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- PDB-8j70: Native SAND domain of protein SP140 with DNA -

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Basic information

Entry
Database: PDB / ID: 8j70
TitleNative 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 SP140
KeywordsDNA BINDING PROTEIN/DNA / Nuclear body protein SP140 SAND / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


PML body / fibrillar center / defense response / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleus / metal ion binding
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
selenourea / DNA / DNA (> 10) / Nuclear body protein SP140
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7055
Polymers30,5824
Non-polymers1231
Water1,874104
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)76.629, 119.071, 64.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-701-

SEY

21A-701-

SEY

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Components

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


Mass: 11321.329 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: Chemical ChemComp-SEY / selenourea


Mass: 123.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2Se
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.64 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 6% v/v Tacsimate pH 6.0, 22% w/v PEG 3350, 10 mM FeCl3

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 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: 25564 / % possible obs: 99.8 % / Redundancy: 12.2 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.02 / Rrim(I) all: 0.07 / Χ2: 1.307 / Net I/σ(I): 9.9 / Num. measured all: 312594
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.85-1.88120.69912580.9440.9850.2060.7290.467100
1.88-1.9212.60.65412560.960.990.1890.6820.47399.8
1.92-1.9512.60.50512670.9730.9930.1470.5270.497100
1.95-1.9912.10.51312400.9640.9910.1540.5360.947100
1.99-2.0412.40.36912700.9850.9960.1080.3850.551100
2.04-2.08130.29512860.9910.9980.0840.3070.577100
2.08-2.14130.26412470.9920.9980.0760.2750.625100
2.14-2.1912.80.21512610.9940.9990.0620.2240.683100
2.19-2.2612.50.17112780.9960.9990.050.1780.754100
2.26-2.339.60.22412440.9720.9930.080.2391.5198.4
2.33-2.41130.13312750.9950.9990.0380.1380.924100
2.41-2.5111.80.14812760.990.9970.0470.1551.39599.8
2.51-2.6312.10.11812580.9950.9990.0360.1241.28699.7
2.63-2.76120.08812870.9980.9990.0260.0921.307100
2.76-2.9412.60.08412910.9980.9990.0250.0881.86999.9
2.94-3.1612.80.06812740.99810.020.0711.864100
3.16-3.4811.60.06312970.99910.0190.0662.713100
3.48-3.9912.60.05513100.99910.0160.0572.57899.9
3.99-5.02120.0513190.99810.0150.0522.649100
5.02-5011.40.04813700.99810.0150.0512.58998.7

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→28.42 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 1296 5.08 %
Rwork0.2005 --
obs0.2023 25505 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→28.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1379 486 4 104 1973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081979
X-RAY DIFFRACTIONf_angle_d0.8772774
X-RAY DIFFRACTIONf_dihedral_angle_d27.859775
X-RAY DIFFRACTIONf_chiral_restr0.053295
X-RAY DIFFRACTIONf_plane_restr0.008268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.920.33081540.26112587X-RAY DIFFRACTION98
1.92-2.010.26441420.24962650X-RAY DIFFRACTION100
2.01-2.120.25681340.21722666X-RAY DIFFRACTION100
2.12-2.250.28871670.21272668X-RAY DIFFRACTION100
2.25-2.420.30741240.2462662X-RAY DIFFRACTION99
2.42-2.670.27461280.2492697X-RAY DIFFRACTION100
2.67-3.050.24231290.22042730X-RAY DIFFRACTION100
3.05-3.840.23241580.18932726X-RAY DIFFRACTION100
3.84-28.420.19841600.17152823X-RAY DIFFRACTION99
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)
12.3508-1.9827-1.4412.7554-0.81014.680.10390.6705-0.4133-0.55870.11451.2396-0.3871-0.6583-0.12010.40570.1285-0.04430.61170.0610.4209-39.5118-7.19821.9306
22.9568-0.5326-1.09131.0502-0.08682.54720.21980.0811-0.0261-0.0295-0.174-0.0615-0.15620.1848-0.03610.2835-0.01960.01220.22270.00460.2989-30.9021-9.265912.258
33.0076-0.4428-4.21111.96571.26076.1196-0.3158-0.922-0.0971-0.00640.1063-0.30860.05830.78280.04770.27630.0202-0.05270.32830.00270.3514-29.9885-12.704819.5744
43.10510.2011-1.08731.7449-0.13441.99550.15120.3526-0.1202-0.1056-0.13390.07910.30310.3301-0.01750.19840.06860.01330.25550.01720.2611-24.1513-16.25096.6645
54.48520.8863-0.03725.7373-2.67388.6876-0.00020.98920.3651-1.2217-0.3621-0.32410.25550.04010.39510.52210.08950.04720.48140.10340.3411-27.934-8.5716-2.1192
61.1519-0.6651-0.39842.60952.07953.94420.13070.69060.669-0.1618-0.4911-0.6605-1.1310.44680.14740.4106-0.04570.07340.58280.21080.5124-24.7231-2.97052.7857
73.8177-2.18380.41061.6166-0.38732.25660.1334-0.47280.0656-0.12610.22520.2207-1.0644-0.362-0.24750.77540.13070.09510.37710.06530.424-20.7572-7.0598-22.6137
82.135-1.0878-0.01264.1517-0.02554.08030.270.7472-0.151-1.4014-0.34580.2081-0.6218-0.12620.07380.58910.1923-0.07480.44590.01690.3086-22.3348-15.0765-27.2632
92.4514-0.41340.20692.3386-0.30632.63260.16140.3631-0.0968-0.6617-0.1172-0.2997-0.00580.4859-0.03570.44980.16910.08940.4704-0.00230.3317-14.5106-20.2756-23.3265
102.1398-1.13370.84572.069-0.45493.69340.2188-0.29320.1168-0.3585-0.13520.5994-0.0452-0.2837-0.07030.46210.11720.02080.33540.0170.3895-24.9276-16.1942-15.3279
112.0869-1.2906-1.34994.5293-0.32173.71180.3016-0.13730.1382-0.0143-0.1045-0.48210.12120.2729-0.15290.27540.0748-0.05680.45460.02580.325-15.1847-21.4628-1.7193
124.1839-1.00321.12612.4543-0.77473.92990.3846-0.3949-0.0251-0.1842-0.2177-0.37130.12180.0056-0.11980.27850.07320.03530.4466-0.00230.3663-14.9134-21.8315-3.3212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 582 through 588 )
2X-RAY DIFFRACTION2chain 'A' and (resid 589 through 618 )
3X-RAY DIFFRACTION3chain 'A' and (resid 619 through 624 )
4X-RAY DIFFRACTION4chain 'A' and (resid 625 through 650 )
5X-RAY DIFFRACTION5chain 'A' and (resid 651 through 656 )
6X-RAY DIFFRACTION6chain 'A' and (resid 657 through 666 )
7X-RAY DIFFRACTION7chain 'B' and (resid 582 through 596 )
8X-RAY DIFFRACTION8chain 'B' and (resid 597 through 608 )
9X-RAY DIFFRACTION9chain 'B' and (resid 609 through 639 )
10X-RAY DIFFRACTION10chain 'B' and (resid 640 through 668 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 12 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 12 )

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