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- PDB-2y4t: Crystal structure of the human co-chaperone P58(IPK) -

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Basic information

Entry
Database: PDB / ID: 2y4t
TitleCrystal structure of the human co-chaperone P58(IPK)
ComponentsDNAJ HOMOLOG SUBFAMILY C MEMBER 3
KeywordsCHAPERONE / ENDOPLASMIC RETICULUM / PROTEIN FOLDING / TETRATRICOPEPTIDEREPEAT / J DOMAIN / UNFOLDED PROTEIN RESPONSE
Function / homology
Function and homology information


positive regulation of translation initiation in response to endoplasmic reticulum stress / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / protein folding in endoplasmic reticulum / XBP1(S) activates chaperone genes / misfolded protein binding / cellular response to cold / protein kinase inhibitor activity / smooth endoplasmic reticulum / Viral mRNA Translation / response to unfolded protein ...positive regulation of translation initiation in response to endoplasmic reticulum stress / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / protein folding in endoplasmic reticulum / XBP1(S) activates chaperone genes / misfolded protein binding / cellular response to cold / protein kinase inhibitor activity / smooth endoplasmic reticulum / Viral mRNA Translation / response to unfolded protein / proteolysis involved in protein catabolic process / Post-translational protein phosphorylation / PKR-mediated signaling / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / extracellular vesicle / azurophil granule lumen / protein-folding chaperone binding / defense response to virus / endoplasmic reticulum lumen / Neutrophil degranulation / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / extracellular exosome / extracellular region / membrane / cytosol / cytoplasm
Similarity search - Function
DnaJ domain / Tetratricopeptide repeat / DnaJ domain / Tetratricopeptide repeat / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Tetratricopeptide repeat 1 / Tetratricopeptide repeat ...DnaJ domain / Tetratricopeptide repeat / DnaJ domain / Tetratricopeptide repeat / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DnaJ homolog subfamily C member 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSvard, M. / Biterova, E.I. / Bourhis, J.-M. / Guy, J.E.
CitationJournal: Plos One / Year: 2011
Title: The Crystal Structure of the Human Co-Chaperone P58Ipk
Authors: Svard, M. / Biterova, E.I. / Bourhis, J.-M. / Guy, J.E.
History
DepositionJan 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release

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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 3
B: DNAJ HOMOLOG SUBFAMILY C MEMBER 3
C: DNAJ HOMOLOG SUBFAMILY C MEMBER 3


Theoretical massNumber of molelcules
Total (without water)155,8413
Polymers155,8413
Non-polymers00
Water45025
1
A: DNAJ HOMOLOG SUBFAMILY C MEMBER 3


Theoretical massNumber of molelcules
Total (without water)51,9471
Polymers51,9471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNAJ HOMOLOG SUBFAMILY C MEMBER 3


Theoretical massNumber of molelcules
Total (without water)51,9471
Polymers51,9471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNAJ HOMOLOG SUBFAMILY C MEMBER 3


Theoretical massNumber of molelcules
Total (without water)51,9471
Polymers51,9471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)212.250, 212.250, 283.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2009-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.4497, 0.8931, 0.01416), (0.8931, -0.4498, 0.008273), (0.01376, 0.008923, -0.9999)-1.346, 3.614, -89.41
2given(0.4432, 0.8964, 0.01124), (0.8963, -0.4433, 0.01285), (0.01651, 0.004378, -0.9999)-1.443, 4.663, -180.6
3given(1, 0.007427, -0.003283), (-0.007413, 1, 0.004333), (0.003315, -0.004308, 1)-0.501, -0.269, 91.2

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Components

#1: Protein DNAJ HOMOLOG SUBFAMILY C MEMBER 3 / INTERFERON-INDUCED\ / DOUBLE-STRANDED RNA-ACTIVATED PROTEIN KINASE INHIBITOR / PROTEIN KINASE ...INTERFERON-INDUCED\ / DOUBLE-STRANDED RNA-ACTIVATED PROTEIN KINASE INHIBITOR / PROTEIN KINASE INHIBITOR OF 58 KDA / PROTEIN KINASE INHIBITOR P58 / P58IPK


Mass: 51946.836 Da / Num. of mol.: 3 / Fragment: RESIDUES 35-461
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: P58IPK_6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q13217
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.9 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growDetails: 0.1 M HEPES, PH 8.2, 1.4 M SUCCINIC ACID, 1% (W/V) PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 44987 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 74.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.5
Reflection shellResolution: 3→3.08 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.2 / % possible all: 79.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0081refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→25 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 39.464 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R: 1.211 / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. THE REGIONS THAT CORRESPOND TO AMINO ACIDS 400-406, 451-452 OF CHAIN B AND 400-409, 449- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. THE REGIONS THAT CORRESPOND TO AMINO ACIDS 400-406, 451-452 OF CHAIN B AND 400-409, 449-450 OF CHAIN C ARE LOCALIZED TO VERY FLEXIBLE LOOPS, CONTAIN VERY WEAK ELECTRON DENSITY AND HAVE BEEN MODELED BASED ON THE POSITION OF RESPECTIVE AMINO ACIDS OF BETTER ORDERED CHAIN A. IN CHAINS B AND C, THE LOOP BETWEEN HELICES I AND II OF THE J DOMAIN (AMINO ACID RESIDUES 402-408) AND THE LOOP IN THE J DOMAIN (RESIDUES 425-428) HAVE VERY WEAK DENSITY AND ARE MODELED BASED ON THEIR POSITION IN CHAIN A.
RfactorNum. reflection% reflectionSelection details
Rfree0.29058 2416 5.1 %RANDOM
Rwork0.24338 ---
obs0.24582 44987 96.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 107.121 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20.94 Å20 Å2
2--1.88 Å20 Å2
3----2.82 Å2
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10234 0 0 25 10259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210390
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0431.97513934
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.67451262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33625.141531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.699152082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9011569
X-RAY DIFFRACTIONr_chiral_restr0.0740.21505
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027751
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 144 -
Rwork0.326 2511 -
obs--74.52 %
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)
10.42220.1733-0.02990.2975-0.03210.2407-0.01670.06550.1265-0.0788-0.02330.1837-0.0488-0.14660.040.0749-0.0057-0.060.1878-0.04910.130581.1791-49.378724.0866
20.5292-0.22420.08210.7409-0.12780.27570.0262-0.0997-0.13480.1887-0.05190.25210.0341-0.11690.02580.0944-0.00320.06570.2641-0.05090.112281.2235-73.3271-20.705
30.46210.1346-0.0650.3753-0.10350.36920.00430.06690.1649-0.0978-0.0180.2469-0.0602-0.19050.01380.1297-0.0335-0.0730.2297-0.05420.199281.1394-49.5399-67.1397
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 455
2X-RAY DIFFRACTION2B35 - 455
3X-RAY DIFFRACTION3C34 - 455

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