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- PDB-7y3i: Structure of DNA bound SALL4 -

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Basic information

Entry
Database: PDB / ID: 7y3i
TitleStructure of DNA bound SALL4
Components
  • (DNA (12-mer)) x 2
  • Sal-like protein 4
KeywordsDNA/DNA BINDING PROTEIN / SALL4 / zinc finger / DNA BINDING PROTEIN / DNA-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Transcriptional regulation of pluripotent stem cells / embryonic limb morphogenesis / ventricular septum development / inner cell mass cell proliferation / somatic stem cell population maintenance / heterochromatin / Regulation of PTEN gene transcription / neural tube closure / DNA-binding transcription factor activity, RNA polymerase II-specific ...POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Transcriptional regulation of pluripotent stem cells / embryonic limb morphogenesis / ventricular septum development / inner cell mass cell proliferation / somatic stem cell population maintenance / heterochromatin / Regulation of PTEN gene transcription / neural tube closure / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Sal-like protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsRu, W. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Citation
Journal: J.Biol.Chem. / Year: 2022
Title: Structural studies of SALL family protein zinc finger cluster domains in complex with DNA reveal preferential binding to an AATA tetranucleotide motif.
Authors: Ru, W. / Koga, T. / Wang, X. / Guo, Q. / Gearhart, M.D. / Zhao, S. / Murphy, M. / Kawakami, H. / Corcoran, D. / Zhang, J. / Zhu, Z. / Yao, X. / Kawakami, Y. / Xu, C.
#1: Journal: J.Biol.Chem. / Year: 2022
Title: Structural studies of SALL family protein zinc finger cluster domains in complex with DNA reveal preferential binding to an AATA tetranucleotide motif
Authors: Ru, W. / Koga, T. / Wang, X. / Guo, Q. / Gearhart, M.D. / Zhao, S. / Murphy, M. / Kawakami, H. / Corcoran, D. / Zhang, J. / Zhu, Z. / Yao, X. / Kawakami, Y. / Xu, C.
History
DepositionJun 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Nov 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: DNA (12-mer)
K: DNA (12-mer)
G: DNA (12-mer)
H: DNA (12-mer)
A: Sal-like protein 4
B: Sal-like protein 4
C: Sal-like protein 4
D: Sal-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,34914
Polymers48,9578
Non-polymers3926
Water2,630146
1
L: DNA (12-mer)
K: DNA (12-mer)
B: Sal-like protein 4
D: Sal-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6757
Polymers24,4784
Non-polymers1963
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-33 kcal/mol
Surface area8720 Å2
MethodPISA
2
G: DNA (12-mer)
H: DNA (12-mer)
A: Sal-like protein 4
C: Sal-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6757
Polymers24,4784
Non-polymers1963
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-35 kcal/mol
Surface area8370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.975, 69.197, 110.295
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (12-mer)


Mass: 3670.430 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (12-mer)


Mass: 3652.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein
Sal-like protein 4 / Zinc finger protein 797 / Zinc finger protein SALL4


Mass: 8577.798 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SALL4, ZNF797 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJQ4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.91 Å3/Da / Density % sol: 35.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-tris, pH 6.5, 25% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 97 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.45→48.98 Å / Num. obs: 14297 / % possible obs: 99.8 % / Redundancy: 13.2 % / CC1/2: 0.996 / Net I/σ(I): 9.9
Reflection shellResolution: 2.45→2.63 Å / Num. unique obs: 14297 / CC1/2: 0.739

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→43.127 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2422 678 4.74 %
Rwork0.1942 13619 -
obs0.1966 14297 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.15 Å2 / Biso mean: 35.9218 Å2 / Biso min: 18.04 Å2
Refinement stepCycle: final / Resolution: 2.45→43.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1221 984 6 146 2357
Biso mean--32.87 34.27 -
Num. residues----208
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4501-2.63920.34731200.25422669100
2.6392-2.90480.29681370.25032694100
2.9048-3.32490.24791320.20362686100
3.3249-4.18850.20021490.1628271399
4.1885-43.1270.23581400.1807285799
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)
10.2614-0.19710.02150.79040.33840.1960.0603-0.00410.03170.01890.22890.3026-0.0313-0.11050.00070.33180.0226-0.04220.30940.08590.273615.1392-0.961622.4278
21.241-0.1841-0.30641.46580.71130.3736-0.06360.28550.13920.5196-0.03760.2358-0.26630.3418-0.00130.2606-0.0003-0.0320.30720.0670.33317.4056-1.419723.4245
30.6651-0.5019-0.31910.6070.55680.57930.07270.0587-0.13720.0001-0.02250.1293-0.01870.17010.00010.2698-0.01270.0410.31240.05010.202939.40780.39690.7345
40.946-0.0890.28940.76990.50290.46830.00910.0285-0.1433-0.24160.13190.06240.18320.04310.00020.2854-0.01590.00650.270.05880.228141.47010.5634-0.2975
50.45630.34270.10971.5376-0.96420.9119-0.1922-0.19020.00430.1780.08460.1405-0.0647-0.0485-0.00010.22820.0082-0.01730.27260.01770.306241.75829.6523.7671
60.20470.4665-0.42732.1492-0.67311.010.07270.06690.0001-0.2171-0.06830.28480.1002-0.104200.2384-0.0028-0.02140.1918-0.01610.247517.7247-10.754219.9738
70.31190.1452-0.17220.33940.10050.2109-0.0945-0.1361-0.1258-0.2213-0.040.0463-0.07190.0158-0.00090.34170.00120.04820.3282-0.00320.325544.99-7.3329-13.2709
80.2236-0.00220.06370.37070.08280.3051-0.3692-0.2823-0.01110.1208-0.00930.3035-0.1419-0.16840.00010.3380.0102-0.01680.3526-0.010.378716.319110.67335.4541
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'L' and resid 1 through 12)L1 - 12
2X-RAY DIFFRACTION2(chain 'K' and resid 0 through 11)K0 - 11
3X-RAY DIFFRACTION3(chain 'G' and resid 1 through 12)G1 - 12
4X-RAY DIFFRACTION4(chain 'H' and resid 1 through 12)H1 - 12
5X-RAY DIFFRACTION5(chain 'A' and resid 868 through 921)A868 - 921
6X-RAY DIFFRACTION6(chain 'B' and resid 869 through 921)B869 - 921
7X-RAY DIFFRACTION7(chain 'C' and resid 895 through 921)C895 - 921
8X-RAY DIFFRACTION8(chain 'D' and resid 896 through 921)D896 - 921

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