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- PDB-5yel: Crystal structure of CTCF ZFs6-11-gb7CSE -

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Basic information

Entry
Database: PDB / ID: 5yel
TitleCrystal structure of CTCF ZFs6-11-gb7CSE
Components
  • (DNA (26-MER)) x 2
  • Transcriptional repressor CTCF
KeywordsDNA BINDING PROTEIN/DNA / zinc fingers / insulators / enhancers / promoters / 3D genome / topological domains / contact loops / higher-order chromatin structure / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


chromatin insulator sequence binding / regulation of centromeric sister chromatid cohesion / genomic imprinting / protein localization to chromosome, centromeric region / chromatin looping / negative regulation of gene expression via chromosomal CpG island methylation / chromosome, centromeric region / epigenetic regulation of gene expression / condensed chromosome / male germ cell nucleus ...chromatin insulator sequence binding / regulation of centromeric sister chromatid cohesion / genomic imprinting / protein localization to chromosome, centromeric region / chromatin looping / negative regulation of gene expression via chromosomal CpG island methylation / chromosome, centromeric region / epigenetic regulation of gene expression / condensed chromosome / male germ cell nucleus / transcription coregulator binding / chromosome segregation / DNA-binding transcription repressor activity, RNA polymerase II-specific / Activation of anterior HOX genes in hindbrain development during early embryogenesis / sequence-specific DNA binding / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
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) / Transcriptional repressor CTCF
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsYin, M. / Wang, J. / Wang, M. / Li, X. / Wang, Y.
Funding support China, 7items
OrganizationGrant numberCountry
National Natural Science Foundation of China31630015 China
National Natural Science Foundation of China91440201 China
National Natural Science Foundation of China31571335 China
National Natural Science Foundation of China31400640 China
National Natural Science Foundation of China31630039 China
National Natural Science Foundation of China91640118 China
National Natural Science Foundation of China31470820 China
CitationJournal: Cell Res. / Year: 2017
Title: Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites
Authors: Yin, M. / Wang, J. / Wang, M. / Li, X. / Zhang, M. / Wu, Q. / Wang, Y.
History
DepositionSep 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: DNA (26-MER)
A: Transcriptional repressor CTCF
B: Transcriptional repressor CTCF
C: DNA (26-MER)
F: DNA (26-MER)
E: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,57618
Polymers73,7916
Non-polymers78512
Water00
1
D: DNA (26-MER)
B: Transcriptional repressor CTCF
C: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2889
Polymers36,8963
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-51 kcal/mol
Surface area18210 Å2
MethodPISA
2
A: Transcriptional repressor CTCF
F: DNA (26-MER)
E: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2889
Polymers36,8963
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-52 kcal/mol
Surface area17980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.993, 69.631, 84.445
Angle α, β, γ (deg.)90.00, 116.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain DNA (26-MER)


Mass: 7940.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Transcriptional repressor CTCF / 11-zinc finger protein / CCCTC-binding factor / CTCFL paralog


Mass: 20922.227 Da / Num. of mol.: 2 / Fragment: UNP residues 405-580 / Mutation: C504S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTCF / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P49711
#3: DNA chain DNA (26-MER)


Mass: 8033.187 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn

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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: 3.41 Å3/Da / Density % sol: 63.96 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 0.1M Bis-tris pH 5.6-6.0, 0.1M Sodium chloride, 17-20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→37.87 Å / Num. obs: 30548 / % possible obs: 99.6 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.029 / Net I/σ(I): 30.6
Reflection shellResolution: 2.96→3.01 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 4.3 / Rpim(I) all: 0.221 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.96→37.874 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 34.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2856 1029 5 %
Rwork0.2678 --
obs0.2687 20571 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.96→37.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2642 2118 12 0 4772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095084
X-RAY DIFFRACTIONf_angle_d1.317285
X-RAY DIFFRACTIONf_dihedral_angle_d32.2912002
X-RAY DIFFRACTIONf_chiral_restr0.074776
X-RAY DIFFRACTIONf_plane_restr0.006575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9602-3.11620.4421650.39082762X-RAY DIFFRACTION99
3.1162-3.31140.31451150.35522741X-RAY DIFFRACTION95
3.3114-3.56690.30771600.31242682X-RAY DIFFRACTION96
3.5669-3.92550.30831560.2832835X-RAY DIFFRACTION99
3.9255-4.49270.26331530.26122797X-RAY DIFFRACTION100
4.4927-5.65740.2691360.24692883X-RAY DIFFRACTION100
5.6574-37.87720.24751440.21462842X-RAY DIFFRACTION97
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)
18.5134-0.38710.7744.7093-0.6091.5857-0.0956-0.0705-0.13860.3510.1461-0.1008-0.0783-0.0359-0.05950.40440.0355-0.0650.5596-0.06670.304389.067914.9713125.6457
26.27391.54862.07081.90330.39991.81610.10490.1976-0.7331-0.17290.25520.53690.1709-0.251-0.26320.50660.1891-0.22660.6019-0.03240.7532369.018514.6126113.7829
35.2704-0.41781.54641.3347-0.18641.23340.18470.0461-0.90090.21590.2515-0.06650.2778-0.4372-0.35640.70720.141-0.58240.9098-0.13281.813337.097413.214597.2166
41.0575-0.1026-0.98580.13880.28851.21890.0134-0.12840.40030.1527-0.10930.1562-0.9684-0.18680.04591.02830.1929-0.17610.81-0.14510.8952305.984260.1986141.6625
50.00580.00440.0020.0028-0.00610.0087-0.135-0.01340.0342-0.03730.00790.0328-0.1166-0.042900.33690.12870.06850.165-0.15880.4104320.852841.7044136.1259
60.0038-0.00250.00060.0062-0.00060.0048-0.0512-0.03630.04480.056-0.0721-0.0353-0.0934-0.0107-00.2978-0.01720.02110.3869-0.07290.3494339.717136.8921134.6999
70.0019-0.0003-0.0016-0.00210.00530.00180.00710.0311-0.0111-0.0340.06050.00470.0027-0.016400.5766-0.0493-0.01980.5198-0.16850.4362359.939741.6473139.4741
8-0.00320.0060.0002-0.0034-0.00110.00510.04160.0207-0.08130.01020.03310.06340.0199-0.0253-00.3107-0.39370.46960.52220.4075-0.3598371.231758.8917142.6635
90.0011-0.0015-0.0005-0.0042-0.0005-0.00020.01230.0309-0.02460.0482-0.0250.03030.01650.0249-00.3157-0.02880.0850.16660.04790.0813365.896156.0541169.1424
100.8225-0.18790.19430.085-0.23010.988-0.03660.2684-0.4207-0.29230.04420.09620.49130.10090.0930.71320.0965-0.03671.1877-0.18410.9285336.21517.429780.8069
110.00990.0012-0.00530.0035-0.00620.0062-0.06060.0741-0.1445-0.05090.0154-0.016-0.0117-0.0126-00.35670.0084-0.0370.2459-0.26140.3514340.730526.036695.7842
120.00150.0019-0.00070.00150.00550.00450.01580.001-0.0602-0.0035-0.0985-0.06360.01930.029700.36730.0969-0.00470.22710.00540.2566351.098130.7738111.6859
130.003-0.0092-0.0018-0.00060.00350.00240.0078-0.01040.04390.00070.03210.0402-0.0061-0.0168-00.05850.32510.02450.1474-0.22130.4305367.185826.0454124.797
140.0005-0.0012-0.00590.0031-0.00750.0009-0.0628-0.01740.05770.0021-0.03530.0202-0.0146-0.024200.1218-0.00070.55920.48530.5123-0.2338376.60378.7083131.6979
150.4244-0.11920.59992.4669-0.35170.83870.07460.07250.0713-0.3718-0.0559-0.2660.04170.08520.0192-0.20940.07970.3690.00180.1327-0.1308394.490311.6262111.24
165.88772.25764.07614.74740.89043.128-0.18940.49180.1876-0.39760.2906-0.0326-0.44940.2309-0.02180.4574-0.0303-0.11570.44760.07360.7164327.24118.339788.718
175.6402-0.01972.21450.0025-0.00690.88680.25480.0001-0.56020.01510.2488-0.13460.4160.0881-0.36331.04320.0172-0.54790.9875-0.08871.2345347.278912.6508102.5645
184.96470.10281.48562.09520.02212.3280.0214-0.34580.36860.04560.15440.2387-0.3-0.2917-0.17330.65830.0458-0.16960.46330.06450.7062377.792516.6893119.3366
193.2890.25963.22052.2146-0.24265.5843-0.11570.0206-0.0933-0.06640.1609-0.2679-0.1245-0.0868-0.02270.3489-0.03260.03750.7528-0.04420.4743373.929152.7346156.3409
205.1051-0.90582.60781.6487-0.80252.3935-0.38350.15610.5133-0.26750.24160.3683-0.2114-0.29680.07780.4659-0.0962-0.17980.645-0.17670.8065352.327853.123147.6317
214.13560.08482.64331.6590.25592.4738-0.2150.22520.6748-0.15230.3217-0.2215-0.5054-0.26010.08210.84490.0305-0.70480.8304-0.12271.509319.739454.4831132.3932
227.5835-1.69641.24373.7418-0.44680.9181-0.176-0.1935-0.31810.18110.08620.1220.1087-0.24190.04440.4625-0.0442-0.14240.4657-0.02490.7341307.032249.3746129.8181
235.28860.81243.54370.130.53922.3773-0.2608-0.00390.51380.04850.3044-0.1637-0.22520.12290.01040.6574-0.0004-0.23270.93510.05741.5719330.174655.0819137.2009
245.0572-0.1281.89311.5629-0.17832.2790.02930.3101-0.3222-0.33770.19880.17080.2290.0763-0.30010.445-0.1075-0.07330.46160.01610.7382362.065551.0341151.2469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 5 )D1 - 5
2X-RAY DIFFRACTION2chain 'D' and (resid 6 through 15 )D6 - 15
3X-RAY DIFFRACTION3chain 'D' and (resid 16 through 26 )D16 - 26
4X-RAY DIFFRACTION4chain 'A' and (resid 406 through 430 )A406 - 430
5X-RAY DIFFRACTION5chain 'A' and (resid 436 through 461 )A436 - 461
6X-RAY DIFFRACTION6chain 'A' and (resid 466 through 491 )A466 - 491
7X-RAY DIFFRACTION7chain 'A' and (resid 494 through 518 )A494 - 518
8X-RAY DIFFRACTION8chain 'A' and (resid 522 through 547 )A522 - 547
9X-RAY DIFFRACTION9chain 'A' and (resid 554 through 577 )A554 - 577
10X-RAY DIFFRACTION10chain 'B' and (resid 406 through 430 )B406 - 430
11X-RAY DIFFRACTION11chain 'B' and (resid 436 through 461 )B436 - 461
12X-RAY DIFFRACTION12chain 'B' and (resid 466 through 491 )B466 - 491
13X-RAY DIFFRACTION13chain 'B' and (resid 494 through 518 )B494 - 518
14X-RAY DIFFRACTION14chain 'B' and (resid 522 through 547 )B522 - 547
15X-RAY DIFFRACTION15chain 'B' and (resid 554 through 578 )B554 - 578
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 5 )C1 - 5
17X-RAY DIFFRACTION17chain 'C' and (resid 6 through 15 )C6 - 15
18X-RAY DIFFRACTION18chain 'C' and (resid 16 through 26 )C16 - 26
19X-RAY DIFFRACTION19chain 'F' and (resid 1 through 5 )F1 - 5
20X-RAY DIFFRACTION20chain 'F' and (resid 6 through 15 )F6 - 15
21X-RAY DIFFRACTION21chain 'F' and (resid 16 through 26 )F16 - 26
22X-RAY DIFFRACTION22chain 'E' and (resid 1 through 5 )E1 - 5
23X-RAY DIFFRACTION23chain 'E' and (resid 6 through 15 )E6 - 15
24X-RAY DIFFRACTION24chain 'E' and (resid 16 through 26 )E16 - 26

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