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- PDB-6jrp: Crystal structure of CIC-HMG-ETV5-DNA complex -

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Basic information

Entry
Database: PDB / ID: 6jrp
TitleCrystal structure of CIC-HMG-ETV5-DNA complex
Components
  • DNA (5'-D(*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*A)-3')
  • DNA (5'-D(*TP*TP*TP*TP*CP*AP*TP*TP*CP*AP*T)-3')
  • Protein capicua homolog
KeywordsTRANSCRIPTION / repressor / protein-DNA complex
Function / homology
Function and homology information


social behavior / learning / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development / memory / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II ...social behavior / learning / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development / memory / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
High mobility group box domain / DNA Binding (I), subunit A / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein capicua homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsSong, J.J. / Lee, H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)2016K1A1A2912057 Korea, Republic Of
National Research Foundation (Korea)2016R1A2B3006293 Korea, Republic Of
CitationJournal: Febs J. / Year: 2019
Title: The crystal structure of Capicua HMG-box domain complexed with the ETV5-DNA and its implications for Capicua-mediated cancers.
Authors: Lee, H. / Song, J.J.
History
DepositionApr 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein capicua homolog
B: DNA (5'-D(*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*A)-3')
C: DNA (5'-D(*TP*TP*TP*TP*CP*AP*TP*TP*CP*AP*T)-3')
D: Protein capicua homolog
E: DNA (5'-D(*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*A)-3')
F: DNA (5'-D(*TP*TP*TP*TP*CP*AP*TP*TP*CP*AP*T)-3')
G: Protein capicua homolog
H: DNA (5'-D(*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*A)-3')
I: DNA (5'-D(*TP*TP*TP*TP*CP*AP*TP*TP*CP*AP*T)-3')
J: Protein capicua homolog
K: DNA (5'-D(*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*A)-3')
L: DNA (5'-D(*TP*TP*TP*TP*CP*AP*TP*TP*CP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)66,33412
Polymers66,33412
Non-polymers00
Water0
1
A: Protein capicua homolog
B: DNA (5'-D(*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*A)-3')
C: DNA (5'-D(*TP*TP*TP*TP*CP*AP*TP*TP*CP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)16,5843
Polymers16,5843
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-6 kcal/mol
Surface area8070 Å2
MethodPISA
2
D: Protein capicua homolog
E: DNA (5'-D(*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*A)-3')
F: DNA (5'-D(*TP*TP*TP*TP*CP*AP*TP*TP*CP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)16,5843
Polymers16,5843
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-8 kcal/mol
Surface area8010 Å2
MethodPISA
3
G: Protein capicua homolog
H: DNA (5'-D(*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*A)-3')
I: DNA (5'-D(*TP*TP*TP*TP*CP*AP*TP*TP*CP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)16,5843
Polymers16,5843
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-10 kcal/mol
Surface area8060 Å2
MethodPISA
4
J: Protein capicua homolog
K: DNA (5'-D(*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*A)-3')
L: DNA (5'-D(*TP*TP*TP*TP*CP*AP*TP*TP*CP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)16,5843
Polymers16,5843
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-11 kcal/mol
Surface area8070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.082, 66.082, 158.285
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Protein capicua homolog


Mass: 9880.117 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CIC, KIAA0306
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q96RK0
#2: DNA chain
DNA (5'-D(*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*A)-3')


Mass: 3414.287 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain
DNA (5'-D(*TP*TP*TP*TP*CP*AP*TP*TP*CP*AP*T)-3')


Mass: 3289.169 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium acetate, PEG3350, Bis-tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.9778, 0.9785
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 5, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97781
20.97851
Reflection

Entry-ID: 6JRP / Diffraction-ID: 1 / Redundancy: 10.5 % / % possible obs: 100 % / Resolution: 3→50 Å

Num. obsRmerge(I) obsNet I/σ(I)
154740.10926.56
155420.10325.48
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.704 / Num. unique obs: 727

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 3→38.791 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 0.3 / Phase error: 38.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3343 1521 9.93 %
Rwork0.2968 --
obs0.3006 15323 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→38.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2576 1784 0 0 4360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044666
X-RAY DIFFRACTIONf_angle_d1.0676656
X-RAY DIFFRACTIONf_dihedral_angle_d25.0481844
X-RAY DIFFRACTIONf_chiral_restr0.114676
X-RAY DIFFRACTIONf_plane_restr0.004544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0004-3.09720.45931390.36441193X-RAY DIFFRACTION97
3.0972-3.20790.39611320.32861213X-RAY DIFFRACTION98
3.2079-3.33620.3671420.28071268X-RAY DIFFRACTION99
3.3362-3.4880.3561350.29661299X-RAY DIFFRACTION100
3.488-3.67170.32041390.29731260X-RAY DIFFRACTION100
3.6717-3.90160.35541460.27931240X-RAY DIFFRACTION100
3.9016-4.20250.32661360.31421255X-RAY DIFFRACTION100
4.2025-4.62480.30361420.29251272X-RAY DIFFRACTION100
4.6248-5.29260.28991380.27951261X-RAY DIFFRACTION100
5.2926-6.66260.31410.28081270X-RAY DIFFRACTION100
6.6626-38.79460.30891310.29381271X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 13.4356 Å / Origin y: -72.1185 Å / Origin z: -9.1999 Å
111213212223313233
T0.0766 Å20.2409 Å20.1348 Å2-0.2558 Å2-0.085 Å2--0.0484 Å2
L0.0923 °2-0.025 °2-0.0762 °2-0.2377 °20.0697 °2--0.0471 °2
S0.0538 Å °-0.0914 Å °0.0535 Å °-0.185 Å °-0.0608 Å °-0.095 Å °0.056 Å °0.0385 Å °0.1101 Å °
Refinement TLS groupSelection details: all

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