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- PDB-5dje: Crystal structure of the zuotin homology domain (ZHD) from yeast Zuo1 -

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Basic information

Entry
Database: PDB / ID: 5dje
TitleCrystal structure of the zuotin homology domain (ZHD) from yeast Zuo1
ComponentsZuotin
KeywordsCHAPERONE / HSP-40 / J-PROTEIN / MOLECULAR CHAPERONE / RIBOMSOME ASSOCIATION
Function / homology
Function and homology information


translational frameshifting / 'de novo' cotranslational protein folding / protein folding chaperone complex / ribosomal subunit export from nucleus / regulation of translational fidelity / Hsp70 protein binding / rRNA processing / ribosome binding / protein folding / transcription coactivator activity ...translational frameshifting / 'de novo' cotranslational protein folding / protein folding chaperone complex / ribosomal subunit export from nucleus / regulation of translational fidelity / Hsp70 protein binding / rRNA processing / ribosome binding / protein folding / transcription coactivator activity / ribosome / intracellular signal transduction / nucleolus / mitochondrion / DNA binding / cytosol / cytoplasm
Similarity search - Function
Ribosome-associated complex head domain / Ribosome-associated complex head domain superfamily / J-protein Zuotin/DnaJC2 / Ribosome-associated complex head domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Zuotin
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsShrestha, O.K. / Bingman, C.A. / Craig, E.A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM31107 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01GM098248 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54GM094584 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01GM094622 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Dual interaction of the Hsp70 J-protein cochaperone Zuotin with the 40S and 60S ribosomal subunits.
Authors: Lee, K. / Sharma, R. / Shrestha, O.K. / Bingman, C.A. / Craig, E.A.
History
DepositionSep 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 16, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zuotin
B: Zuotin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2146
Polymers33,7312
Non-polymers4844
Water7,674426
1
A: Zuotin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9722
Polymers16,8651
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Zuotin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2434
Polymers16,8651
Non-polymers3773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.480, 70.260, 95.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Zuotin / / DnaJ-related protein ZUO1 / J protein ZUO1 / Heat shock protein 40 homolog ZUO1 / Ribosome- ...DnaJ-related protein ZUO1 / J protein ZUO1 / Heat shock protein 40 homolog ZUO1 / Ribosome-associated complex subunit ZUO1


Mass: 16865.471 Da / Num. of mol.: 2 / Fragment: UNP residues 166-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ZUO1, YGR285C / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P32527
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: protein at 15 mg/ml was dissolved in 100 mM NaCl, 5 mM HEPES, 5 mM DTT, pH 7.5. One microliter of protein solution was mixed with one microliter of reservoir solution, 30% PEG 3350, 30 mM ...Details: protein at 15 mg/ml was dissolved in 100 mM NaCl, 5 mM HEPES, 5 mM DTT, pH 7.5. One microliter of protein solution was mixed with one microliter of reservoir solution, 30% PEG 3350, 30 mM MgCl2, 100 mM BisTris, pH 6.5, 5 mM DTT and equilibrated against the reservoir at 4C (277K)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2014
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 31477 / % possible obs: 99.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.93
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.49 / Mean I/σ(I) obs: 1.21 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.85→47.675 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 1902 5.73 %Thin shells
Rwork0.1739 ---
obs0.1765 31477 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→47.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 32 426 2762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112428
X-RAY DIFFRACTIONf_angle_d1.2413251
X-RAY DIFFRACTIONf_dihedral_angle_d12.638969
X-RAY DIFFRACTIONf_chiral_restr0.049308
X-RAY DIFFRACTIONf_plane_restr0.007423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8501-1.87350.34511930.31722238X-RAY DIFFRACTION100
1.8735-1.89811000000000.29222479X-RAY DIFFRACTION98
1.8981-1.92420.34261970.28362257X-RAY DIFFRACTION100
1.9242-1.95160.30611940.2692299X-RAY DIFFRACTION99
1.9516-1.98080.28711920.24152275X-RAY DIFFRACTION100
1.9808-2.01171000000000.23082473X-RAY DIFFRACTION99
2.0117-2.04470.24621960.21632257X-RAY DIFFRACTION100
2.0447-2.080.27181940.22232279X-RAY DIFFRACTION100
2.08-2.11780.28841920.21572288X-RAY DIFFRACTION100
2.1178-2.15851000000000.20382437X-RAY DIFFRACTION99
2.1585-2.20260.27271960.20422271X-RAY DIFFRACTION100
2.2026-2.25050.24461940.19192306X-RAY DIFFRACTION100
2.2505-2.30281000000000.17722456X-RAY DIFFRACTION100
2.3028-2.36040.2221930.17352272X-RAY DIFFRACTION100
2.3604-2.42420.24521930.17672314X-RAY DIFFRACTION100
2.4242-2.49560.23671940.16962283X-RAY DIFFRACTION100
2.4956-2.57611000000000.18142477X-RAY DIFFRACTION100
2.5761-2.66820.26981920.18282251X-RAY DIFFRACTION100
2.6682-2.7750.2411930.19382314X-RAY DIFFRACTION100
2.775-2.90130.28761890.18652286X-RAY DIFFRACTION100
2.9013-3.05421000000000.18022487X-RAY DIFFRACTION100
3.0542-3.24550.22741880.17962275X-RAY DIFFRACTION100
3.2455-3.4960.2191920.16472305X-RAY DIFFRACTION100
3.496-3.84770.16921840.14452297X-RAY DIFFRACTION100
3.8477-4.40411000000000.1412486X-RAY DIFFRACTION100
4.4041-5.54740.1541850.12972287X-RAY DIFFRACTION100
5.5474-47.69080.15931780.14122305X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 43.7221 Å / Origin y: 45.1083 Å / Origin z: 71.7817 Å
111213212223313233
T0.1759 Å2-0.0092 Å2-0.008 Å2-0.2095 Å20.0056 Å2--0.2131 Å2
L0.1587 °2-0.0051 °2-0.0003 °2-0.0907 °20.1919 °2--0.3264 °2
S0.0308 Å °0.0001 Å °-0.002 Å °0.0025 Å °0.0002 Å °-0.017 Å °-0.0264 Å °-0.0377 Å °-0.0219 Å °
Refinement TLS groupSelection details: all

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