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- PDB-2y4u: Crystal structure of human P58(IPK) in space group P312 -

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Basic information

Entry
Database: PDB / ID: 2y4u
TitleCrystal structure of human P58(IPK) in space group P312
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 / negative regulation of translation in response to endoplasmic reticulum stress / protein folding in endoplasmic reticulum / XBP1(S) activates chaperone genes / misfolded protein binding / cellular response to cold / protein kinase inhibitor activity / 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 / negative regulation of translation in response to endoplasmic reticulum stress / protein folding in endoplasmic reticulum / XBP1(S) activates chaperone genes / misfolded protein binding / cellular response to cold / protein kinase inhibitor activity / 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) / azurophil granule lumen / extracellular vesicle / protein-folding chaperone binding / defense response to virus / endoplasmic reticulum lumen / Neutrophil degranulation / protein kinase binding / negative regulation of apoptotic process / endoplasmic reticulum / extracellular exosome / extracellular region / membrane / cytosol / cytoplasm
Similarity search - Function
: / DnaJ domain / Tetratricopeptide repeat / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Tetratricopeptide repeat / Chaperone J-domain superfamily / DnaJ domain / Tetratricopeptide repeat ...: / DnaJ domain / Tetratricopeptide repeat / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Tetratricopeptide repeat / Chaperone J-domain superfamily / DnaJ domain / 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 / Helix Hairpins / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / 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: 3.2 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. / Guy, J.E.
History
DepositionJan 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)52,3691
Polymers52,3691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DNAJ HOMOLOG SUBFAMILY C MEMBER 3

A: DNAJ HOMOLOG SUBFAMILY C MEMBER 3

A: DNAJ HOMOLOG SUBFAMILY C MEMBER 3


Theoretical massNumber of molelcules
Total (without water)157,1073
Polymers157,1073
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area6820 Å2
ΔGint-19.8 kcal/mol
Surface area67440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.620, 124.620, 92.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number149
Space group name H-MP312

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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 P58IPK


Mass: 52368.887 Da / Num. of mol.: 1 / 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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growDetails: 0.1 M TRIS, PH 8.5, 1.3 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: ID23-1 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 12967 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.9
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IEG

3ieg


Resolution: 3.2→29.93 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.913 / SU B: 56.174 / SU ML: 0.435 / Cross valid method: THROUGHOUT / ESU R: 0.899 / ESU R Free: 0.479 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.28631 677 5 %RANDOM
Rwork0.24418 ---
obs0.24626 12967 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 118.539 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20.78 Å20 Å2
2--1.56 Å20 Å2
3----2.35 Å2
Refinement stepCycle: LAST / Resolution: 3.2→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3429 0 0 0 3429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223481
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.9744668
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9865423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54925.169178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.78515698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1571523
X-RAY DIFFRACTIONr_chiral_restr0.0850.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022597
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 3.2→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 64 -
Rwork0.328 938 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -34.6234 Å / Origin y: -32.986 Å / Origin z: -22.5066 Å
111213212223313233
T0.3079 Å2-0.0805 Å20.1064 Å2-0.3633 Å20.1218 Å2--0.3016 Å2
L0.2456 °20.0587 °2-0.0135 °2-0.79 °20.0719 °2--0.034 °2
S-0.0013 Å °0.2734 Å °0.0402 Å °0.0171 Å °-0.0606 Å °-0.2108 Å °0.0336 Å °-0.0127 Å °0.0619 Å °

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