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Basic information

Entry
Database: PDB / ID: 8cuc
TitleCrystal structure analysis of SALL4 zinc finger domain in complex with DNA
Components
  • DNA (5'-D(P*CP*GP*AP*AP*AP*TP*AP*TP*TP*AP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*TP*AP*AP*TP*AP*TP*TP*TP*CP*G)-3')
  • Sal-like protein 4
KeywordsTRANSCRIPTION/DNA / Transcription factor / Zinc finger / Protein-DNA complex / TRANSCRIPTION-DNA 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsSeo, H.S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Crystal Structure Analysis of SALL4 Zinc Finger domain in complex with DNA
Authors: Seo, H.S. / Dhe-Paganon, S.
History
DepositionMay 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 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
A: DNA (5'-D(P*CP*GP*AP*AP*AP*TP*AP*TP*TP*AP*GP*C)-3')
B: DNA (5'-D(P*GP*CP*TP*AP*AP*TP*AP*TP*TP*TP*CP*G)-3')
C: DNA (5'-D(P*CP*GP*AP*AP*AP*TP*AP*TP*TP*AP*GP*C)-3')
D: DNA (5'-D(P*GP*CP*TP*AP*AP*TP*AP*TP*TP*TP*CP*G)-3')
E: Sal-like protein 4
F: Sal-like protein 4
G: Sal-like protein 4
H: Sal-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,22414
Polymers44,8328
Non-polymers3926
Water4,179232
1
A: DNA (5'-D(P*CP*GP*AP*AP*AP*TP*AP*TP*TP*AP*GP*C)-3')
B: DNA (5'-D(P*GP*CP*TP*AP*AP*TP*AP*TP*TP*TP*CP*G)-3')
F: Sal-like protein 4
H: Sal-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6127
Polymers22,4164
Non-polymers1963
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(P*CP*GP*AP*AP*AP*TP*AP*TP*TP*AP*GP*C)-3')
D: DNA (5'-D(P*GP*CP*TP*AP*AP*TP*AP*TP*TP*TP*CP*G)-3')
E: Sal-like protein 4
G: Sal-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6127
Polymers22,4164
Non-polymers1963
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.250, 70.510, 112.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D
13(chain E and ((resid 895 through 896 and (name N...
23(chain H and ((resid 895 through 896 and (name N...
14(chain F and resid 870 through 921)
24(chain G and (resid 870 through 917 or (resid 918...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111DCDCDCDCchain AAA1 - 121 - 12
211DCDCDCDCchain CCC1 - 121 - 12
112DGDGDGDGchain BBB1 - 121 - 12
212DGDGDGDGchain DDD1 - 121 - 12
113GLUGLULYSLYS(chain E and ((resid 895 through 896 and (name N...EE895 - 89634 - 35
123GLUGLUHISHIS(chain E and ((resid 895 through 896 and (name N...EE895 - 92034 - 59
133GLUGLUHISHIS(chain E and ((resid 895 through 896 and (name N...EE895 - 92034 - 59
143GLUGLUHISHIS(chain E and ((resid 895 through 896 and (name N...EE895 - 92034 - 59
153GLUGLUHISHIS(chain E and ((resid 895 through 896 and (name N...EE895 - 92034 - 59
213GLUGLULYSLYS(chain H and ((resid 895 through 896 and (name N...HH895 - 89634 - 35
223GLYGLYGLYGLY(chain H and ((resid 895 through 896 and (name N...HH894 - 92133 - 60
233GLYGLYGLYGLY(chain H and ((resid 895 through 896 and (name N...HH894 - 92133 - 60
243GLYGLYGLYGLY(chain H and ((resid 895 through 896 and (name N...HH894 - 92133 - 60
253GLYGLYGLYGLY(chain H and ((resid 895 through 896 and (name N...HH894 - 92133 - 60
114HISHISGLYGLY(chain F and resid 870 through 921)FF870 - 9219 - 60
214HISHISTYRTYR(chain G and (resid 870 through 917 or (resid 918...GG870 - 9179 - 56
224METMETMETMET(chain G and (resid 870 through 917 or (resid 918...GG91857
234GLNGLNGLYGLY(chain G and (resid 870 through 917 or (resid 918...GG869 - 9218 - 60
244GLNGLNGLYGLY(chain G and (resid 870 through 917 or (resid 918...GG869 - 9218 - 60
254GLNGLNGLYGLY(chain G and (resid 870 through 917 or (resid 918...GG869 - 9218 - 60
264GLNGLNGLYGLY(chain G and (resid 870 through 917 or (resid 918...GG869 - 9218 - 60

NCS ensembles :
ID
1
2
3
4

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Components

#1: DNA chain DNA (5'-D(P*CP*GP*AP*AP*AP*TP*AP*TP*TP*AP*GP*C)-3')


Mass: 3670.430 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(P*GP*CP*TP*AP*AP*TP*AP*TP*TP*TP*CP*G)-3')


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


Mass: 7546.546 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 BL21(DE3) (bacteria) / References: UniProt: Q9UJQ4
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% PEG3350, 40 mM ammonium sulfate, Bis-Tris, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2827 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2827 Å / Relative weight: 1
ReflectionResolution: 2.09→70.51 Å / Num. obs: 23766 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 39.27 Å2 / Rpim(I) all: 0.099 / Rrim(I) all: 0.232 / Net I/σ(I): 6.7 / Num. measured all: 124824
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2.09-2.135.51.3640211710.9842.34399.9
5.67-70.554.815.1634013190.0420.097100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
xia2data scaling
SOLVEphasing
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.09→59.68 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2307 1132 4.77 %
Rwork0.2022 22580 -
obs0.2035 23712 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.98 Å2 / Biso mean: 41.2448 Å2 / Biso min: 8.75 Å2
Refinement stepCycle: final / Resolution: 2.09→59.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1234 984 6 232 2456
Biso mean--46.54 41.72 -
Num. residues----209
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A234X-RAY DIFFRACTION4.204TORSIONAL
12C234X-RAY DIFFRACTION4.204TORSIONAL
21B234X-RAY DIFFRACTION4.204TORSIONAL
22D234X-RAY DIFFRACTION4.204TORSIONAL
31E140X-RAY DIFFRACTION4.204TORSIONAL
32H140X-RAY DIFFRACTION4.204TORSIONAL
41F312X-RAY DIFFRACTION4.204TORSIONAL
42G312X-RAY DIFFRACTION4.204TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.09-2.190.38771430.317827662909100
2.19-2.30.31441540.275627622916100
2.3-2.440.29511390.263628132952100
2.44-2.630.29571350.25327772912100
2.63-2.90.27091440.225728212965100
2.9-3.320.20791270.20122809293699
3.32-4.180.19161460.15852834298099
4.18-59.680.19521440.17962998314299
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)
12.65280.61960.09981.66410.19781.01760.02610.12130.00790.05090.10970.2241-0.14980.10020.00050.39370.0474-0.00830.32710.04570.345715.706634.161778.8686
22.70630.6323-0.063.05970.05031.66620.07370.50680.0180.2919-0.18990.1543-0.3750.236100.41310.0246-0.00420.42060.01450.324417.67734.057979.1938
32.6004-0.6907-0.05551.9725-0.30391.1232-0.0369-0.03650.03780.02940.15710.28860.07750.1401-0.00030.3444-0.0382-0.00170.32650.05820.307640.043935.848756.4083
41.5864-0.3882-0.01431.667-0.43881.8471-0.1242-0.1537-0.1121-0.29330.19470.18530.5208-0.0864-00.4068-0.00470.0080.37120.00660.335941.86235.59456.054
50.2001-0.1081-0.29790.15160.25370.5623-0.028-0.1724-0.1522-0.45240.0090.57820.3372-0.4511-0.00030.4252-0.00260.00850.4205-0.02320.44142.65427.422439.659
60.56770.0665-0.48060.28120.3791.3542-0.0472-0.40030.17180.05770.0318-0.19570.28910.5206-0.00230.43820.00860.0570.43410.00690.354848.553728.189345.5628
70.13760.23060.0310.5971-0.11721.63610.1750.2185-0.1044-0.16950.030.78370.2787-0.94440.01080.44550.0082-0.0430.52030.03150.62026.616123.850475.4946
81.3116-1.0291-0.57182.1301-0.78062.03060.01140.3037-0.0058-0.0626-0.0684-0.11910.02170.1879-0.00010.34210.0133-0.00340.32890.00130.356627.550224.625876.5937
90.5071-0.071-0.12110.2395-0.25820.661-0.2343-0.42390.10840.27270.74910.55950.2371-1.17830.00480.4240.00550.00960.69770.05050.639628.223244.917159.9242
100.37860.02120.08390.08720.04020.0655-0.4749-0.4190.48440.55220.36860.454-0.07860.0248-0.00240.38920.03150.00470.41580.07850.495636.04347.352661.6346
113.88410.76850.86071.2865-0.24640.33270.6073-1.10581.63241.3563-0.2070.9987-0.2061-0.54140.02750.6163-0.02770.02730.3976-0.08850.556545.82549.831562.1725
120.21140.2-0.01830.17450.04340.1248-0.3581-0.14680.66870.1168-0.0513-0.0439-0.67770.3649-0.00070.3687-0.0168-0.03610.38910.020.386653.615547.150958.8463
130.6360.9369-0.69091.7777-0.17212.63430.1109-0.1302-0.8708-0.4134-0.2827-0.32740.48360.651-0.0150.3391-0.0014-0.02210.38490.05530.418154.140239.707257.1658
148.4466-1.2777-6.41390.21930.99624.9297-0.157-0.1977-0.9438-0.6545-0.0514-1.40680.63911.3164-0.08160.4683-0.03170.06730.45790.01140.488123.458549.340385.3127
151.0076-0.02180.45191.37970.16270.7976-0.0464-0.4719-0.57550.3723-0.21520.73980.1714-0.4265-0.00030.4143-0.017-0.00530.5563-0.02780.492915.324245.855992.6042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 12 )A1 - 12
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 12 )B1 - 12
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 12 )C1 - 12
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 12 )D1 - 12
5X-RAY DIFFRACTION5chain 'E' and (resid 895 through 909 )E895 - 909
6X-RAY DIFFRACTION6chain 'E' and (resid 910 through 920 )E910 - 920
7X-RAY DIFFRACTION7chain 'F' and (resid 868 through 893 )F868 - 893
8X-RAY DIFFRACTION8chain 'F' and (resid 894 through 921 )F894 - 921
9X-RAY DIFFRACTION9chain 'G' and (resid 869 through 881 )G869 - 881
10X-RAY DIFFRACTION10chain 'G' and (resid 882 through 893 )G882 - 893
11X-RAY DIFFRACTION11chain 'G' and (resid 894 through 898 )G894 - 898
12X-RAY DIFFRACTION12chain 'G' and (resid 899 through 909 )G899 - 909
13X-RAY DIFFRACTION13chain 'G' and (resid 910 through 921 )G910 - 921
14X-RAY DIFFRACTION14chain 'H' and (resid 894 through 898 )H894 - 898
15X-RAY DIFFRACTION15chain 'H' and (resid 899 through 921 )H899 - 921

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