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- PDB-4jvh: Structure of the star domain of quaking protein in complex with RNA -

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Basic information

Entry
Database: PDB / ID: 4jvh
TitleStructure of the star domain of quaking protein in complex with RNA
Components
  • Protein quaking
  • RNA (5'-R(*UP*UP*CP*AP*CP*UP*AP*AP*CP*AP*A)-3')
KeywordsRNA BINDING PROTEIN / STAR domain / RNA regulator / TRANSLATION
Function / homology
Function and homology information


regulation of macrophage differentiation / internal N(7)-methylguanine-containing RNA reader activity / 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 / positive regulation of myelination ...regulation of macrophage differentiation / internal N(7)-methylguanine-containing RNA reader activity / 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 / positive regulation of myelination / intracellular mRNA localization / 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 / Signaling by BRAF and RAF1 fusions / transcription coactivator activity / negative regulation of translation / mRNA binding / synapse / positive regulation of gene expression / DNA binding / RNA binding / nucleus / cytosol
Similarity search - Function
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 / KH domain / Ribosomal Protein S8; Chain: A, domain 1 ...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 / KH domain / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / KH domain-containing RNA-binding protein QKI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.501 Å
AuthorsTeplova, M. / Hafner, M. / Teplov, D. / Essig, K. / Tuschl, T. / Patel, D.J.
CitationJournal: Genes Dev. / Year: 2013
Title: Structure-function studies of STAR family Quaking proteins bound to their in vivo RNA target sites.
Authors: Teplova, M. / Hafner, M. / Teplov, D. / Essig, K. / Tuschl, T. / Patel, D.J.
History
DepositionMar 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 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
D: RNA (5'-R(*UP*UP*CP*AP*CP*UP*AP*AP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8304
Polymers27,6382
Non-polymers1922
Water00
1
A: Protein quaking
D: RNA (5'-R(*UP*UP*CP*AP*CP*UP*AP*AP*CP*AP*A)-3')
hetero molecules

A: Protein quaking
D: RNA (5'-R(*UP*UP*CP*AP*CP*UP*AP*AP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6608
Polymers55,2764
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+2/31
2
A: Protein quaking
D: RNA (5'-R(*UP*UP*CP*AP*CP*UP*AP*AP*CP*AP*A)-3')
hetero molecules

A: Protein quaking
D: RNA (5'-R(*UP*UP*CP*AP*CP*UP*AP*AP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6608
Polymers55,2764
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area6010 Å2
ΔGint-51 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.634, 98.634, 103.137
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Protein quaking / Hqk / HqkI


Mass: 24202.705 Da / Num. of mol.: 1 / Fragment: STAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QKI, HKQ / Production host: Escherichia coli (E. coli) / References: UniProt: Q96PU8
#2: RNA chain RNA (5'-R(*UP*UP*CP*AP*CP*UP*AP*AP*CP*AP*A)-3')


Mass: 3435.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
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: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: PEG, pH 7.5, VAPOR DIFFUSION, temperature 298.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 120.13 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXAutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.501→19.73 Å / Occupancy max: 1 / Occupancy min: 0.81 / FOM work R set: 0.7236 / SU ML: 0.43 / σ(F): 0 / Phase error: 31.91 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3156 397 9.97 %random
Rwork0.2429 ---
obs0.2496 3983 98.74 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 427.48 Å2 / Biso mean: 101.9961 Å2 / Biso min: 6.32 Å2
Refinement stepCycle: LAST / Resolution: 3.501→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1412 170 10 0 1592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091628
X-RAY DIFFRACTIONf_angle_d0.8712222
X-RAY DIFFRACTIONf_chiral_restr0.054253
X-RAY DIFFRACTIONf_plane_restr0.003257
X-RAY DIFFRACTIONf_dihedral_angle_d16.501670
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5009-4.00380.34551270.26261139126697
4.0038-5.03050.3231300.26051179130999
5.0305-19.73040.30351400.2291268140899
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)
10.30520.1019-0.14470.4222-0.14210.1428-1.28940.50042.31850.98040.135-0.7565-0.29630.6671-0.2562-0.3194-0.2011-0.3356-0.119-1.0855-2.545448.446949.297948.8075
20.0184-0.0135-0.0223-0.00110.0160.010.2337-0.10050.6125-0.00880.58870.0087-0.0783-0.1263-00.65760.0002-0.24550.4027-0.29981.103242.205455.386351.9189
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 203 )A0
2X-RAY DIFFRACTION2chain 'D' and (resid 4 through 11 )D0

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