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- PDB-5elk: Crystal structure of mouse Unkempt zinc fingers 4-6 (ZnF4-6), bou... -

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Basic information

Entry
Database: PDB / ID: 5elk
TitleCrystal structure of mouse Unkempt zinc fingers 4-6 (ZnF4-6), bound to RNA
Components
  • RING finger protein unkempt homolog
  • RNA
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: 2.3 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 1.3Apr 6, 2016Group: Source and taxonomy
Revision 1.4Sep 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 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 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
R: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3035
Polymers17,1072
Non-polymers1963
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.192, 51.203, 37.460
Angle α, β, γ (deg.)90.00, 97.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 15231.030 Da / Num. of mol.: 1 / Fragment: UNP residues 204-335
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


Mass: 1876.173 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.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.1 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Hepes pH 7.0, 17 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2828 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2828 Å / Relative weight: 1
ReflectionResolution: 2.29→41.25 Å / Num. obs: 5787 / % possible obs: 96.7 % / Redundancy: 3.7 % / Net I/σ(I): 16

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SCALAdata scaling
AutoSolphasing
RefinementResolution: 2.3→19.348 Å / FOM work R set: 0.7947 / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 26.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2235 263 4.6 %
Rwork0.1805 5458 -
obs0.1824 5721 96.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.94 Å2 / Biso mean: 52.74 Å2 / Biso min: 22.77 Å2
Refinement stepCycle: final / Resolution: 2.3→19.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 90 3 19 1095
Biso mean--60.89 42.22 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081129
X-RAY DIFFRACTIONf_angle_d1.1641549
X-RAY DIFFRACTIONf_chiral_restr0.061146
X-RAY DIFFRACTIONf_plane_restr0.006191
X-RAY DIFFRACTIONf_dihedral_angle_d16.366447
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.89630.29681320.22462665279794
2.8963-19.34890.20631310.1712793292498
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)
16.98650.89650.54151.4856-0.68172.2561-0.125-0.7992-0.41590.390.01180.13040.0625-0.05630.10820.3760.08920.05710.32360.02640.354815.60034.459627.4412
23.00062.29761.81776.533-2.4726.7488-0.3718-0.1071.254-0.57720.29630.40.0676-1.60860.66780.63430.045-0.12820.3659-0.03450.535515.323113.660623.3703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 204 through 324)A0
2X-RAY DIFFRACTION2chain 'R' and (resid 2 through 7 )R0

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