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- PDB-5yeg: Crystal structure of CTCF ZFs4-8-Hs5-1a complex -

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Basic information

Entry
Database: PDB / ID: 5yeg
TitleCrystal structure of CTCF ZFs4-8-Hs5-1a complex
Components
  • (Transcriptional repressor ...) x 2
  • DNA (5'-D(*AP*CP*TP*TP*TP*AP*AP*CP*CP*AP*GP*CP*AP*GP*AP*GP*GP*GP*CP*G)-3')
  • DNA (5'-D(*TP*CP*GP*CP*CP*CP*TP*CP*TP*GP*CP*TP*GP*GP*TP*TP*AP*AP*AP*G)-3')
KeywordsDNA BINDING PROTEIN / zinc fingers / insulators / enhancers / promoters / 3D genome / topological domains / contact loops / higher-order chromatin structure
Function / homology
Function and homology information


chromatin loop anchoring activity / chromatin insulator sequence binding / regulation of centromeric sister chromatid cohesion / genomic imprinting / protein localization to chromosome, centromeric region / chromatin looping / chromosome, centromeric region / condensed chromosome / transcription coregulator binding / chromosome segregation ...chromatin loop anchoring activity / chromatin insulator sequence binding / regulation of centromeric sister chromatid cohesion / genomic imprinting / protein localization to chromosome, centromeric region / chromatin looping / chromosome, centromeric region / condensed chromosome / transcription coregulator binding / chromosome segregation / epigenetic regulation of gene expression / 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 gene expression / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / nucleoplasm / zinc ion binding / nucleus
Similarity search - Function
: / : / C2H2-type zinc-finger domain / C2H2 zinc finger / 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 / SAD / Resolution: 2 Å
AuthorsYin, M. / Wang, J. / Wang, M. / Li, X.
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 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Structure summary / Category: entity / Item: _entity.src_method
Revision 1.2Mar 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

Downloads & links

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Assembly

Deposited unit
A: Transcriptional repressor CTCF
B: Transcriptional repressor CTCF
D: DNA (5'-D(*TP*CP*GP*CP*CP*CP*TP*CP*TP*GP*CP*TP*GP*GP*TP*TP*AP*AP*AP*G)-3')
C: DNA (5'-D(*AP*CP*TP*TP*TP*AP*AP*CP*CP*AP*GP*CP*AP*GP*AP*GP*GP*GP*CP*G)-3')
E: DNA (5'-D(*TP*CP*GP*CP*CP*CP*TP*CP*TP*GP*CP*TP*GP*GP*TP*TP*AP*AP*AP*G)-3')
F: DNA (5'-D(*AP*CP*TP*TP*TP*AP*AP*CP*CP*AP*GP*CP*AP*GP*AP*GP*GP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,32216
Polymers58,6686
Non-polymers65410
Water10,935607
1
A: Transcriptional repressor CTCF
D: DNA (5'-D(*TP*CP*GP*CP*CP*CP*TP*CP*TP*GP*CP*TP*GP*GP*TP*TP*AP*AP*AP*G)-3')
C: DNA (5'-D(*AP*CP*TP*TP*TP*AP*AP*CP*CP*AP*GP*CP*AP*GP*AP*GP*GP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7268
Polymers29,3993
Non-polymers3275
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-77 kcal/mol
Surface area14040 Å2
MethodPISA
2
B: Transcriptional repressor CTCF
E: DNA (5'-D(*TP*CP*GP*CP*CP*CP*TP*CP*TP*GP*CP*TP*GP*GP*TP*TP*AP*AP*AP*G)-3')
F: DNA (5'-D(*AP*CP*TP*TP*TP*AP*AP*CP*CP*AP*GP*CP*AP*GP*AP*GP*GP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5978
Polymers29,2703
Non-polymers3275
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-43 kcal/mol
Surface area14160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.167, 56.502, 67.486
Angle α, β, γ (deg.)78.41, 79.31, 78.60
Int Tables number1
Space group name H-MP1

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Components

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Transcriptional repressor ... , 2 types, 2 molecules AB

#1: Protein Transcriptional repressor CTCF / 11-zinc finger protein / CCCTC-binding factor / CTCFL paralog


Mass: 16825.561 Da / Num. of mol.: 1 / Fragment: UNP residues 349-490
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
#2: Protein Transcriptional repressor CTCF / 11-zinc finger protein / CCCTC-binding factor / CTCFL paralog


Mass: 16696.379 Da / Num. of mol.: 1 / Fragment: UNP residues 349-489
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

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DNA chain , 2 types, 4 molecules DECF

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


Mass: 6405.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*AP*CP*TP*TP*TP*AP*AP*CP*CP*AP*GP*CP*AP*GP*AP*GP*GP*GP*CP*G)-3')


Mass: 6168.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 617 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal growTemperature: 289.15 K / Method: evaporation
Details: 0.1M Bis-tris pH 5.6-6.0, 0.2M Sodium chloride, 17-24% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→39.84 Å / Num. obs: 42594 / % possible obs: 97.1 % / Redundancy: 4 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.035 / Net I/σ(I): 20.9
Reflection shellResolution: 2→39.84 Å / Redundancy: 4 % / Rmerge(I) obs: 0.37 / Rpim(I) all: 0.21 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→39.838 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 22
RfactorNum. reflection% reflection
Rfree0.2042 2036 4.78 %
Rwork0.1863 --
obs0.1872 42552 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→39.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2284 1627 10 607 4528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084165
X-RAY DIFFRACTIONf_angle_d1.0045940
X-RAY DIFFRACTIONf_dihedral_angle_d22.222207
X-RAY DIFFRACTIONf_chiral_restr0.053636
X-RAY DIFFRACTIONf_plane_restr0.006478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9965-2.04290.3031150.26042593X-RAY DIFFRACTION92
2.0429-2.0940.19671490.23812732X-RAY DIFFRACTION97
2.094-2.15060.23251240.22982660X-RAY DIFFRACTION97
2.1506-2.21390.271560.22432700X-RAY DIFFRACTION97
2.2139-2.28540.24241520.21972669X-RAY DIFFRACTION97
2.2854-2.3670.23431290.21512683X-RAY DIFFRACTION95
2.367-2.46180.23611230.22292758X-RAY DIFFRACTION98
2.4618-2.57380.25941440.21752726X-RAY DIFFRACTION98
2.5738-2.70950.22811390.21412713X-RAY DIFFRACTION98
2.7095-2.87920.28191220.21382690X-RAY DIFFRACTION96
2.8792-3.10140.23151390.21372727X-RAY DIFFRACTION98
3.1014-3.41340.18891350.18552716X-RAY DIFFRACTION97
3.4134-3.90690.20221210.15952725X-RAY DIFFRACTION97
3.9069-4.92090.16711420.14592739X-RAY DIFFRACTION98
4.9209-39.84570.14961460.152685X-RAY DIFFRACTION96
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)
10.94380.14930.04631.4078-0.54651.4215-0.05720.55670.3894-0.19060.06490.4809-0.2592-0.47210.01760.30350.0318-0.08960.45880.04010.34664.9717-13.1736-14.7166
21.23870.66970.50050.50580.21620.817-0.03050.015-0.1582-0.032-0.0775-0.03230.1426-0.00640.08490.2327-0.02660.02380.1423-0.00160.180819.4787-25.8919-6.0225
30.82250.83050.39061.570.73930.7368-0.0290.0785-0.0108-0.04130.189-0.35630.0830.2242-0.1290.12160.0134-0.00850.2016-0.02810.225435.0425-10.9259-1.0099
41.5615-0.3795-0.31331.3370.03441.2876-0.0915-0.0129-0.01410.05630.0338-0.00570.123-0.00770.05880.1484-0.0040.01120.1287-0.01360.156618.4306-0.511912.5158
51.14541.0285-0.44411.06930.13970.70430.3465-0.3272-0.02070.4239-0.346-0.2288-0.52940.4962-0.0220.3828-0.1280.01450.42030.06790.196710.6273-2.038329.8379
60.9967-0.0691-0.29571.26030.2971.39030.0231-0.1790.25080.03370.1108-0.3396-0.5599-0.2002-0.09390.50230.0171-0.01530.2723-0.08040.421312.94332.137615.9283
70.5620.1618-0.25750.96570.20180.95390.063-0.1390.1903-0.00880.0099-0.1732-0.17120.2273-0.08260.125-0.0298-0.00310.1443-0.0340.212421.653615.60216.1875
82.03070.62660.11810.66190.17970.47450.04080.0435-0.26320.05050.0613-0.0130.0685-0.1137-0.08240.137-0.0053-0.01860.18940.01150.27222.62083.77832.3029
90.8216-0.36920.09930.74660.00160.847-0.2476-0.3679-0.2656-0.29080.31160.1534-0.1608-0.5021-0.14190.30840.13370.10220.49980.15170.3117-3.783521.5955-11.6184
100.98880.39910.12671.08-0.55610.4803-0.2510.0901-0.18330.11340.08230.21870.6268-0.46330.13250.4643-0.03250.12720.31050.03130.2328-2.55929.5291-29.5681
111.17970.2770.24242.6854-0.15923.1028-0.09430.82-0.4304-0.8104-0.34170.0771-0.0472-0.75230.3340.38760.02370.00050.6052-0.08510.291217.9748-19.2402-21.4308
121.3186-0.33620.4471.80320.78163.2158-0.10630.0067-0.02030.0965-0.0002-0.0410.0024-0.01140.14550.2279-0.04510.01430.1656-0.03840.235721.9078-12.45063.2422
130.18160.39560.42131.74670.68241.17120.568-0.06290.17640.32480.6204-1.0419-0.75140.184-0.4290.92650.15520.0060.8181-0.34950.6630.2343-5.72525.2886
141.85971.18371.34470.78480.811.01960.4371-0.5873-0.2850.55970.5276-0.97590.41530.2696-0.25811.07270.0821-0.15470.7356-0.05660.351827.0842-10.785431.8638
151.1756-0.2216-0.11321.31030.5180.60010.01460.20120.0581-0.11510.08330.09750.0474-0.0447-0.01120.2057-0.01840.0120.23390.03560.16921.5422-12.1304-2.5691
161.2198-0.34180.17951.7264-0.24432.29460.035-0.15790.07190.30680.1299-0.2365-0.3219-0.0501-0.17520.25770.0211-0.04670.2192-0.04250.227210.187616.71715.8106
171.58840.19850.13740.15670.32650.87421.44170.4066-0.6629-0.230.74170.4328-0.7636-1.0553-0.49960.39180.2376-1.54960.6680.4744-0.9419-0.11948.8077-23.8618
180.7359-0.2840.31210.35270.16671.54890.45230.4047-0.4053-0.65140.2440.1550.3473-0.163-0.39760.47980.0549-0.08380.4704-0.04430.27733.940311.0298-21.0006
190.9726-0.12560.11111.32330.14751.70560.0928-0.23070.0480.31020.0929-0.1356-0.1722-0.2005-0.1770.2540.0178-0.0230.18760.00320.17419.963418.316911.3767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 350 through 374 )
2X-RAY DIFFRACTION2chain 'A' and (resid 378 through 403 )
3X-RAY DIFFRACTION3chain 'A' and (resid 406 through 431 )
4X-RAY DIFFRACTION4chain 'A' and (resid 436 through 461 )
5X-RAY DIFFRACTION5chain 'A' and (resid 466 through 487 )
6X-RAY DIFFRACTION6chain 'B' and (resid 350 through 374 )
7X-RAY DIFFRACTION7chain 'B' and (resid 378 through 403 )
8X-RAY DIFFRACTION8chain 'B' and (resid 406 through 431 )
9X-RAY DIFFRACTION9chain 'B' and (resid 436 through 461 )
10X-RAY DIFFRACTION10chain 'B' and (resid 466 through 489 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 5 )
12X-RAY DIFFRACTION12chain 'D' and (resid 6 through 15 )
13X-RAY DIFFRACTION13chain 'D' and (resid 16 through 20 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 5 )
15X-RAY DIFFRACTION15chain 'C' and (resid 6 through 20 )
16X-RAY DIFFRACTION16chain 'E' and (resid 1 through 15 )
17X-RAY DIFFRACTION17chain 'E' and (resid 16 through 20 )
18X-RAY DIFFRACTION18chain 'F' and (resid 1 through 10 )
19X-RAY DIFFRACTION19chain 'F' and (resid 11 through 20 )

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