520.07660.67252.32150.24532.5957-0.0730.12850.0757-0.11470.1166-0.1242-0.23870.20920.00130.3059-0.04480.03220.2406-0.01870.255344.56376.13210.9226
72.51051.1435-1.94451.70760.1411.92430.02870.2199-0.1550.050.0352-0.0714-0.20950.01210.00150.2231-0.0660.05550.268-0.06250.217765.4194-18.67754.381
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 116 )
2X-RAY DIFFRACTION2chain 'A' and (resid 117 through 233)
3X-RAY DIFFRACTION3chain 'A' and (resid 234 through 347)
4X-RAY DIFFRACTION4chain 'A' and (resid 348 through 453)
5X-RAY DIFFRACTION5chain 'A' and (resid 454 through 555)
6X-RAY DIFFRACTION6chain 'A' and (resid 556 through 668)
7X-RAY DIFFRACTION7chain 'A' and (resid 669 through 783)

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