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- PDB-5yeh: Crystal structure of CTCF ZFs4-8-eCBS -

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Basic information

Entry
Database: PDB / ID: 5yeh
TitleCrystal structure of CTCF ZFs4-8-eCBS
Components
  • DNA (5'-D(*AP*CP*GP*GP*TP*TP*TP*CP*CP*GP*CP*TP*AP*GP*AP*GP*GP*GP*CP*G)-3')
  • DNA (5'-D(*TP*CP*GP*CP*CP*CP*TP*CP*TP*AP*GP*CP*GP*GP*AP*AP*AP*CP*CP*G)-3')
  • 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 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 / 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: 2.328 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 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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


Theoretical massNumber of molelcules
Total (without water)58,84716
Polymers58,1936
Non-polymers65410
Water1,27971
1
A: Transcriptional repressor CTCF
C: DNA (5'-D(*AP*CP*GP*GP*TP*TP*TP*CP*CP*GP*CP*TP*AP*GP*AP*GP*GP*GP*CP*G)-3')
D: DNA (5'-D(*TP*CP*GP*CP*CP*CP*TP*CP*TP*AP*GP*CP*GP*GP*AP*AP*AP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4248
Polymers29,0963
Non-polymers3275
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-71 kcal/mol
Surface area13860 Å2
MethodPISA
2
B: Transcriptional repressor CTCF
E: DNA (5'-D(*AP*CP*GP*GP*TP*TP*TP*CP*CP*GP*CP*TP*AP*GP*AP*GP*GP*GP*CP*G)-3')
F: DNA (5'-D(*TP*CP*GP*CP*CP*CP*TP*CP*TP*AP*GP*CP*GP*GP*AP*AP*AP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4248
Polymers29,0963
Non-polymers3275
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-30 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.845, 54.876, 66.938
Angle α, β, γ (deg.)81.17, 80.11, 79.72
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: 16825.561 Da / Num. of mol.: 2 / 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: DNA chain DNA (5'-D(*AP*CP*GP*GP*TP*TP*TP*CP*CP*GP*CP*TP*AP*GP*AP*GP*GP*GP*CP*G)-3')


Mass: 6190.991 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*CP*GP*CP*CP*CP*TP*CP*TP*AP*GP*CP*GP*GP*AP*AP*AP*CP*CP*G)-3')


Mass: 6079.932 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.: 71 / 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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 0.1 M Bis-tris pH 5.6-6.0, 0.2 M Sodium chloride and 17-24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.33→32.71 Å / Num. obs: 25836 / % possible obs: 96.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.034 / Net I/av σ(I): 20.2 / Net I/σ(I): 20.2
Reflection shellResolution: 2.34→2.38 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.54 / Rpim(I) all: 0.306 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YEG

5yeg


Resolution: 2.328→32.706 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 33.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2695 1291 5.01 %
Rwork0.2219 --
obs0.2243 25750 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.328→32.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 1624 10 71 3853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014022
X-RAY DIFFRACTIONf_angle_d1.2085760
X-RAY DIFFRACTIONf_dihedral_angle_d27.8491576
X-RAY DIFFRACTIONf_chiral_restr0.067626
X-RAY DIFFRACTIONf_plane_restr0.008460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3279-2.4210.35571460.29762663X-RAY DIFFRACTION93
2.421-2.53120.36381260.28662754X-RAY DIFFRACTION97
2.5312-2.66460.37731530.2932767X-RAY DIFFRACTION97
2.6646-2.83140.32621390.29032679X-RAY DIFFRACTION96
2.8314-3.04990.33011350.29072794X-RAY DIFFRACTION97
3.0499-3.35660.30191530.26312685X-RAY DIFFRACTION95
3.3566-3.84160.2821390.19962727X-RAY DIFFRACTION96
3.8416-4.83750.2171470.18032721X-RAY DIFFRACTION97
4.8375-32.70910.21111530.17892669X-RAY DIFFRACTION94
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)
10.04010.0108-0.01840.00620.00270.02430.41330.18520.0856-0.36230.2760.023-0.34550.2111-0.00270.70140.0611-0.03840.82010.1590.58825.3051-10.0994-14.7984
20.0249-0.0258-0.05650.05930.00720.1715-0.09630.27690.3408-0.247-0.11920.31340.11540.2279-0.00430.28120.0189-0.09060.2706-0.01780.396319.1857-24.672-7.071
30.1178-0.0621-0.04970.0750.06410.28570.15920.15380.2531-0.1637-0.2364-0.3079-0.074-0.0748-0.01010.2023-0.03940.05170.2861-0.02130.449835.7244-10.4497-0.6111
40.0287-0.04280.05310.0231-0.07950.2492-0.2542-0.4365-0.3364-0.04-0.2127-0.1492-0.06130.1735-0.05830.1940.01940.08850.31030.07950.291719.0671-0.231612.5985
50.2934-0.35420.18160.4562-0.25730.16480.28340.3681-0.2022-0.20670.32120.0868-0.19830.29170.04330.6023-0.08150.15620.75390.22570.2919.9707-0.92929.8273
60.0885-0.00060.0060.0881-0.01160.00120.24640.0725-0.13310.12710.52540.26620.2321-0.2019-0.0050.8612-0.0552-0.20190.65850.02730.457126.9579-10.934331.1749
71.94761.01140.58690.52250.32120.6230.00410.2154-0.46630.19860.3272-0.2735-0.0058-0.09960.16630.31640.0186-0.01630.25050.05990.286723.334-12.27915.9147
80.0433-0.02750.02350.04440.00660.02030.11790.07320.0024-0.0660.31090.07910.0453-0.1333-0.00120.6130.1472-0.04180.9039-0.03630.36319.3358-8.559-19.2441
90.19140.15740.08720.37110.00460.0698-0.1258-0.0566-0.2569-0.0516-0.1565-0.20720.0873-0.0337-0.02740.8376-0.062-0.06421.0423-0.09870.350718.0114-16.7382-21.8405
100.1051-0.03860.08050.2290.20670.18420.2678-0.0579-0.296-0.07450.2223-0.0449-0.0001-0.19670.00070.37260.0207-0.00610.339-0.00050.312222.0615-11.94193.3958
110.0103-0.0089-0.01750.0180.00940.02950.1282-0.1611-0.2520.2720.0754-0.387-0.226-0.0402-0.00060.72410.0405-0.14940.5531-0.11640.579430.316-6.146424.6293
120.0896-0.0571-0.04660.1279-0.00840.05560.1977-0.22210.03440.084-0.03210.0151-0.10420.0540.13831.25540.4595-0.39920.6023-0.86010.71313.909632.829215.0519
130.32990.56880.77731.30961.20781.80580.121-0.63350.01070.0911-0.50190.4716-0.0994-0.5537-0.10820.1762-0.0489-0.02330.0915-0.0240.283122.990415.99577.2597
140.02880.0074-0.07050.0921-0.1050.3793-0.0236-0.12310.2869-0.08690.17520.189-0.0841-0.08110.02120.1235-0.02460.00510.23760.050.36453.9994.05492.0269
150.7966-0.23280.68450.3712-0.22980.6676-0.1389-0.2811-0.02050.03740.09860.023-0.292-0.3751-0.01560.3429-0.02070.01660.24170.0020.3229-2.675122.8267-11.0097
160.45370.507-0.37440.7467-0.28920.43070.2660.0942-0.01440.3909-0.39380.0725-0.01210.10680.4170.65370.0690.06540.51840.02530.2211-1.779832.0654-28.4314
170.0376-0.01060.02590.0127-0.02160.03120.10080.15-0.06980.2289-0.01610.0585-0.0852-0.02890.00830.82590.00540.04040.6066-0.28670.47716.157912.7018-29.8639
180.54130.3563-0.23570.8048-0.08510.1220.0221-0.52410.17630.19890.1697-0.5136-0.4577-0.28280.03160.37210.1125-0.05980.3709-0.13590.30678.658716.92063.8196
190.2178-0.29680.00660.41280.0114-0.00430.32170.2891-0.6726-0.16230.0417-0.13470.11830.12610.17580.7290.0223-0.19340.9774-0.60110.218916.09418.738622.7623
200.11950.12980.00530.10020.03740.08370.1156-0.02390.1041-0.17160.2142-0.1145-0.6119-0.39690.00010.40140.07060.02460.4812-0.06210.43889.024116.717-2.1578
210.2759-0.3422-0.09420.43630.11720.03340.39290.2993-0.2021-0.10370.29920.1899-0.2945-0.33670.1280.74060.1613-0.16320.73330.06870.41850.396510.7328-23.2159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 349 through 374 )A349 - 374
2X-RAY DIFFRACTION2chain 'A' and (resid 378 through 403 )A378 - 403
3X-RAY DIFFRACTION3chain 'A' and (resid 406 through 431 )A406 - 431
4X-RAY DIFFRACTION4chain 'A' and (resid 436 through 461 )A436 - 461
5X-RAY DIFFRACTION5chain 'A' and (resid 466 through 487 )A466 - 487
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 5 )C1 - 5
7X-RAY DIFFRACTION7chain 'C' and (resid 6 through 15 )C6 - 15
8X-RAY DIFFRACTION8chain 'C' and (resid 16 through 20 )C16 - 20
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 5 )D1 - 5
10X-RAY DIFFRACTION10chain 'D' and (resid 6 through 15 )D6 - 15
11X-RAY DIFFRACTION11chain 'D' and (resid 16 through 20 )D16 - 20
12X-RAY DIFFRACTION12chain 'B' and (resid 352 through 374 )B352 - 374
13X-RAY DIFFRACTION13chain 'B' and (resid 378 through 402 )B378 - 402
14X-RAY DIFFRACTION14chain 'B' and (resid 406 through 431 )B406 - 431
15X-RAY DIFFRACTION15chain 'B' and (resid 436 through 461 )B436 - 461
16X-RAY DIFFRACTION16chain 'B' and (resid 466 through 487 )B466 - 487
17X-RAY DIFFRACTION17chain 'E' and (resid 1 through 5 )E1 - 5
18X-RAY DIFFRACTION18chain 'E' and (resid 6 through 20 )E6 - 20
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 20 )F16 - 20

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