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- PDB-5t00: Human CTCF ZnF3-7 and methylated DNA complex -

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Basic information

Entry
Database: PDB / ID: 5t00
TitleHuman CTCF ZnF3-7 and methylated DNA complex
Components
  • DNA (5'-GCCAGCAGGGGG(5CM)GCTA-3')
  • DNA (5'-TAG(5CM)GCCCCCTGCTGGC-3')
  • Transcriptional repressor CTCF
KeywordsTRANSCRIPTION REGULATOR/DNA / CCCTC-binding factor / zinc finger / CTCF / TRANSCRIPTION REGULATOR-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
C2H2-type zinc-finger domain / 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: 2.19 Å
AuthorsHashimoto, H. / Wang, D. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245 United States
CitationJournal: Mol. Cell / Year: 2017
Title: Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA.
Authors: Hashimoto, H. / Wang, D. / Horton, J.R. / Zhang, X. / Corces, V.G. / Cheng, X.
History
DepositionAug 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional repressor CTCF
B: DNA (5'-TAG(5CM)GCCCCCTGCTGGC-3')
C: DNA (5'-GCCAGCAGGGGG(5CM)GCTA-3')
D: Transcriptional repressor CTCF
E: DNA (5'-TAG(5CM)GCCCCCTGCTGGC-3')
F: DNA (5'-GCCAGCAGGGGG(5CM)GCTA-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,63016
Polymers55,9766
Non-polymers65410
Water1,74797
1
A: Transcriptional repressor CTCF
B: DNA (5'-TAG(5CM)GCCCCCTGCTGGC-3')
C: DNA (5'-GCCAGCAGGGGG(5CM)GCTA-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3158
Polymers27,9883
Non-polymers3275
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-39 kcal/mol
Surface area11630 Å2
MethodPISA
2
D: Transcriptional repressor CTCF
E: DNA (5'-TAG(5CM)GCCCCCTGCTGGC-3')
F: DNA (5'-GCCAGCAGGGGG(5CM)GCTA-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3158
Polymers27,9883
Non-polymers3275
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-39 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.990, 44.910, 86.800
Angle α, β, γ (deg.)98.33, 92.40, 94.80
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 17541.293 Da / Num. of mol.: 2 / Fragment: UNP residues 321-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTCF / Plasmid: pXC1551 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): codon plus / References: UniProt: P49711
#2: DNA chain DNA (5'-TAG(5CM)GCCCCCTGCTGGC-3')


Mass: 5154.338 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-GCCAGCAGGGGG(5CM)GCTA-3')


Mass: 5292.438 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.: 10 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% (w/v) PEG 3350, 0.2 M NaCl, 0.1 M HEPES-NaOH, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 9, 2016
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→41.956 Å / Num. obs: 31307 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 43.92 Å2 / CC1/2: 0.994 / Rsym value: 0.109 / Net I/σ(I): 6.56
Reflection shellResolution: 2.18→2.24 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.687 / % possible all: 84.5

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Processing

Software
NameVersionClassification
PHENIX(dev_2257: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KKQ

5kkq


Resolution: 2.19→41.956 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 30.06
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 1553 5.01 %Random
Rwork0.2184 ---
obs0.2196 30975 98.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.19→41.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3043 682 10 97 3832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063994
X-RAY DIFFRACTIONf_angle_d0.6845606
X-RAY DIFFRACTIONf_dihedral_angle_d20.9612136
X-RAY DIFFRACTIONf_chiral_restr0.041595
X-RAY DIFFRACTIONf_plane_restr0.002478
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
2.19-2.26070.33221310.3204248191
2.2607-2.34150.31931410.29222679100
2.3415-2.43530.33031430.28842719100
2.4353-2.54610.32861430.29222721100
2.5461-2.68030.29621410.27262677100
2.6803-2.84820.3461430.27292708100
2.8482-3.0680.25131420.26172709100
3.068-3.37670.27914350.2346266098
3.3767-3.8650.234314150.1997266999
3.865-4.86830.21114350.18252709100
4.8683-41.9560.170414250.166269099
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)
11.2046-0.9999-0.52851.05480.41510.25190.07190.5252-0.5709-0.94390.1776-0.02220.53630.5195-0.02351.2245-0.03860.14031.1774-0.33210.750810.0369-27.4025-32.6371
22.40020.72071.04370.86470.83032.7747-0.44470.24040.1966-0.38610.2760.1256-0.65920.55340.14750.5737-0.0792-0.01790.3363-0.0120.3374-1.2909-13.8856-17.6348
31.4534-1.16650.48282.0972-0.63172.53080.09960.21130.0668-0.5899-0.02830.07-0.00330.0452-0.07610.47660.037-0.05420.2693-0.04640.3735-13.6992-32.9047-11.2991
42.00280.90870.81913.0707-0.03573.7682-0.0842-0.17440.220.16560.4129-0.00080.21220.1667-0.35150.29140.10560.02760.5081-0.09470.4447-6.509-34.989710.2057
53.63971.7385-3.33292.5931-3.90956.1024-0.6369-0.55780.52210.4604-0.35010.5947-0.6201-0.15630.61790.82530.18590.05840.9109-0.34980.7329-9.9441-27.853817.9183
63.24290.9846-0.82371.2303-0.16571.0786-0.42870.3830.84350.2354-0.0189-0.4114-0.28040.43650.28931.1026-0.2751-0.07441.03120.25410.7674-2.9848-11.7107-28.3523
71.9371-0.0470.49984.72960.25524.9503-0.1810.9140.4505-0.6480.60860.39020.1269-0.4525-0.43910.7958-0.14350.08660.5970.1110.5288-7.5956-25.468-20.0907
83.410.0628-1.96474.1645-0.68984.45850.3468-1.31180.7359-0.25020.3733-0.21530.1140.7934-0.69540.3640.00030.00150.6560.02340.5474-6.4055-26.4536-2.3391
91.0106-0.3064-0.19522.5146-1.34862.80.0321-0.90390.2642-0.29380.24610.60780.0788-0.4895-0.31740.27530.03760.05390.43520.07410.5422-21.5072-30.8774.1721
103.885-0.2593-0.70083.0919-0.90453.35680.1204-0.4211-0.0597-0.2693-0.5192-0.12880.29370.28710.31070.16640.03240.00820.25150.06120.4407-15.7613-36.02191.3438
111.65090.2951-0.5822.96120.32562.3441-0.0121-0.07820.2422-0.55810.2580.36260.03930.2154-0.18930.4539-0.0031-0.01380.35790.04080.3861-8.055-21.168-9.4473
120.73731.09231.68551.98692.11995.50860.32841.2269-0.009-0.51570.57030.33990.18080.1259-0.56510.7982-0.21450.05981.21780.17190.4976-2.1941-20.8867-29.8417
131.6861-1.8171-1.07926.32790.00781.0131-0.16680.2709-0.8327-0.45570.05510.78360.135-0.3948-0.54250.8524-0.5728-0.12241.34390.55421.019-11.1181-26.494535.4436
140.0814-0.0618-0.03850.12890.07070.11560.8854-0.93340.80960.00870.6250.7381-0.7264-0.2003-1.12480.7142-0.05470.19941.32680.14871.069-16.048-18.073833.7067
151.20490.8488-0.77911.1984-0.83341.53370.4936-1.03260.34550.9374-0.36780.2435-0.34440.0733-0.16230.9952-0.34620.14981.36520.15970.7253-2.3542-5.215840.7518
162.81740.7281-0.35484.6-1.08713.30080.3607-0.4789-0.4420.0491-0.6304-0.26050.60430.14420.26620.3986-0.01860.01250.43440.0520.48648.2339-4.071417.2915
171.8402-2.63260.0723.93250.65093.3764-0.6874-0.35661.5461.14470.00780.2259-1.5465-0.46390.4480.7245-0.02140.07740.5093-0.1171.20830.843920.880313.8
182.09930.1398-2.99340.2091-0.1734.2469-0.022-0.94680.09420.7605-0.09720.2775-0.14450.1697-0.15640.8379-0.58820.31321.76430.67280.8714-2.1164-18.012146.0708
193.29-4.35350.42666.1862-2.23526.84761.318-1.122-0.55860.7703-1.1167-0.1879-0.10931.50730.24680.7137-0.3053-0.03341.00750.26940.57984.4925-16.660430.5653
203.78550.1879-0.88272.4556-1.4992.6590.3194-0.28390.9878-0.25390.11321.14410.3059-0.6723-0.45220.5409-0.06760.11860.79620.19070.68441.6193-0.896921.8341
215.81240.72380.23544.5007-1.06792.89330.3456-1.14350.36020.1883-0.51920.3411-0.46840.86930.1340.2957-0.01470.04250.62750.09210.48216.78965.043616.767
221.9413-1.46620.55332.9293-1.81132.34660.3508-0.5340.2012-0.5593-0.4917-0.42460.5001-0.02370.04410.31940.04420.01040.41610.09240.516311.95720.82210.8159
235.13161.4446-2.14192.5204-1.55794.43551.0019-0.7391-0.11140.9711-0.5486-0.31050.1692-0.2149-0.32820.5688-0.13480.01580.77080.1680.517710.057-2.756325.4086
244.49191.06210.36281.6557-1.03841.7540.9222-1.07760.27110.5037-0.6027-0.0705-0.339-0.1502-0.28210.7673-0.20990.18010.94050.21910.5656-3.1774-12.084131.8924
252.03780.1713-0.12141.5352-0.7280.34860.6665-0.3943-0.1742-0.14610.29110.43880.3389-0.6102-0.67091.168-0.17360.12141.27670.53860.89741.0477-25.816942.4102
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 320:333)
2X-RAY DIFFRACTION2(chain A and resid 334:386)
3X-RAY DIFFRACTION3(chain A and resid 387:432)
4X-RAY DIFFRACTION4(chain A and resid 433:458)
5X-RAY DIFFRACTION5(chain A and resid 459:462)
6X-RAY DIFFRACTION6(chain B and resid 1:4)
7X-RAY DIFFRACTION7(chain B and resid 5:9)
8X-RAY DIFFRACTION8(chain B and resid 10:13)
9X-RAY DIFFRACTION9(chain B and resid 14:17)
10X-RAY DIFFRACTION10(chain C and resid 1:5)
11X-RAY DIFFRACTION11(chain C and resid 6:11)
12X-RAY DIFFRACTION12(chain C and resid 12:17)
13X-RAY DIFFRACTION13(chain D and resid 322:343)
14X-RAY DIFFRACTION14(chain D and resid 344:348)
15X-RAY DIFFRACTION15(chain D and resid 349:383)
16X-RAY DIFFRACTION16(chain D and resid 384:459)
17X-RAY DIFFRACTION17(chain D and resid 460:464)
18X-RAY DIFFRACTION18(chain E and resid 1:4)
19X-RAY DIFFRACTION19(chain E and resid 5:9)
20X-RAY DIFFRACTION20(chain E and resid 10:13)
21X-RAY DIFFRACTION21(chain E and resid 14:17)
22X-RAY DIFFRACTION22(chain F and resid 1:4)
23X-RAY DIFFRACTION23(chain F and resid 5:8)
24X-RAY DIFFRACTION24(chain F and resid 9:13)
25X-RAY DIFFRACTION25(chain F and resid 14:17)

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