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- PDB-4dnn: Crystal structure of the Quaking Qua1 homodimerization domain -

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Basic information

Entry
Database: PDB / ID: 4dnn
TitleCrystal structure of the Quaking Qua1 homodimerization domain
ComponentsProtein quaking
KeywordsSPLICING / Helix-turn-helix / HYDROPHOBIC HOMODIMER INTERFACE / PERPENDICULAR STACKING OF Protomers / DEVELOPMENTAL PROTEIN / RNA-binding / TRANSLATION REGULATION
Function / homology
Function and homology information


internal N(7)-methylguanine-containing RNA reader activity / positive regulation of 3'-UTR-mediated mRNA stabilization / negative regulation of miRNA catabolic process / myofibroblast contraction / negative regulation of 3'-UTR-mediated mRNA stabilization / spliceosome-depend formation of circular RNA / regulation of astrocyte differentiation / vascular associated smooth muscle cell differentiation / negative regulation of macrophage differentiation / axon ensheathment ...internal N(7)-methylguanine-containing RNA reader activity / positive regulation of 3'-UTR-mediated mRNA stabilization / negative regulation of miRNA catabolic process / myofibroblast contraction / negative regulation of 3'-UTR-mediated mRNA stabilization / spliceosome-depend formation of circular RNA / regulation of astrocyte differentiation / vascular associated smooth muscle cell differentiation / negative regulation of macrophage differentiation / axon ensheathment / positive regulation of myelination / intracellular mRNA localization / 3'-UTR-mediated mRNA destabilization / regulation of epithelial to mesenchymal transition / microglia differentiation / regulation of mRNA splicing, via spliceosome / mRNA stabilization / long-chain fatty acid biosynthetic process / miRNA binding / negative regulation of cold-induced thermogenesis / negative regulation of type I interferon production / spermatid development / positive regulation of oligodendrocyte differentiation / mRNA transport / vasculogenesis / myelination / negative regulation of angiogenesis / mRNA 3'-UTR binding / positive regulation of cholesterol biosynthetic process / SH3 domain binding / cytoplasmic stress granule / transcription coactivator activity / negative regulation of translation / mRNA binding / synapse / positive regulation of gene expression / DNA binding / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4010 / Protein quaking, putative nuclear localisation signal / Putative nuclear localisation signal of quaking / STAR protein, homodimerisation region / Homodimerisation region of STAR domain protein / : / KHDC4/BBP-like, KH-domain type I / KH domain-containing BBP-like / K Homology domain, type 1 superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4010 / Protein quaking, putative nuclear localisation signal / Putative nuclear localisation signal of quaking / STAR protein, homodimerisation region / Homodimerisation region of STAR domain protein / : / KHDC4/BBP-like, KH-domain type I / KH domain-containing BBP-like / K Homology domain, type 1 superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / K Homology domain / K homology RNA-binding domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
KH domain-containing RNA-binding protein QKI
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsBeuck, C. / Qu, S. / Williamson, J.R.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural Analysis of the Quaking Homodimerization Interface.
Authors: Beuck, C. / Qu, S. / Fagg, W.S. / Ares, M. / Williamson, J.R.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein quaking
B: Protein quaking
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4203
Polymers13,3802
Non-polymers401
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-20 kcal/mol
Surface area6830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.983, 36.024, 92.814
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 Protein quaking / MqkI / qkI


Mass: 6689.929 Da / Num. of mol.: 2 / Fragment: UNP residues 14-67 domain / Mutation: C35S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Qk, Qk1, Qka1, Qki, Quaking / Plasmid: modified pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) / References: UniProt: Q9QYS9
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: sodium cacodylate, calcium acetate, PEG 600, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9791358, 0.9184018, 0.979569
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2011 / Details: Rh coated flat mirror
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97913581
20.91840181
30.9795691
ReflectionResolution: 2.1→50 Å / Num. obs: 7046 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 41.1 Å2 / Rsym value: 0.036 / Net I/σ(I): 35.1
Reflection shellResolution: 2.1→2.65 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 578 / Rsym value: 0.288

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→31.911 Å / SU ML: 0.49 / σ(F): 0 / Phase error: 24.97 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 316 4.47 %random 5%
Rwork0.2163 ---
obs0.2179 7067 99.69 %-
all-7067 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.555 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3079 Å20 Å2-0 Å2
2--1.7713 Å20 Å2
3----2.0792 Å2
Refinement stepCycle: LAST / Resolution: 2.1→31.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 0 1 44 871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008871
X-RAY DIFFRACTIONf_angle_d1.1021172
X-RAY DIFFRACTIONf_dihedral_angle_d12.149352
X-RAY DIFFRACTIONf_chiral_restr0.068129
X-RAY DIFFRACTIONf_plane_restr0.006152
LS refinement shellResolution: 2.1→2.6456 Å
RfactorNum. reflection% reflection
Rfree0.2466 149 -
Rwork0.2203 3313 -
obs-3462 100 %
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)
12.1253-0.5391-0.34493.58381.73064.8439-0.27390.2427-0.1446-0.35440.05210.12110.39290.10070.12960.2694-0.00910.06030.21290.00670.194130.706915.466628.6974
24.0255-0.1022-1.40512.66261.31035.2299-0.1310.0228-0.0544-0.04690.0982-0.01320.31170.25220.00450.11580.0052-0.00760.1131-0.01030.165723.936522.689941.9519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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