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- PDB-7m5w: Crystal structure of the HMG-C1 domain of human capicua bound to DNA -

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Basic information

Entry
Database: PDB / ID: 7m5w
TitleCrystal structure of the HMG-C1 domain of human capicua bound to DNA
Components
  • DNA (5'-D(*GP*CP*TP*TP*TP*TP*TP*CP*AP*TP*TP*CP*AP*TP*AP*AP*CP*C)-3')
  • DNA (5'-D(*GP*GP*TP*TP*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*AP*AP*GP*C)-3')
  • Protein capicua homolog
KeywordsDNA BINDING PROTEIN/DNA / helix-turn-helix / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


lung alveolus development / social behavior / learning / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development / memory / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle ...lung alveolus development / social behavior / learning / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development / memory / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus
Similarity search - Function
Domain of unknown function DUF4819 / Domain of unknown function (DUF4819) / : / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein capicua homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
Model detailsHMG box, HTH, DNA complex
AuthorsWebb, J.P. / Liew, J.J.M. / Gnann, A.D. / Dowling, D.P.
CitationJournal: Biorxiv / Year: 2022
Title: Molecular basis of DNA recognition by the HMG-box-C1 module of Capicua
Authors: Webb, J. / Gnann, A.D. / Liew, J.J. / Patterson, M. / Paul, S. / Fores, M. / Jimenez, G. / Veraksa, A. / Dowling, D.P.
History
DepositionMar 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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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(*GP*GP*TP*TP*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*AP*AP*GP*C)-3')
C: DNA (5'-D(*GP*CP*TP*TP*TP*TP*TP*CP*AP*TP*TP*CP*AP*TP*AP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0314
Polymers32,9913
Non-polymers401
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-25 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.890, 79.920, 106.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Protein capicua homolog


Mass: 21962.199 Da / Num. of mol.: 1
Fragment: HMG box domain UNP residues 188-280 fused with C1 domain UNP residues 1457-1527
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CIC, KIAA0306 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: Q96RK0
#2: DNA chain DNA (5'-D(*GP*GP*TP*TP*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*AP*AP*GP*C)-3')


Mass: 5612.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ThermoFisher Custom DNA Oligo Synthesis / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*TP*TP*TP*TP*TP*CP*AP*TP*TP*CP*AP*TP*AP*AP*CP*C)-3')


Mass: 5416.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ThermoFisher Custom DNA Oligo Synthesis / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsHMG box domain UNP residues 188-280 fused with C1 domain UNP residues 1457-1527. Residue F95 was ...HMG box domain UNP residues 188-280 fused with C1 domain UNP residues 1457-1527. Residue F95 was inserted within the flexible linker region to increase UV absorption properties for purification.

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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: 2.84 Å3/Da / Density % sol: 56.7 % / Description: orthorhombic
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM MES, 100 mM CaCl2, 100 mM NaCl, and 16% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.95→23.844 Å / Num. obs: 8838 / % possible obs: 98.8 % / Redundancy: 8.943 % / Biso Wilson estimate: 45.45 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.088 / Χ2: 0.864 / Net I/σ(I): 22.47 / Num. measured all: 79037
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.95-3.138.9280.5064.3812044138613490.970.53697.3
3.13-3.349.1740.16711.9712165132613260.9970.178100
3.34-3.69.1570.1315.411071120912090.9980.138100
3.6-3.949.1080.09619.9810365113811380.9990.102100
3.94-4.399.1450.06426.699209103210070.9990.06897.6
4.39-5.049.0310.05531.9182909299180.9990.05998.8
5.04-6.18.8310.05631.9971628118110.9990.06100
6.1-8.368.5690.03844.0256046546540.9990.04100
8.36-23.8447.340.02857.7131274614260.9990.0392.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JRP

2jrp


Resolution: 2.95→23.84 Å / SU ML: 0.2704 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.0489
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 437 4.98 %Random selection
Rwork0.2093 8332 --
obs0.2111 8769 98.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.44 Å2
Refinement stepCycle: LAST / Resolution: 2.95→23.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 732 1 15 1912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272018
X-RAY DIFFRACTIONf_angle_d0.45812873
X-RAY DIFFRACTIONf_chiral_restr0.0337302
X-RAY DIFFRACTIONf_plane_restr0.0018243
X-RAY DIFFRACTIONf_dihedral_angle_d22.8865803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.380.31351390.24712705X-RAY DIFFRACTION98.37
3.38-4.250.22721440.21242746X-RAY DIFFRACTION98.7
4.25-23.840.23031540.19212881X-RAY DIFFRACTION98.99
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)
11.443726601650.65245500185-0.1010856966173.232371814220.02394539362131.30734227006-0.0608795876407-0.0613437822391-0.03115840117020.174568618590.04215345112790.0121973716117-0.259699441356-0.0648552680674-3.69714419757E-70.5494268819960.07618330758550.04468422580610.4035496149590.02094429704240.3149691668671.9179461051419.368347633225.7398309026
20.439221473199-0.242602880037-0.3324064570971.62426184986-0.5209549028530.5581263573750.0209165707310.07419129389360.196657546785-0.188871501353-0.01674817781010.144312721608-0.072010696435-0.175303611993-9.67313513554E-80.485029370156-0.0267742938048-0.01224922754510.3832664659120.01727680925510.415829444323-5.27337496328-2.8020486649618.4521602897
32.37487199134-0.618604908861-1.010057915931.07588230189-0.1492423623750.5910350491650.189490890515-0.0858964664809-0.2714881729310.4719399109840.399662231969-0.4215716848790.5566353041820.3152632437640.02914051371020.8406521926320.0730397858581-0.08761871506830.476706320185-0.009350679870970.4989890692958.581774993375.3772131133228.7408454135
41.37332430190.720272766437-0.9382458891361.98602111741-0.2232783413660.6383086458090.1099417749670.0881789334037-0.3317114788050.2705796791070.072598209179-0.517100906082-0.1365138411870.5413903088050.004435844299770.6834172422520.102340252916-0.01720891182410.5168928181990.004350623845730.4874750101599.202726048166.9781857295327.9662578925
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 32 through 105 )AA32 - 1051 - 75
22chain 'A' and (resid 118 through 181 )AA118 - 18176 - 139
33chain 'B'BB1 - 18
44chain 'C'CC1 - 18

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