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- PDB-1zzk: Crystal Structure of the third KH domain of hnRNP K at 0.95A reso... -

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Basic information

Entry
Database: PDB / ID: 1zzk
TitleCrystal Structure of the third KH domain of hnRNP K at 0.95A resolution
ComponentsHeterogeneous nuclear ribonucleoprotein K
KeywordsDNA BINDING PROTEIN / KH domian / alpha-beta fold
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 / SUMOylation of RNA binding proteins / podosome / 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 / SUMOylation of RNA binding proteins / podosome / 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 / cytoplasmic stress granule / positive regulation of receptor-mediated endocytosis / ribonucleoprotein complex / cadherin binding / 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 / identical protein binding / membrane / 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
Heterogeneous nuclear ribonucleoprotein K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 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: 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

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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoprotein K


Theoretical massNumber of molelcules
Total (without water)8,9101
Polymers8,9101
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.848, 30.876, 42.413
Angle α, β, γ (deg.)90.00, 102.74, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Heterogeneous nuclear ribonucleoprotein K / hnRNP K / Transformation up-regulated nuclear protein / TUNP


Mass: 8910.091 Da / Num. of mol.: 1 / 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 1.9 Å3/Da / Density % sol: 33.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulphate, PEG 400, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 30, 2001
RadiationMonochromator: Khozu double crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 0.95→40 Å / Num. all: 95636 / Num. obs: 40192 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.4
Reflection shellResolution: 0.95→1 Å / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 5 / % possible all: 91.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.95→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.127 2007 Random
Rwork0.119 --
all0.124 40192 -
obs0.124 38185 -
Refinement stepCycle: LAST / Resolution: 0.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms712 0 0 58 770
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.037
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.123
X-RAY DIFFRACTIONs_zero_chiral_vol0.081
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.042
X-RAY DIFFRACTIONs_approx_iso_adps0.101

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