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- PDB-8j71: Selenomethionine mutant (L601Sem/L654Sem) of SAND domain of prote... -

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Basic information

Entry
Database: PDB / ID: 8j71
TitleSelenomethionine mutant (L601Sem/L654Sem) of SAND domain of protein SP140 with DNA
Components
  • DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3')
  • Nuclear body protein SP140Nuclear bodies
KeywordsDNA BINDING PROTEIN/DNA / Nuclear body protein SP140 SAND domain DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


defense response / PML body / fibrillar center / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / metal ion binding / nucleus
Similarity search - Function
Nuclear body protein Sp140 / HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily ...Nuclear body protein Sp140 / HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear body protein SP140
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsLi, H.T. / Liu, W.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Molecular basis for Speckled protein SP140 bivalent recognition of histone H3 and DNA
Authors: Li, H.T. / Liu, W.Q.
History
DepositionApr 26, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear body protein SP140
B: Nuclear body protein SP140
C: DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3')
D: DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)30,9354
Polymers30,9354
Non-polymers00
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry, ITC results indicate that the binding ratio of SAND domain and dsDNA is 2:1
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.131, 59.748, 124.956
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nuclear body protein SP140 / Nuclear bodies / Lymphoid-restricted homolog of Sp100 / LYSp100 / Nuclear autoantigen Sp-140 / Speckled 140 kDa


Mass: 11498.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SP140, LYSP100
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q13342
#2: DNA chain DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3')


Mass: 3969.561 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.12 M DL-Malic acid pH 7.0, 14% w/v PEG 3350 0.025% v/v Dichloromethane

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 26673 / % possible obs: 98.3 % / Redundancy: 8.7 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.046 / Rrim(I) all: 0.136 / Χ2: 1.472 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.85-1.8890.67312830.910.9760.230.7120.57396.4
1.88-1.929.10.61312870.9090.9760.210.6490.62296.8
1.92-1.958.70.53613070.9060.9750.1880.570.63297
1.95-1.998.90.48812680.9190.9790.1690.5170.64496.4
1.99-2.048.60.41312940.9180.9780.1460.440.78597.4
2.04-2.087.80.37412970.9210.9790.1390.4010.87397.4
2.08-2.1490.33513180.9540.9880.1150.3550.91997.8
2.14-2.1990.313130.9550.9880.1040.3180.93797.7
2.19-2.268.90.27313010.9660.9910.0940.291.02897.7
2.26-2.338.70.23713050.9730.9930.0830.2511.08597.9
2.33-2.418.40.21213390.9750.9940.0760.2261.1798.5
2.41-2.517.90.19213110.9720.9930.0710.2051.32298.3
2.51-2.638.70.17913350.9760.9940.0630.191.48798.7
2.63-2.768.80.15913360.9780.9950.0560.1691.64398.9
2.76-2.948.70.14513590.9830.9960.0520.1551.98799.1
2.94-3.168.40.13113670.9860.9960.0470.142.23599.6
3.16-3.488.40.11313530.9840.9960.0450.1222.54499.6
3.48-3.999.30.09813850.9880.9970.0350.1042.62899.9
3.99-5.028.80.08614070.9950.9990.0310.0912.62899.9
5.02-508.70.09515080.9940.9990.0340.1013.13699.6

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
SHELXphasing
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→39.07 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.26 / Phase error: 23.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2235 1342 5.04 %
Rwork0.1941 --
obs0.1956 26601 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1456 490 0 262 2208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082046
X-RAY DIFFRACTIONf_angle_d1.0152859
X-RAY DIFFRACTIONf_dihedral_angle_d21.207811
X-RAY DIFFRACTIONf_chiral_restr0.052299
X-RAY DIFFRACTIONf_plane_restr0.006279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.880.29931400.25212509X-RAY DIFFRACTION94
1.88-1.920.27391520.24252578X-RAY DIFFRACTION97
1.92-1.970.25561250.22672643X-RAY DIFFRACTION97
1.97-2.010.30011240.23092595X-RAY DIFFRACTION97
2.01-2.060.27641440.22182656X-RAY DIFFRACTION98
2.06-2.120.29631720.21892546X-RAY DIFFRACTION98
2.12-2.180.25151380.2172625X-RAY DIFFRACTION98
2.18-2.250.24381130.20142661X-RAY DIFFRACTION99
2.25-2.330.24941470.21032608X-RAY DIFFRACTION98
2.33-2.420.26821600.20732645X-RAY DIFFRACTION98
2.42-2.530.20941220.21252664X-RAY DIFFRACTION99
2.53-2.670.3011520.21912622X-RAY DIFFRACTION99
2.67-2.830.21421660.21242642X-RAY DIFFRACTION99
2.83-3.050.2076830.20432715X-RAY DIFFRACTION99
3.05-3.360.23041560.19992674X-RAY DIFFRACTION99
3.36-3.840.17741240.16622677X-RAY DIFFRACTION99
3.85-4.840.20291190.15352709X-RAY DIFFRACTION100
4.85-39.070.18011800.18262637X-RAY DIFFRACTION100

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