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- PDB-8ssu: ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 19mer DNA -

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Basic information

Entry
Database: PDB / ID: 8ssu
TitleZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 19mer DNA
Components
  • (DNA (19-MER) Strand ...) x 2
  • Transcriptional repressor CTCF,LIM domain-binding protein 1
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DNA BINDING PROTEIN / transcription factor / zinc fingers / insulator/chromatin architecture / transcription-dna complex / TRANSCRIPTION
Function / homology
Function and homology information


Expression and translocation of olfactory receptors / regulation of kinase activity / cellular component assembly / chromatin insulator sequence binding / negative regulation of erythrocyte differentiation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / epithelial structure maintenance / regulation of centromeric sister chromatid cohesion / beta-catenin-TCF complex ...Expression and translocation of olfactory receptors / regulation of kinase activity / cellular component assembly / chromatin insulator sequence binding / negative regulation of erythrocyte differentiation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / epithelial structure maintenance / regulation of centromeric sister chromatid cohesion / beta-catenin-TCF complex / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / LIM domain binding / genomic imprinting / protein localization to chromosome, centromeric region / chromatin looping / gastrulation with mouth forming second / negative regulation of gene expression via chromosomal CpG island methylation / Cardiogenesis / anterior/posterior axis specification / regulation of focal adhesion assembly / cell leading edge / somatic stem cell population maintenance / chromosome, centromeric region / positive regulation of cell adhesion / hair follicle development / epigenetic regulation of gene expression / condensed chromosome / regulation of cell migration / male germ cell nucleus / chromosome segregation / transcription coregulator binding / positive regulation of transcription elongation by RNA polymerase II / neuron differentiation / Wnt signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / Regulation of expression of SLITs and ROBOs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / : / nervous system development / RUNX1 regulates transcription of genes involved in differentiation of HSCs / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / transcription coactivator activity / transcription cis-regulatory region binding / cell adhesion / 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 / chromatin binding / chromatin / positive regulation of gene expression / nucleolus / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile. / 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 / LIM domain-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsHorton, J.R. / Yang, J. / Cheng, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR160029 United States
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structures of CTCF-DNA complexes including all 11 zinc fingers.
Authors: Yang, J. / Horton, J.R. / Liu, B. / Corces, V.G. / Blumenthal, R.M. / Zhang, X. / Cheng, X.
History
DepositionMay 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional repressor CTCF,LIM domain-binding protein 1
B: DNA (19-MER) Strand I
C: DNA (19-MER) Strand II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,44413
Polymers51,7973
Non-polymers64710
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-38 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.464, 80.464, 187.598
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Transcriptional repressor CTCF,LIM domain-binding protein 1


Mass: 40142.430 Da / Num. of mol.: 1
Fragment: Zinc finger domains 3-11 of CTCF, Residues 195-258 of LDB1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTCF, LDB1, CLIM2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus / References: UniProt: P49711, UniProt: Q86U70

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DNA (19-MER) Strand ... , 2 types, 2 molecules BC

#2: DNA chain DNA (19-MER) Strand I


Mass: 5724.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (19-MER) Strand II


Mass: 5929.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 16 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.4 Å3/Da / Density % sol: 63.78 %
Description: 0.04 M Citric acid, 0.06 M BIS-TRIS propane)/pH 6.4, 20% w/v Polyethylene glycol 3,350
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.04 M Citric acid, 0.06 M BIS-TRIS propane/pH 6.4, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→39.34 Å / Num. obs: 30234 / % possible obs: 99.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 78.7 Å2 / CC1/2: 0.974 / Rpim(I) all: 0.065 / Net I/σ(I): 12.8
Reflection shellResolution: 2.89→2.99 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3041 / CC1/2: 0.706 / Rpim(I) all: 0.86

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→39.34 Å / SU ML: 0.4767 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.1391
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2403 1460 4.93 %
Rwork0.1998 28168 -
obs0.2018 29628 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.66 Å2
Refinement stepCycle: LAST / Resolution: 2.89→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 772 16 6 2679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312852
X-RAY DIFFRACTIONf_angle_d0.50294020
X-RAY DIFFRACTIONf_chiral_restr0.0347427
X-RAY DIFFRACTIONf_plane_restr0.003380
X-RAY DIFFRACTIONf_dihedral_angle_d21.83181131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-30.47261400.38782686X-RAY DIFFRACTION91.93
3-3.120.36911450.37522810X-RAY DIFFRACTION98.4
3.12-3.260.38631440.32872780X-RAY DIFFRACTION96.31
3.26-3.430.38381490.30762666X-RAY DIFFRACTION93.65
3.43-3.640.28821470.24232856X-RAY DIFFRACTION97.12
3.64-3.920.22731520.19812833X-RAY DIFFRACTION99.24
3.92-4.320.24531390.18632872X-RAY DIFFRACTION99.9
4.32-4.940.22051560.16732891X-RAY DIFFRACTION99.77
4.95-6.220.20031460.15792886X-RAY DIFFRACTION99.97
6.23-39.340.15971420.14232888X-RAY DIFFRACTION99.64
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)
15.53908334657-1.675628228051.944804976987.595701838591.505334560056.68760604961-0.1296464303980.992719683938-0.420457018088-1.05113868106-0.0216106559919-0.9048841978890.9041787211871.289921744320.0982493741340.931671569661-0.1212316424070.201688172431.00043102924-0.185208043490.59710970017951.7286662376-23.38005090857.01600437892
21.251503137690.6813705401610.2129125074192.840696847510.3937504094956.66376453163-0.032638264388-0.078146806055-0.2259300766370.1854867428260.267655882643-0.2593863204650.3280043660130.474300984809-0.2294115450670.8011109614350.119787180869-0.02659752852180.68872719442-0.0602655183940.47582260075939.4197599835-13.882091920638.7345031935
31.534249349140.842379659846-0.6302211443713.43430118812.941554405993.874514272990.2409213149270.238640249993-0.0836775944999-0.708138414824-0.558748956573-0.03454276176890.0181542080013-0.07149374882340.3103253792061.201487226420.180253954509-0.01095416719050.9265864391310.2080091015790.65655522028346.97054583043.28537485532106.452754859
46.890876877841.396946328175.571423227754.676064055614.371428175448.311041455631.01958703465-1.23177116585-0.4156646633191.20460781093-0.167231604114-0.1240681034831.66828141585-0.170435224181-0.7148169935431.11385909719-0.00895989564104-0.00484801043861.09266507711-0.001481053362280.42031235286139.6254215065-21.91813068620.9918316193
55.87536881117-1.689598048753.951208769818.34921231336-5.336443087847.108476947050.192666714689-0.796456393954-0.590979522172-0.4349869595620.8702540756730.5139114285411.17737723895-1.08748952621-0.9918332937791.323668390720.0761382126234-0.06229376273461.002833132720.05519592391730.44037758034837.3451536023-18.592760567750.5344007801
62.22452075418-0.0394555901449-0.8910192802221.44386256560.798194091651.128439033490.005155303807170.00418192337602-0.1685490831620.2002965545460.2372184731760.04321416648490.3169203221790.273414882246-0.1765947442741.373175807690.0712534873254-0.08758602285210.921761679084-0.0009080478036230.4288952269838.8920335813-17.499480461440.6802800303
74.369625002345.064609316085.270685499048.040885984595.231427482626.72674037607-1.501641240020.79646211161-0.111437292267-1.285372256330.492538301880.166494012666-0.9394876198480.6685398354630.9902291072451.14600728296-0.162940143120.06129544639170.834065734703-0.08666199365130.42831992737840.9895715882-28.038834066510.9086380988
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 320 through 344 )AA320 - 3441 - 25
22chain 'A' and (resid 345 through 487 )AA345 - 48726 - 168
33chain 'A' and (resid 488 through 552 )AA488 - 552169 - 233
44chain 'B' and (resid 1 through 10 )BC1 - 10
55chain 'B' and (resid 11 through 19 )BC11 - 19
66chain 'C' and (resid 1 through 15 )CE1 - 15
77chain 'C' and (resid 16 through 19 )CE16 - 19

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