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- PDB-7cre: hnRNPK KH3 domain in complex with a ssDNA fragment from the SIRLO... -

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Basic information

Entry
Database: PDB / ID: 7cre
TitlehnRNPK KH3 domain in complex with a ssDNA fragment from the SIRLOIN element
Components
  • Heterogeneous nuclear ribonucleoprotein K
  • ssDNA fragment
KeywordsDNA BINDING PROTEIN/DNA / SRILOIN / hnRNPK / KH3 / complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


podosome / anchoring junction / spliceosomal complex / DNA binding / RNA binding / nucleoplasm / cytoplasm
Similarity search - Function
ROK, N-terminal / ROKNT (NUC014) domain / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain
Similarity search - Domain/homology
DNA / DNA (> 10) / Heterogeneous nuclear ribonucleoprotein K
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsYao, J. / Sun, Q.
CitationJournal: Cell.Mol.Life Sci. / Year: 2021
Title: Nuclear import receptors and hnRNPK mediates nuclear import and stress granule localization of SIRLOIN.
Authors: Yao, J. / Tu, Y. / Shen, C. / Zhou, Q. / Xiao, H. / Jia, D. / Sun, Q.
History
DepositionAug 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoprotein K
C: ssDNA fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9833
Polymers12,9602
Non-polymers231
Water19811
1
A: Heterogeneous nuclear ribonucleoprotein K
C: ssDNA fragment
hetero molecules

A: Heterogeneous nuclear ribonucleoprotein K
C: ssDNA fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9676
Polymers25,9214
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z1
Unit cell
Length a, b, c (Å)61.611, 61.611, 144.544
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-500-

NA

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Components

#1: Protein Heterogeneous nuclear ribonucleoprotein K


Mass: 8205.230 Da / Num. of mol.: 1 / Fragment: KH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: B4DUQ1
#2: DNA chain ssDNA fragment


Mass: 4755.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SIRLOIN element / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.06 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25 % w/v Polyethylene glycol 3350, 100 mM BIS-TRIS pH 5.5, 200 mM Ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 3670 / % possible obs: 98.8 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.049 / Rrim(I) all: 0.159 / Χ2: 1.003 / Net I/σ(I): 13.7 / Num. measured all: 42330
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3-3.1111.13560.3240.8890.765100
3.11-3.2311.93550.7960.3080.864100
3.23-3.3812.13480.9650.1491.0311000.5450.566
3.38-3.5612.13570.9620.1161.04199.40.4190.436
3.56-3.7811.73510.9830.0671.05598.90.240.25
3.78-4.07123640.9850.0551.03999.20.1930.201
4.07-4.4811.83660.9940.0321.07199.50.1140.119
4.48-5.1311.43750.9940.0271.02399.20.0870.091
5.13-6.4611.63740.9930.0271.05898.40.0930.097
6.46-509.94240.9790.0541.06694.90.1630.172

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZZI

1zzi


Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2938 / WRfactor Rwork: 0.2824 / FOM work R set: 0.5831 / SU B: 95.111 / SU ML: 0.624 / SU Rfree: 0.4102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2792 365 10.1 %RANDOM
Rwork0.2579 ---
obs0.26 3239 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 457.39 Å2 / Biso mean: 142.491 Å2 / Biso min: 76.14 Å2
Baniso -1Baniso -2Baniso -3
1--9.41 Å2-4.71 Å2-0 Å2
2---9.41 Å20 Å2
3---30.54 Å2
Refinement stepCycle: final / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms546 159 1 11 717
Biso mean--107.89 175.78 -
Num. residues----80
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.012726
X-RAY DIFFRACTIONr_bond_other_d0.0270.018627
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.5281009
X-RAY DIFFRACTIONr_angle_other_deg1.9921.7891471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.553571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5424.61526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.43115108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.805153
X-RAY DIFFRACTIONr_chiral_restr0.0440.2107
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02695
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02129
X-RAY DIFFRACTIONr_rigid_bond_restr17.8273724
LS refinement shellResolution: 3→3.158 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.398 57 -
Rwork0.41 446 -
all-503 -
obs--100 %

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