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- PDB-1zzj: Structure of the third KH domain of hnRNP K in complex with 15-me... -

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Basic information

Entry
Database: PDB / ID: 1zzj
TitleStructure of the third KH domain of hnRNP K in complex with 15-mer ssDNA
Components
  • 5'-D(*TP*TP*CP*CP*CP*CP*TP*CP*CP*CP*CP*AP*TP*TP*T)-3'
  • Heterogeneous nuclear ribonucleoprotein K
KeywordsSTRUCTURAL PROTEIN/DNA / PROTEIN-DNA 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 / positive regulation of low-density lipoprotein particle clearance / random inactivation of X chromosome / regulatory ncRNA-mediated heterochromatin formation / regulation of mRNA splicing, via spliceosome / SUMOylation of RNA binding proteins / podosome / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / RNA processing ...regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of low-density lipoprotein particle clearance / random inactivation of X chromosome / regulatory ncRNA-mediated heterochromatin formation / regulation of mRNA splicing, via spliceosome / SUMOylation of RNA binding proteins / podosome / 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 / cadherin binding / ribonucleoprotein complex / protein domain specific binding / focal adhesion / negative regulation of DNA-templated transcription / mRNA binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / 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 / DNA (> 10) / Heterogeneous nuclear ribonucleoprotein K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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
D: 5'-D(*TP*TP*CP*CP*CP*CP*TP*CP*CP*CP*CP*AP*TP*TP*T)-3'
A: Heterogeneous nuclear ribonucleoprotein K
B: Heterogeneous nuclear ribonucleoprotein K
C: Heterogeneous nuclear ribonucleoprotein K


Theoretical massNumber of molelcules
Total (without water)31,1374
Polymers31,1374
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.008, 54.008, 149.656
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C
101A
111B
121C
131A
141B
151C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYSERSER2AB11 - 274 - 20
21GLYGLYSERSER2BC11 - 274 - 20
31GLYGLYSERSER2CD11 - 274 - 20
42ILEILEARGARG5AB28 - 3521 - 28
52ILEILEARGARG5BC28 - 3521 - 28
62ILEILEARGARG5CD28 - 3521 - 28
73ILEILEASPASP2AB36 - 5029 - 43
83ILEILEASPASP2BC36 - 5029 - 43
93ILEILEASPASP2CD36 - 5029 - 43
104GLUGLUGLUGLU5AB51 - 5744 - 50
114GLUGLUGLUGLU5BC51 - 5744 - 50
124GLUGLUGLUGLU5CD51 - 5744 - 50
135ASPASPVALVAL2AB58 - 8151 - 74
145ASPASPVALVAL2BC58 - 8151 - 74
155ASPASPVALVAL2CD58 - 8151 - 74

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Components

#1: DNA chain 5'-D(*TP*TP*CP*CP*CP*CP*TP*CP*CP*CP*CP*AP*TP*TP*T)-3'


Mass: 4406.860 Da / Num. of mol.: 1 / 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.: 3 / 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


Mass: 18.015 Da / Num. of mol.: 80 / 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: 38.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, SODIUM ACETATE, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM ACETATE11
2PEG 800011
3MES11
4H2O11
5PEG 800012
6MES12
7H2O13

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 26, 2001
RadiationMonochromator: Khozu double crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.3→46.6 Å / Num. all: 11572 / Num. obs: 11572 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.3
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.3 / % possible all: 84.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.906 / SU B: 18.684 / SU ML: 0.224 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.358 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28279 559 4.8 %RANDOM
Rwork0.20972 ---
all0.21315 10975 --
obs0.21315 10975 97.35 %-
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: 53.216 Å2
Baniso -1Baniso -2Baniso -3
1-2.32 Å21.16 Å20 Å2
2--2.32 Å20 Å2
3----3.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.279 Å0.359 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1622 153 0 80 1855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221805
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0582.082472
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1935219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.26226.56264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.34715291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.196158
X-RAY DIFFRACTIONr_chiral_restr0.1320.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021278
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.2765
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21250
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8281.51123
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42721766
X-RAY DIFFRACTIONr_scbond_it2.5543763
X-RAY DIFFRACTIONr_scangle_it3.8474.5706
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A224tight positional0.090.05
2B224tight positional0.080.05
3C224tight positional0.070.05
1A253medium positional0.540.5
2B253medium positional0.590.5
3C253medium positional0.610.5
1A31loose positional0.845
2B31loose positional0.65
3C31loose positional0.615
1A224tight thermal0.230.5
2B224tight thermal0.210.5
3C224tight thermal0.210.5
1A253medium thermal1.122
2B253medium thermal0.962
3C253medium thermal1.172
1A31loose thermal1.6210
2B31loose thermal1.9310
3C31loose thermal1.7110
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 26 -
Rwork0.273 620 -
obs--75.73 %
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)
14.3119-2.5991.590211.6752-4.591611.6250.23150.18120.1735-0.322-0.09310.7472-0.3903-0.2679-0.1384-0.24050.00160.0069-0.3777-0.0039-0.23646.561415.806733.0611
22.63510.01230.833912.31989.135715.07340.67050.0501-0.54521.30610.139-0.86732.0037-0.0912-0.80950.1228-0.0024-0.2175-0.39370.004-0.125115.293534.430849.8141
34.14272.78061.29017.895-1.699913.81790.6876-0.1777-0.8130.0621-0.1645-0.04621.37640.5564-0.52310.01570.2762-0.0883-0.18720.0334-0.142514.2737-6.59132.5379
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AB11 - 834 - 76
2X-RAY DIFFRACTION1DA2 - 53 - 6
3X-RAY DIFFRACTION2BC9 - 812 - 74
4X-RAY DIFFRACTION2DA6 - 97 - 10
5X-RAY DIFFRACTION3CD8 - 811 - 74

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