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- PDB-7y3m: Structure of SALL4 ZFC1 bound with 16 bp AT-rich dsDNA -

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Basic information

Entry
Database: PDB / ID: 7y3m
TitleStructure of SALL4 ZFC1 bound with 16 bp AT-rich dsDNA
Components
  • (DNA (16-mer)) x 2
  • Sal-like protein 4
KeywordsDNA/DNA BINDING PROTEIN / SALL4 / zinc finger / DNA / 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 / 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 / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / 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 / MOLECULAR REPLACEMENT / Resolution: 2.723 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 11, 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 1.3Nov 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
G: DNA (16-mer)
H: DNA (16-mer)
D: DNA (16-mer)
E: DNA (16-mer)
B: Sal-like protein 4
C: Sal-like protein 4
A: Sal-like protein 4
F: Sal-like protein 4
J: Sal-like protein 4
K: DNA (16-mer)
L: DNA (16-mer)
I: Sal-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,06824
Polymers83,28312
Non-polymers78512
Water00
1
G: DNA (16-mer)
H: DNA (16-mer)
B: Sal-like protein 4
A: Sal-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0238
Polymers27,7614
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-43 kcal/mol
Surface area11830 Å2
MethodPISA
2
D: DNA (16-mer)
E: DNA (16-mer)
C: Sal-like protein 4
F: Sal-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0238
Polymers27,7614
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-46 kcal/mol
Surface area13440 Å2
MethodPISA
3
J: Sal-like protein 4
K: DNA (16-mer)
L: DNA (16-mer)
I: Sal-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0238
Polymers27,7614
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-40 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.587, 65.706, 102.980
Angle α, β, γ (deg.)90.000, 106.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain DNA (16-mer)


Mass: 4896.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (16-mer)


Mass: 4896.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein
Sal-like protein 4 / Zinc finger protein 797 / Zinc finger protein SALL4


Mass: 8984.367 Da / Num. of mol.: 6
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.: 12 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M HEPES, pH 6.5, 10% polyethylene glycol 6000, 5% (v/v) 2-Methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.72→67.89 Å / Num. obs: 25181 / % possible obs: 98.6 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 15.8
Reflection shellResolution: 2.72→2.87 Å / Num. unique obs: 25181 / CC1/2: 0.93

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Y3I

7y3i


Resolution: 2.723→33.789 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 35.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2682 1978 7.86 %
Rwork0.223 23203 -
obs0.2266 25181 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 286.57 Å2 / Biso mean: 113.4613 Å2 / Biso min: 46.12 Å2
Refinement stepCycle: final / Resolution: 2.723→33.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 1968 12 0 4703
Biso mean--100.61 --
Num. residues----450
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7234-2.79150.37811480.34166199
2.7915-2.86690.40381340.3449169499
2.8669-2.95120.42621360.3899165199
2.9512-3.04640.45381510.3548165298
3.0464-3.15520.40661320.3242156593
3.1552-3.28140.33781420.3098158293
3.2814-3.43070.36331340.2865163896
3.4307-3.61130.32621350.2406164698
3.6113-3.83730.25951480.2188167298
3.8373-4.13310.27411390.2221166297
4.1331-4.54810.22811420.2003167599
4.5481-5.20420.29641480.2152168199
5.2042-6.54890.21991450.1943169998
6.5489-33.7890.19171440.1651172598
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)
12.35880.7239-1.28254.3263-1.92761.56980.2773-0.3233-1.9502-0.02280.79680.05910.2242-0.31440.01290.63360.0301-0.08610.6397-0.02930.820928.339815.90283.5173
22.1322-1.1353-2.05162.107-0.72663.54970.2277-0.1755-1.49670.55980.6635-0.3620.2289-0.03070.05480.73640.0305-0.23130.58980.01440.970930.826514.14064.6004
30.44440.3617-0.92983.94220.32211.4946-0.2753-1.0044-0.44530.59760.29810.0026-0.2948-0.24540.00060.79940.1892-0.02871.15150.11880.759813.187939.08426.6665
41.2294-1.9839-0.4362.4337-0.56991.494-0.3412-0.79230.42940.26540.11940.131-0.8482-0.61060.00020.85660.0968-0.07271.0689-0.01640.748112.30640.535623.9374
51.1842-0.26442.07781.7697-0.08173.54070.32550.094-1.27130.25530.4301-0.38470.06410.39170.51090.7361-0.0667-0.03440.5095-0.13511.444740.74749.17433.0308
61.170.71860.99110.36750.33662.5915-0.1245-0.6946-0.17980.58320.04060.53650.0923-0.59090.00070.85050.15660.16091.0640.03940.774310.673735.656835.8236
73.0240.0873-0.20151.26660.02791.6616-0.4364-0.50480.20770.0780.46240.1007-0.1075-0.9544-0.00480.6052-0.00310.00710.53920.10230.394322.703924.37343.5233
82.1678-2.01210.10932.0331-0.57820.1671-0.14840.4342-0.2715-0.2384-0.14330.3846-0.31940.1287-0.00270.70970.045-0.03180.7086-0.00080.780712.400744.085413.0171
91.0382-0.24620.91590.4809-0.13160.6664-0.23160.90720.37140.24930.2439-0.56030.0681-1.08110.00090.9704-0.07880.09351.28770.13460.89912.503617.703540.8352
101.46290.0544-0.2122.79361.73240.7584-0.17791.1436-0.8217-0.0693-0.03740.7744-0.9374-0.1281-0.00011.1812-0.1133-0.09031.48030.23881.0668-9.859111.696840.1634
110.6165-1.1411-0.31483.694-0.13770.3763-0.06940.7355-0.69490.208-0.29410.3704-0.88761.08190.00051.2628-0.1017-0.21681.68670.18911.1884-6.798311.775240.1506
120.4172-0.03390.14190.32190.44210.27090.1528-0.0976-0.42080.3154-0.87240.1516-0.1249-0.1835-0.00051.14290.03160.08221.1282-0.15571.2802-18.93459.568343.9286
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'G' and resid 1 through 16)G1 - 16
2X-RAY DIFFRACTION2(chain 'H' and resid 1 through 16)H1 - 16
3X-RAY DIFFRACTION3(chain 'D' and resid 1 through 16)D1 - 16
4X-RAY DIFFRACTION4(chain 'E' and resid 1 through 16)E1 - 16
5X-RAY DIFFRACTION5(chain 'B' and resid 382 through 436)B382 - 436
6X-RAY DIFFRACTION6(chain 'C' and resid 380 through 449)C380 - 449
7X-RAY DIFFRACTION7(chain 'A' and resid 380 through 435)A380 - 435
8X-RAY DIFFRACTION8(chain 'F' and resid 381 through 446)F381 - 446
9X-RAY DIFFRACTION9(chain 'J' and resid 382 through 434)J382 - 434
10X-RAY DIFFRACTION10(chain 'K' and resid 1 through 16)K1 - 16
11X-RAY DIFFRACTION11(chain 'L' and resid 1 through 16)L1 - 16
12X-RAY DIFFRACTION12(chain 'I' and resid 381 through 434)I381 - 434

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