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- PDB-3vke: Contribution of the first K-homology domain of poly(C)-binding pr... -

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Basic information

Entry
Database: PDB / ID: 3vke
TitleContribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides
Components
  • DNA (5'-D(P*AP*CP*CP*CP*CP*A)-3')
  • Poly(rC)-binding protein 1
KeywordsDNA BINDING PROTEIN/DNA / PCBP-1 / DNA RNA BINDING PROTEIN / KH DOMAIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


sequence-specific single stranded DNA binding / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / cytoplasmic ribonucleoprotein granule / single-stranded DNA binding / postsynaptic density / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / cadherin binding / ribonucleoprotein complex ...sequence-specific single stranded DNA binding / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / cytoplasmic ribonucleoprotein granule / single-stranded DNA binding / postsynaptic density / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / cadherin binding / ribonucleoprotein complex / viral RNA genome replication / mRNA binding / positive regulation of transcription by RNA polymerase II / 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
DNA / Poly(rC)-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsTraore, D.A.K. / Wilce, M.C.J. / Wilce, J.A.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides
Authors: Yoga, Y.M.K. / Traore, D.A.K. / Sidiqi, M. / Szeto, C. / Pendini, N.R. / Barker, A. / Leedman, P.J. / Wilce, J.A. / Wilce, M.C.J.
History
DepositionNov 15, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly(rC)-binding protein 1
B: Poly(rC)-binding protein 1
C: Poly(rC)-binding protein 1
D: Poly(rC)-binding protein 1
R: DNA (5'-D(P*AP*CP*CP*CP*CP*A)-3')
S: DNA (5'-D(P*AP*CP*CP*CP*CP*A)-3')
T: DNA (5'-D(P*AP*CP*CP*CP*CP*A)-3')
U: DNA (5'-D(P*AP*CP*CP*CP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)40,8048
Polymers40,8048
Non-polymers00
Water1,27971
1
A: Poly(rC)-binding protein 1
R: DNA (5'-D(P*AP*CP*CP*CP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)10,2012
Polymers10,2012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(rC)-binding protein 1
S: DNA (5'-D(P*AP*CP*CP*CP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)10,2012
Polymers10,2012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Poly(rC)-binding protein 1
T: DNA (5'-D(P*AP*CP*CP*CP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)10,2012
Polymers10,2012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Poly(rC)-binding protein 1
U: DNA (5'-D(P*AP*CP*CP*CP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)10,2012
Polymers10,2012
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.597, 114.887, 43.429
Angle α, β, γ (deg.)90.00, 93.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Poly(rC)-binding protein 1 / Alpha-CP1 / Heterogeneous nuclear ribonucleoprotein E1 / hnRNP E1 / Nucleic acid-binding protein SUB2.3


Mass: 8462.802 Da / Num. of mol.: 4 / Fragment: KH1 domain / Mutation: C54S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCBP1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15365
#2: DNA chain
DNA (5'-D(P*AP*CP*CP*CP*CP*A)-3')


Mass: 1738.183 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1M phosphate-citrate, 40%(v/v) PEG 300, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.77→38.51 Å / Num. obs: 36143 / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZTG

1ztg


Resolution: 1.77→27.16 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0 / SU B: 4.484 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 1808 5 %RANDOM
Rwork0.161 ---
obs0.1636 35997 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 90.59 Å2 / Biso mean: 31.5288 Å2 / Biso min: 13.06 Å2
Baniso -1Baniso -2Baniso -3
1--2.36 Å2-0 Å2-1.68 Å2
2--1.63 Å2-0 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.77→27.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 388 0 71 2696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222632
X-RAY DIFFRACTIONr_angle_refined_deg2.2432.1593602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4335293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11123.28873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2315433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.7031517
X-RAY DIFFRACTIONr_chiral_restr0.1570.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211739
X-RAY DIFFRACTIONr_mcbond_it2.4091.51448
X-RAY DIFFRACTIONr_mcangle_it3.96222330
X-RAY DIFFRACTIONr_scbond_it5.8531184
X-RAY DIFFRACTIONr_scangle_it8.2774.51270
X-RAY DIFFRACTIONr_rigid_bond_restr3.11532632
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 137 -
Rwork0.187 2592 -
all-2729 -
obs--100 %

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