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- PDB-2py9: Protein-RNA Interaction involving KH1 domain from Human Poly(C)-B... -

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Basic information

Entry
Database: PDB / ID: 2py9
TitleProtein-RNA Interaction involving KH1 domain from Human Poly(C)-Binding Protein-2
Components
  • 12-mer C-rich strand of human telomeric RNA
  • Poly(rC)-binding protein 2
KeywordsRNA AND DNA binding protein/RNA / PROTEIN-RNA COMPLEX / RNA AND DNA binding protein-RNA COMPLEX
Function / homology
Function and homology information


mRNA metabolic process / negative regulation of defense response to virus / promoter-enhancer loop anchoring activity / IRES-dependent viral translational initiation / chromatin looping / lncRNA binding / negative regulation of cGAS/STING signaling pathway / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / Negative regulators of DDX58/IFIH1 signaling ...mRNA metabolic process / negative regulation of defense response to virus / promoter-enhancer loop anchoring activity / IRES-dependent viral translational initiation / chromatin looping / lncRNA binding / negative regulation of cGAS/STING signaling pathway / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / Negative regulators of DDX58/IFIH1 signaling / SARS-CoV-1 activates/modulates innate immune responses / single-stranded DNA binding / defense response to virus / proteasome-mediated ubiquitin-dependent protein catabolic process / postsynaptic density / ribonucleoprotein complex / viral RNA genome replication / innate immune response / focal adhesion / mRNA binding / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / enzyme binding / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / Type-1 KH domain profile. / 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) / Poly(rC)-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsJames, T.L. / Du, Z. / Lee, J.K.
CitationJournal: Rna / Year: 2007
Title: X-ray crystallographic and NMR studies of protein-protein and protein-nucleic acid interactions involving the KH domains from human poly(C)-binding protein-2.
Authors: Du, Z. / Lee, J.K. / Fenn, S. / Tjhen, R. / Stroud, R.M. / James, T.L.
History
DepositionMay 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / 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_ncs_dom_lim / struct_ref_seq_dif
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: 12-mer C-rich strand of human telomeric RNA
F: 12-mer C-rich strand of human telomeric RNA
A: Poly(rC)-binding protein 2
B: Poly(rC)-binding protein 2
C: Poly(rC)-binding protein 2
D: Poly(rC)-binding protein 2


Theoretical massNumber of molelcules
Total (without water)40,0956
Polymers40,0956
Non-polymers00
Water91951
1
E: 12-mer C-rich strand of human telomeric RNA
A: Poly(rC)-binding protein 2
B: Poly(rC)-binding protein 2


Theoretical massNumber of molelcules
Total (without water)20,0473
Polymers20,0473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: 12-mer C-rich strand of human telomeric RNA
C: Poly(rC)-binding protein 2
D: Poly(rC)-binding protein 2


Theoretical massNumber of molelcules
Total (without water)20,0473
Polymers20,0473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.006, 58.697, 71.496
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 13 - 80 / Label seq-ID: 4 - 71

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AC
21BD
12CE
22DF

NCS ensembles :
ID
1
2
Detailsbiological assembly is 2 homo-dimers binding to 2 independent strands of RNA. One homo-dimer is present in the asymmetric unit. The others are generated via the two-fold axis.

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Components

#1: RNA chain 12-mer C-rich strand of human telomeric RNA


Mass: 3715.288 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein
Poly(rC)-binding protein 2 / Alpha-CP2 / hnRNP-E2


Mass: 8166.099 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCBP2 / Plasmid: pet24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): bl21(de3) / References: UniProt: Q15366
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 25% PEG 8000, 100mM sodium acetate, 100mM sodium cacodylate pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2sodium acetate11
3sodium cacodylate11
4PEG 800012
5sodium acetate12
6sodium cacodylate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 29, 2005 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 2.56→70.1 Å / Num. all: 12378 / Num. obs: 11660 / % possible obs: 94.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.4 % / Rmerge(I) obs: 0.102 / Rsym value: 0.096 / Net I/σ(I): 14.4
Reflection shellResolution: 2.56→2.626 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 3.1 / % possible all: 90.73

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.916 / SU B: 19.899 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.966 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26862 591 4.8 %RANDOM
Rwork0.21798 ---
obs0.22038 11656 94.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.229 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å20 Å20 Å2
2---0.13 Å20 Å2
3---1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.56→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2132 490 0 51 2673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0222692
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.3062.2283704
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4755275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.424.28677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.315458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.6561516
X-RAY DIFFRACTIONr_chiral_restr0.1550.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021736
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2860.21124
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3380.21816
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2111
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3210.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5531.51422
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.13922213
X-RAY DIFFRACTIONr_scbond_it3.4231500
X-RAY DIFFRACTIONr_scangle_it5.0044.51491
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Number: 517 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.430.05
2Ctight positional0.410.05
1Atight thermal0.50.5
2Ctight thermal0.640.5
LS refinement shellResolution: 2.56→2.626 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.469 47 -
Rwork0.365 785 -
obs--90.73 %
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)
13.2547-1.02910.19422.6141.64612.5880.190.40520.7385-0.1125-0.2173-0.07440.0024-0.09230.02730.02690.02190.0546-0.00970.12630.1744-4.1489-16.54739.2691
24.0203-0.9427-0.84092.3005-0.93262.95440.1552-0.41440.70490.07160.0711-0.15940.02360.2817-0.22630.0262-0.0344-0.0090.0072-0.12310.1381.3077-16.89527.2324
35.93470.2890.31532.49191.19910.8001-0.0207-0.4211-0.30010.0624-0.12060.05190.0632-0.23280.14130.05210.0087-0.01630.1665-0.0138-0.035816.062-10.4995-15.6771
41.88980.05710.35115.27710.33354.4422-0.09780.2101-0.53480.1256-0.00490.18220.21430.03620.1028-0.02590.10490.06620.11120.04040.0598-17.9453-7.579452.0541
5000000000000000000000000
6000000000000000000000000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC13 - 804 - 71
2X-RAY DIFFRACTION2BD13 - 804 - 71
3X-RAY DIFFRACTION3CE13 - 804 - 71
4X-RAY DIFFRACTION4DF13 - 804 - 71
5X-RAY DIFFRACTION5EA1 - 121 - 12
6X-RAY DIFFRACTION6FB1 - 121 - 12

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