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- PDB-1zzi: Crystal Structure Analysis of the third KH domain of hnRNP K in c... -

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Basic information

Entry
Database: PDB / ID: 1zzi
TitleCrystal Structure Analysis of the third KH domain of hnRNP K in complex with ssDNA
Components
  • 5'-D(*CP*TP*CP*CP*CP*C)-3'
  • Heterogeneous nuclear ribonucleoprotein K
KeywordsSTRUCTURAL PROTEIN/DNA / PROTEIN-ssDNA COMPLEX / STRUCTURAL PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of low-density lipoprotein particle clearance / regulation of mRNA splicing, via spliceosome / podosome / SUMOylation of RNA binding proteins / positive regulation of low-density lipoprotein receptor activity / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / RNA processing / catalytic step 2 spliceosome ...regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of low-density lipoprotein particle clearance / regulation of mRNA splicing, via spliceosome / podosome / SUMOylation of RNA binding proteins / positive regulation of low-density lipoprotein receptor activity / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / RNA processing / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / HCMV Late Events / cell projection / mRNA splicing, via spliceosome / positive regulation of receptor-mediated endocytosis / cytoplasmic stress granule / cadherin binding / ribonucleoprotein complex / protein domain specific binding / focal adhesion / negative regulation of DNA-templated transcription / mRNA binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / cytoplasm
Similarity search - Function
ROK, N-terminal / ROKNT (NUC014) domain / 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 ...ROK, N-terminal / ROKNT (NUC014) domain / 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 / Heterogeneous nuclear ribonucleoprotein K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBacke, P.H. / Messias, A.C. / Ravelli, R.B. / Sattler, M. / Cusack, S.
CitationJournal: STRUCTURE / Year: 2005
Title: X-Ray Crystallographic and NMR Studies of the Third KH Domain of hnRNP K in Complex with Single-Stranded Nucleic Acids
Authors: Backe, P.H. / Messias, A.C. / Ravelli, R.B. / Sattler, M. / Cusack, S.
History
DepositionJun 14, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*CP*TP*CP*CP*CP*C)-3'
D: 5'-D(*CP*TP*CP*CP*CP*C)-3'
A: Heterogeneous nuclear ribonucleoprotein K
B: Heterogeneous nuclear ribonucleoprotein K


Theoretical massNumber of molelcules
Total (without water)21,2304
Polymers21,2304
Non-polymers00
Water2,450136
1
C: 5'-D(*CP*TP*CP*CP*CP*C)-3'
A: Heterogeneous nuclear ribonucleoprotein K


Theoretical massNumber of molelcules
Total (without water)10,6152
Polymers10,6152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 5'-D(*CP*TP*CP*CP*CP*C)-3'
B: Heterogeneous nuclear ribonucleoprotein K


Theoretical massNumber of molelcules
Total (without water)10,6152
Polymers10,6152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.590, 52.590, 104.891
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsAsymmetric unit contains two KH3-ssDNA complexes (chains A+C and B+D) with approximately 2-fold NCS

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Components

#1: DNA chain 5'-D(*CP*TP*CP*CP*CP*C)-3'


Mass: 1705.144 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Heterogeneous nuclear ribonucleoprotein K / hnRNP K / Transformation up-regulated nuclear protein / TUNP


Mass: 8910.091 Da / Num. of mol.: 2 / Fragment: KH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P61978
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, TRIS HCl, MAGNESIUM CHLORIDE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1MgCl211
2PEG 400011
3TRIS HCl11
4H2O11
5MgCl212
6PEG 400012
7H2O13

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.94 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 2, 2002
RadiationMonochromator: Khozu dual crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 1.8→34.3 Å / Num. all: 15859 / Num. obs: 15859 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 23.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.9 / % possible all: 87.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.41 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24041 795 5 %RANDOM
Rwork0.19458 ---
all0.19685 15825 --
obs0.19685 15030 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.821 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20.44 Å20 Å2
2--0.88 Å20 Å2
3----1.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.147 Å0.152 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1235 209 0 136 1580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221488
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8942.1472041
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8665161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09625.92654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09815243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.933156
X-RAY DIFFRACTIONr_chiral_restr0.1110.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021029
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.2785
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.21065
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2157
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0711.5815
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.74221293
X-RAY DIFFRACTIONr_scbond_it2.7683764
X-RAY DIFFRACTIONr_scangle_it3.7934.5748
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 57 -
Rwork0.243 866 -
obs--80.96 %
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)
11.7683-0.0852.85451.9498-0.423513.07010.1452-0.1007-0.2148-0.0017-0.03290.08720.5184-0.3394-0.1123-0.16960.0086-0.0125-0.17530.0186-0.117857.972539.554621.0852
22.6045-0.15950.74312.8772.36545.35140.0645-0.0550.1095-0.163-0.22210.1032-0.163-0.28750.1576-0.13680.0421-0.008-0.1809-0.009-0.144941.982239.8017-0.9654
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC8 - 891 - 82
2X-RAY DIFFRACTION1CA1 - 61 - 6
3X-RAY DIFFRACTION2BD11 - 894 - 82
4X-RAY DIFFRACTION2DB2 - 62 - 6

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