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- PDB-5elh: Crystal structure of mouse Unkempt zinc fingers 1-3 (ZnF1-3), bou... -

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Basic information

Entry
Database: PDB / ID: 5elh
TitleCrystal structure of mouse Unkempt zinc fingers 1-3 (ZnF1-3), bound to RNA
Components
  • RING finger protein unkempt homolog
  • RNA (5'-R(*UP*UP*AP*UP*U)-3')
KeywordsRNA BINDING PROTEIN/RNA / Unkempt / RNA-binding protein / CCCH zinc fingers / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


mRNA CDS binding / : / : / cell morphogenesis involved in neuron differentiation / negative regulation of cytoplasmic translation / neuron migration / in utero embryonic development / metal ion binding / cytoplasm
Similarity search - Function
Unkempt, zinc finger domain 1 / RING finger protein Unkempt-like / Unkempt Zinc finger domain 1 (Znf1) / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile.
Similarity search - Domain/homology
RNA / RING finger protein unkempt homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsTeplova, M. / Murn, J. / Zarnack, K. / Shi, Y. / Patel, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104962 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Recognition of distinct RNA motifs by the clustered CCCH zinc fingers of neuronal protein Unkempt.
Authors: Murn, J. / Teplova, M. / Zarnack, K. / Shi, Y. / Patel, D.J.
History
DepositionNov 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Jan 20, 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
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: RING finger protein unkempt homolog
B: RING finger protein unkempt homolog
R: RNA (5'-R(*UP*UP*AP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,95513
Polymers36,1783
Non-polymers77710
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-47 kcal/mol
Surface area18230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.194, 56.559, 131.025
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein RING finger protein unkempt homolog / Zinc finger CCCH domain-containing protein 5


Mass: 17334.453 Da / Num. of mol.: 2 / Fragment: UNP residues 31-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Unk, Kiaa1753, Zc3h5, Zc3hdc5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BL48
#2: RNA chain RNA (5'-R(*UP*UP*AP*UP*U)-3')


Mass: 1508.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate, 0.1 M Tris pH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2827 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2827 Å / Relative weight: 1
ReflectionResolution: 1.8→131 Å / Num. obs: 30245 / % possible obs: 99.4 % / Redundancy: 6.6 % / Net I/σ(I): 14.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SCALAdata scaling
AutoSolphasing
RefinementResolution: 1.8→19.941 Å / FOM work R set: 0.7925 / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2155 1525 5.06 %
Rwork0.1782 28589 -
obs0.1801 30114 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.41 Å2 / Biso mean: 29.15 Å2 / Biso min: 9.36 Å2
Refinement stepCycle: final / Resolution: 1.8→19.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 99 26 307 2805
Biso mean--59.88 33.61 -
Num. residues----287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072596
X-RAY DIFFRACTIONf_angle_d1.0273533
X-RAY DIFFRACTIONf_chiral_restr0.065349
X-RAY DIFFRACTIONf_plane_restr0.005441
X-RAY DIFFRACTIONf_dihedral_angle_d14.57972
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.86150.46681410.40132471261297
1.8615-1.9280.34421320.29512544267699
1.928-2.00510.31981390.268525572696100
2.0051-2.09630.24821200.22962599271999
2.0963-2.20670.25841280.18922557268599
2.2067-2.34470.22891310.1812600273199
2.3447-2.52540.23111190.17022620273999
2.5254-2.7790.23851590.18162568272799
2.779-3.17970.221490.172426272776100
3.1797-4.00080.18991520.146526602812100
4.0008-19.94230.15491550.15042786294199
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)
11.93610.23580.29962.0317-0.14692.17920.0616-0.31690.04670.1905-0.00610.1924-0.0161-0.2889-0.03570.1739-0.00970.03190.1984-0.04390.16249.83186.4191113.5322
22.07150.154-0.00580.9808-0.61342.9097-0.00570.02690.09-0.01790.04230.0295-0.0385-0.0812-0.04220.12010.01710.00040.0677-0.00540.12486.7536-24.0251113.5776
30.2468-1.1818-0.22165.9591.01510.206-0.18110.0721-0.04140.04760.4424-0.15230.25430.0543-0.18790.17540.0203-0.04040.192-0.04640.172912.6853-36.3845119.8249
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 172 )A0
2X-RAY DIFFRACTION2chain 'B' and (resid 31 through 170 )B0
3X-RAY DIFFRACTION3chain 'R' and (resid 1 through 5 )R0

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