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- PDB-5und: Crystal Structure of CTCF(ZnF 4-10) With 28-mer DNA -

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Basic information

Entry
Database: PDB / ID: 5und
TitleCrystal Structure of CTCF(ZnF 4-10) With 28-mer DNA
Components
  • (DNA (26-MER)) x 2
  • Transcriptional repressor CTCF
Keywordstranscription/dna / transcription factor zinc finger protein-DNA binding insulator/chromatin architecture / transcription-dna complex
Function / homology
Function and homology information


chromatin loop anchoring activity / chromatin insulator sequence binding / regulation of centromeric sister chromatid cohesion / protein localization to chromosome, centromeric region / genomic imprinting / chromatin looping / cardiac muscle cell development / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / chromosome, centromeric region ...chromatin loop anchoring activity / chromatin insulator sequence binding / regulation of centromeric sister chromatid cohesion / protein localization to chromosome, centromeric region / genomic imprinting / chromatin looping / cardiac muscle cell development / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / chromosome, centromeric region / condensed chromosome / epigenetic regulation of gene expression / transcription coregulator binding / male germ cell nucleus / mitochondrion organization / chromosome segregation / DNA-binding transcription repressor activity, RNA polymerase II-specific / Activation of anterior HOX genes in hindbrain development during early embryogenesis / sequence-specific double-stranded DNA binding / gene expression / sequence-specific DNA binding / in utero embryonic development / 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 / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleolus / 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 zinc finger / C2H2-type zinc-finger domain / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...: / : / C2H2 zinc finger / C2H2-type zinc-finger domain / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional repressor CTCF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.549 Å
AuthorsHorton, J.R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 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
DepositionJan 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 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 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.5Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,14825
Polymers82,8986
Non-polymers1,24919
Water1,38777
1
A: Transcriptional repressor CTCF
C: DNA (26-MER)
D: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,03112
Polymers41,4493
Non-polymers5829
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-85 kcal/mol
Surface area18140 Å2
MethodPISA
2
B: Transcriptional repressor CTCF
E: DNA (26-MER)
F: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,11613
Polymers41,4493
Non-polymers66710
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-41 kcal/mol
Surface area16810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.072, 73.825, 93.289
Angle α, β, γ (deg.)90.00, 91.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 24231.049 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTCF / Production host: Escherichia coli (E. coli) / References: UniProt: P49711

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DNA chain , 2 types, 4 molecules CEDF

#2: DNA chain DNA (26-MER)


Mass: 8526.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (26-MER)


Mass: 8691.582 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 96 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.13 Å3/Da / Density % sol: 60.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 28% PEG 2000 MME 100mM Bis-Tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→34.6 Å / Num. obs: 33435 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 55.3 Å2 / CC1/2: 0.59 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.044 / Net I/av σ(I): 1.94 / Net I/σ(I): 14.9
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.986 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3301 / Rpim(I) all: 0.458 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KKQ

5kkq


Resolution: 2.549→34.613 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2367 3251 5.02 %
Rwork0.2111 --
obs0.2124 64813 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.549→34.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 2102 42 77 4707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044998
X-RAY DIFFRACTIONf_angle_d0.447109
X-RAY DIFFRACTIONf_dihedral_angle_d22.1622580
X-RAY DIFFRACTIONf_chiral_restr0.031765
X-RAY DIFFRACTIONf_plane_restr0.002552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5488-2.58680.40811320.35262506X-RAY DIFFRACTION91
2.5868-2.62720.35471530.32622620X-RAY DIFFRACTION98
2.6272-2.67030.31161330.31612625X-RAY DIFFRACTION99
2.6703-2.71630.33421340.30652672X-RAY DIFFRACTION99
2.7163-2.76570.3041520.27542728X-RAY DIFFRACTION100
2.7657-2.81880.27241520.26392691X-RAY DIFFRACTION100
2.8188-2.87630.35181360.26182664X-RAY DIFFRACTION100
2.8763-2.93880.25731440.27092704X-RAY DIFFRACTION100
2.9388-3.00720.25141330.262739X-RAY DIFFRACTION100
3.0072-3.08230.32411320.25462710X-RAY DIFFRACTION100
3.0823-3.16560.28941450.25582673X-RAY DIFFRACTION100
3.1656-3.25870.25221370.24722657X-RAY DIFFRACTION99
3.2587-3.36380.26231460.21952683X-RAY DIFFRACTION98
3.3638-3.48390.2471300.22452698X-RAY DIFFRACTION99
3.4839-3.62330.22151400.20882660X-RAY DIFFRACTION100
3.6233-3.7880.22011420.2092709X-RAY DIFFRACTION100
3.788-3.98740.24971510.19382664X-RAY DIFFRACTION100
3.9874-4.23680.20451410.18052744X-RAY DIFFRACTION100
4.2368-4.56330.22181420.18462684X-RAY DIFFRACTION100
4.5633-5.02130.2431380.18962712X-RAY DIFFRACTION100
5.0213-5.7450.21321460.17962679X-RAY DIFFRACTION100
5.745-7.22720.20781420.20852687X-RAY DIFFRACTION100
7.2272-34.61570.18931500.16982653X-RAY DIFFRACTION98
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)
10.1731-0.1293-0.40040.5290.32651.0076-0.25730.7252-0.1007-0.0649-0.30321.15760.1352-0.7966-0.61060.5345-0.1357-0.21580.7801-0.13711.43632.87725.468112.0496
20.13540.17350.11990.37340.28490.5039-0.12420.39470.4212-0.0337-0.06950.35980.14750.0558-0.02310.3007-0.0295-0.04160.279-0.03990.490722.245219.402215.947
30.24490.0063-0.14430.01080.06110.04-0.02490.1930.19940.4646-0.16010.35111.00510.2766-0.03380.69990.0001-0.05620.3954-0.14080.298834.29622.33796.8469
40.785-0.40260.36161.8733-1.90162.30410.09060.08910.1320.4128-0.8197-0.4476-0.26010.244-0.64030.5878-0.0925-0.06170.2792-0.20890.409339.3317-3.3043-13.7833
50.00380.00510.01910.0265-0.0146-0.0179-0.0625-0.19920.39450.36090.7903-0.440.07360.43820.0060.943-0.1716-0.33581.2969-0.36211.369566.1859-1.8049-6.9405
60.09060.08970.09690.0991-0.01240.06690.04980.06020.1985-0.14720.2786-0.10420.2849-0.7024-0.00020.5764-0.00610.07920.7725-0.06151.131714.83439.665616.3895
70.2707-0.2371-0.14160.18310.11870.0719-0.41830.4153-0.1873-0.562-0.3926-0.07470.1113-0.0978-0.02630.8235-0.1307-0.18080.92780.11250.480530.314416.7499-0.6635
80.0187-0.0219-0.0923-0.07020.04480.0287-0.6580.76970.4753-0.4640.1316-0.36050.21590.4235-01.2376-0.27430.43191.8770.07881.715955.799513.1384-12.4326
90.0555-0.01110.0387-0.0087-0.07860.07560.5989-0.28670.5317-0.13790.7086-0.44390.3024-0.0073-0.00021.4576-0.08720.46531.93420.23282.006856.832913.1339-13.5299
100.50060.13490.4730.94050.35050.1886-0.28320.1994-0.1556-0.40960.04890.3279-0.1515-0.1155-0.01160.4115-0.0514-0.00080.5527-0.06350.489621.194510.058911.0149
110.0228-0.0282-0.0157-0.00470.00680.01080.0972-0.1215-0.43280.44830.2494-0.26370.05310.05210.12180.35341.0882-0.14842.04751.04831.6225-2.7408-0.956737.5569
120.31840.2214-0.26520.1754-0.22160.3541-0.2425-0.0761-0.00580.1932-0.5066-0.2948-0.28990.3769-0.55120.99740.0919-0.87031.61230.02481.5477-7.679916.329446
13-0.001-0.14360.10690.6832-0.31230.31690.0104-0.2758-0.0849-0.2136-0.3789-0.38960.00880.2022-0.12360.3144-0.0269-0.03530.42490.1210.3383-23.821117.80133.3463
140.06380.3739-0.0420.0306-0.48380.1337-0.1105-0.0601-0.0026-0.2049-0.2434-0.04780.27840.1572-0.50870.61310.11990.06590.28770.09450.3338-37.701-1.58847.9895
150.0774-0.00140.1010.45230.10060.0986-0.07830.14440.3058-0.9994-0.42590.0239-0.1088-0.3874-0.02990.65870.1433-0.10750.48570.02770.3322-48.684-5.99458.7154
160.09760.3640.19851.32570.83960.45940.64850.17540.47980.46980.3435-0.37051.00820.39650.35880.38040.23460.16261.18280.30941.1295-15.75298.698434.6286
170.16310.29630.1610.50140.14950.2009-0.5126-1.2375-0.20790.86250.25541.2094-0.3016-0.0761-0.08380.91780.12230.32340.85020.14830.806-43.500612.446949.6204
180.00440.0113-0.00630.0291-0.01360.01840.1105-0.0896-0.244-0.0861-0.52620.00280.12040.279202.23050.09830.99482.8718-0.00152.6423-66.503412.106363.8413
190.27170.1380.07860.07030.03670.0439-0.01990.0102-0.0179-0.0263-0.05720.00270.01780.01590.00072.57350.11240.242.58890.13412.9155-84.28195.859860.9065
200.01470.0041-0.0171-0.0073-0.00390.00340.44160.01310.002-0.0710.1168-0.18230.0587-0.163301.8823-0.1094-0.02962.7419-0.16792.4803-68.29078.219458.8196
210.003-0.03480.0090.00850.01210.01-0.39630.01390.6225-0.1336-0.17540.4357-0.13650.10750.00021.37110.43820.49451.2642-0.12021.4737-49.69413.804757.0049
220.2245-0.1461-0.17080.78750.11260.3971-0.4259-0.5532-0.78720.4195-0.2246-0.3934-0.33250.674-0.81740.21590.05750.05040.66270.29740.5928-21.95918.922537.4777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 348:390 )A348 - 390
2X-RAY DIFFRACTION2( CHAIN A AND RESID 391:429 )A391 - 429
3X-RAY DIFFRACTION3( CHAIN A AND RESID 430:459 )A430 - 459
4X-RAY DIFFRACTION4( CHAIN A AND RESID 460:491 )A460 - 491
5X-RAY DIFFRACTION5( CHAIN A AND RESID 492:518 )A492 - 518
6X-RAY DIFFRACTION6( CHAIN C AND RESID 1:10 )C1 - 10
7X-RAY DIFFRACTION7( CHAIN C AND RESID 11:15 )C11 - 15
8X-RAY DIFFRACTION8( CHAIN C AND RESID 16:26 )C16 - 26
9X-RAY DIFFRACTION9( CHAIN D AND RESID 3:12 )D3 - 12
10X-RAY DIFFRACTION10( CHAIN D AND RESID 13:28 )D13 - 28
11X-RAY DIFFRACTION11( CHAIN B AND RESID 348:374 )B348 - 374
12X-RAY DIFFRACTION12( CHAIN B AND RESID 375:390 )B375 - 390
13X-RAY DIFFRACTION13( CHAIN B AND RESID 391:429 )B391 - 429
14X-RAY DIFFRACTION14( CHAIN B AND RESID 430:478 )B430 - 478
15X-RAY DIFFRACTION15( CHAIN B AND RESID 479:492 )B479 - 492
16X-RAY DIFFRACTION16( CHAIN E AND RESID 1:10 )E1 - 10
17X-RAY DIFFRACTION17( CHAIN E AND RESID 11:20 )E11 - 20
18X-RAY DIFFRACTION18( CHAIN E AND RESID 21:25 )E21 - 25
19X-RAY DIFFRACTION19( CHAIN E AND RESID 26:26 )E26
20X-RAY DIFFRACTION20( CHAIN F AND RESID 4:8 )F4 - 8
21X-RAY DIFFRACTION21( CHAIN F AND RESID 9:13 )F9 - 13
22X-RAY DIFFRACTION22( CHAIN F AND RESID 14:28 )F14 - 28

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