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- PDB-2axy: Crystal Structure of KH1 domain of human Poly(C)-binding protein-... -

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Basic information

Entry
Database: PDB / ID: 2axy
TitleCrystal Structure of KH1 domain of human Poly(C)-binding protein-2 with C-rich strand of human telomeric DNA
Components
  • C-rich strand of human telomeric dna
  • Poly(rC)-binding protein 2
KeywordsDNA BINDING PROTEIN/DNA / protein-dna complex / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


mRNA metabolic process / regulation of RNA metabolic process / negative regulation of defense response to virus / IRES-dependent viral translational initiation / 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 ...mRNA metabolic process / regulation of RNA metabolic process / negative regulation of defense response to virus / IRES-dependent viral translational initiation / 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 / regulation of gene expression / proteasome-mediated ubiquitin-dependent protein catabolic process / defense response to virus / postsynaptic density / ribonucleoprotein complex / viral RNA genome replication / innate immune response / focal adhesion / mRNA binding / ubiquitin protein ligase binding / enzyme binding / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsDu, Z. / Lee, J.K. / Tjhen, R.J. / Li, S. / Stroud, R.M. / James, T.L.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structure of the First KH Domain of Human Poly(C)-binding Protein-2 in Complex with a C-rich Strand of Human Telomeric DNA at 1.7 A
Authors: Du, Z. / Lee, J.K. / Tjhen, R. / Li, S. / Pan, H. / Stroud, R.M. / James, T.L.
History
DepositionSep 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: C-rich strand of human telomeric dna
F: C-rich strand of human telomeric dna
G: C-rich strand of human telomeric dna
H: C-rich strand of human telomeric dna
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)40,9308
Polymers40,9308
Non-polymers00
Water3,999222
1
E: C-rich strand of human telomeric dna
F: C-rich strand of human telomeric dna
A: Poly(rC)-binding protein 2
B: Poly(rC)-binding protein 2


Theoretical massNumber of molelcules
Total (without water)20,4654
Polymers20,4654
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: C-rich strand of human telomeric dna
H: C-rich strand of human telomeric dna
C: Poly(rC)-binding protein 2
D: Poly(rC)-binding protein 2


Theoretical massNumber of molelcules
Total (without water)20,4654
Polymers20,4654
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.603, 115.176, 45.525
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: DNA chain
C-rich strand of human telomeric dna


Mass: 2066.401 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
Poly(rC)-binding protein 2 / Alpha-CP2 / hnRNP-E2


Mass: 8166.099 Da / Num. of mol.: 4 / Fragment: KH1 domain of human PCBP2 (residues 11-82)
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.: 222 / 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: 2.183 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: PEG 8000, Cacodylate, Acetate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2Cacodylate11
3Acetate11
4H2O11
5PEG 800012
6Cacodylate12
7Acetate12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979594 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2004 / 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: 0.979594 Å / Relative weight: 1
ReflectionRedundancy: 4 % / Number: 67408 / Rmerge(I) obs: 0.072 / Χ2: 1.037 / D res high: 1.75 Å / D res low: 60 Å / % possible obs: 98.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.016092.310.0251.0014.1
3.184.0197.910.0330.9724.2
2.783.1899.110.0480.994.2
2.522.7899.410.0741.0494.2
2.342.5299.810.1071.0714.2
2.22.3410010.1211.044.1
2.092.210010.1561.0094.1
22.0910010.2181.0474.1
1.93210010.3171.074.1
1.861.9310010.4271.0714
1.81.8699.810.561.0723.5
1.751.897.110.6381.0763
ReflectionResolution: 1.7→66.67 Å / Num. obs: 39246 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 6.1
Reflection shellResolution: 1.7→1.81 Å / Redundancy: 6 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 0.7 / Rsym value: 0.887 / % possible all: 96.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
CNSphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.375 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23759 1995 5.1 %RANDOM
Rwork0.21419 ---
obs0.21541 37143 99.28 %-
all-39373 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.586 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2184 444 0 222 2850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222696
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5852.2043688
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.815282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83824.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36915468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0851516
X-RAY DIFFRACTIONr_chiral_restr0.1090.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021767
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21184
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21833
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2201
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.291.51461
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52222272
X-RAY DIFFRACTIONr_scbond_it2.60931467
X-RAY DIFFRACTIONr_scangle_it3.7294.51416
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 122 -
Rwork0.286 2584 -
obs--94.29 %
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)
11.7588-0.29270.27031.1881-0.45982.20890.0107-0.2055-0.02280.1731-0.0326-0.08210.02420.22590.0218-0.0780.0068-0.0136-0.0550.0125-0.066246.010368.613629.1753
22.7059-1.6133-0.13272.9274-0.64571.2720.10690.16430.1302-0.0848-0.1233-0.2014-0.07470.14370.0163-0.07420.010100.01650.0109-0.032357.568568.809215.448
32.07950.07380.82351.15760.4652.6570.00720.22540.0867-0.1767-0.0580.09110.0113-0.03690.0509-0.06150.0303-0.0117-0.0695-0.0019-0.058726.481673.247310.5995
42.6317-0.4335-0.11633.32920.97331.71820.0151-0.1687-0.04630.05970.00410.07810.0316-0.0432-0.0192-0.03960.0315-0.0012-0.06450.0085-0.052816.268578.838124.4559
54.53545.46622.12288.8824.281811.4934-0.2057-0.1242-0.34940.26840.24840.3590.1425-0.1654-0.0427-0.0565-0.01490.0122-0.06640.0394-0.059639.837962.654336.7351
611.383-6.74382.89998.865-3.86767.10560.19760.68360.0926-0.2826-0.3577-0.766-0.16990.23480.1602-0.04770.10380.02330.07730.0376-0.053464.32363.5849.0415
72.04770.2706-0.82694.0031-2.3857.3349-0.14970.2205-0.5032-0.25230.0266-0.27390.47670.08270.1230.02470.0702-0.0014-0.0067-0.0441-0.017130.616364.04964.4309
813.20364.95223.27073.74083.227611.745-0.0234-0.4544-0.60840.81940.19580.44060.5991-0.0556-0.17240.11210.03130.02260.06270.0742-0.042911.469775.553234.5349
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AE10 - 811 - 72
2X-RAY DIFFRACTION2BF12 - 823 - 73
3X-RAY DIFFRACTION3CG10 - 811 - 72
4X-RAY DIFFRACTION4DH12 - 823 - 73
5X-RAY DIFFRACTION5EA499 - 5051 - 7
6X-RAY DIFFRACTION6FB500 - 5042 - 6
7X-RAY DIFFRACTION7GC500 - 5052 - 7
8X-RAY DIFFRACTION8HD499 - 5031 - 5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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