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- PDB-8cpg: Structure of the AT-Hook 1 peptide from the mammalian HMGA protei... -

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Basic information

Entry
Database: PDB / ID: 8cpg
TitleStructure of the AT-Hook 1 peptide from the mammalian HMGA protein in complex with DNA
Components
  • DNA (5'-D(*CP*GP*TP*TP*AP*AP*TP*TP*AP*AP*CP*G)-3')
  • High mobility group protein HMG-I/HMG-Y
KeywordsDNA BINDING PROTEIN / Mammalian High Mobility Group protein (HMGA1) AT-hook peptides
Function / homology
Function and homology information


senescence-associated heterochromatin focus / nuclear retinoic acid receptor binding / peroxisome proliferator activated receptor binding / oncogene-induced cell senescence / nucleosome disassembly / DNA binding, bending / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / 2-LTR circle formation ...senescence-associated heterochromatin focus / nuclear retinoic acid receptor binding / peroxisome proliferator activated receptor binding / oncogene-induced cell senescence / nucleosome disassembly / DNA binding, bending / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / minor groove of adenine-thymine-rich DNA binding / 5'-deoxyribose-5-phosphate lyase activity / nuclear retinoid X receptor binding / cis-regulatory region sequence-specific DNA binding / DNA-(apurinic or apyrimidinic site) endonuclease activity / molecular function activator activity / transcription coregulator binding / transcription coregulator activity / base-excision repair / RNA polymerase II transcription regulator complex / structural constituent of chromatin / molecular adaptor activity / nuclear membrane / transcription regulator complex / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / focal adhesion / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
High mobility group protein HMGA / HMG-I/HMG-Y, DNA-binding, conserved site / HMG-I and HMG-Y DNA-binding domain (A+T-hook). / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif
Similarity search - Domain/homology
DNA / DNA (> 10) / High mobility group protein HMG-I/HMG-Y
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBoer, D.R. / Campos, J.L.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessPID2020-117028GB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesRTI2018-093940-B-I00 Spain
CitationJournal: Sci Rep / Year: 2024
Title: Crystal structure of the HMGA AT-hook 1 domain bound to the minor groove of AT-rich DNA and inhibition by antikinetoplastid drugs.
Authors: Nue-Martinez, J.J. / Maturana, M. / Lagartera, L. / Rodriguez-Gutierrez, J.A. / Boer, R. / Campos, J.L. / Saperas, N. / Dardonville, C.
History
DepositionMar 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*TP*TP*AP*AP*TP*TP*AP*AP*CP*G)-3')
B: DNA (5'-D(*CP*GP*TP*TP*AP*AP*TP*TP*AP*AP*CP*G)-3')
C: DNA (5'-D(*CP*GP*TP*TP*AP*AP*TP*TP*AP*AP*CP*G)-3')
D: DNA (5'-D(*CP*GP*TP*TP*AP*AP*TP*TP*AP*AP*CP*G)-3')
E: DNA (5'-D(*CP*GP*TP*TP*AP*AP*TP*TP*AP*AP*CP*G)-3')
F: DNA (5'-D(*CP*GP*TP*TP*AP*AP*TP*TP*AP*AP*CP*G)-3')
G: High mobility group protein HMG-I/HMG-Y
H: High mobility group protein HMG-I/HMG-Y
I: High mobility group protein HMG-I/HMG-Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,49313
Polymers25,3969
Non-polymers974
Water6,503361
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.635, 43.635, 97.480
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: DNA chain
DNA (5'-D(*CP*GP*TP*TP*AP*AP*TP*TP*AP*AP*CP*G)-3')


Mass: 3661.416 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein/peptide High mobility group protein HMG-I/HMG-Y / HMG-I(Y) / High mobility group AT-hook protein 1 / High mobility group protein A1 / High mobility ...HMG-I(Y) / High mobility group AT-hook protein 1 / High mobility group protein A1 / High mobility group protein R / AT-Hook 1 peptide


Mass: 1142.406 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P17096
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.03 % / Description: long rod
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 6
Details: Crystallization buffer: 0.025mM NiCl2 10 mM MgCl2 2.5% MPD 25 mM NaCaco, pH 6 Final well concentration MPD about 38% Crystallization drops were setup at 285.15 K, using a well solution ...Details: Crystallization buffer: 0.025mM NiCl2 10 mM MgCl2 2.5% MPD 25 mM NaCaco, pH 6 Final well concentration MPD about 38% Crystallization drops were setup at 285.15 K, using a well solution consisting of aqueous MPD at 17% (v/v) concentration. After three days, the temperature was lowererd to 281.15 K. After 3 days at 281.15K, the solution in the well solution was changed to 25% MPD in water. After 1 week, the temperature was changed to 277.15K. The well solution was interchanged to a MPD solution at 30%. and after 8 days it was replaced by a 38% (v/v) MPD solution.

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cold nitrogen gas / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97925 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2017 / Details: KB mirrors, Si surface
RadiationMonochromator: Channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 1.4→37.79 Å / Num. obs: 40810 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Redundancy: 8.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.025 / Rsym value: 0.072 / Net I/σ(I): 18.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible allMean I/σ(I) obs
3.808-37.798.50.05220430.9960.0190.05599.9
1.4-1.4240.57920450.9220.3260.6193.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
autoPROC1.0.5 (20200206)data reduction
pointless1.11.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→37.79 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.504 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15812 1975 4.8 %RANDOM
Rwork0.12424 ---
obs0.12597 38850 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.952 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0.26 Å2-0 Å2
2---0.52 Å2-0 Å2
3---1.7 Å2
Refinement stepCycle: 1 / Resolution: 1.4→37.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms167 1426 4 361 1958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0111771
X-RAY DIFFRACTIONr_bond_other_d0.0020.02996
X-RAY DIFFRACTIONr_angle_refined_deg1.581.2342676
X-RAY DIFFRACTIONr_angle_other_deg1.6052.7482340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.548519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.8579.520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3441539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.447159
X-RAY DIFFRACTIONr_chiral_restr0.0690.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0290.021042
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02387
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4051.28183
X-RAY DIFFRACTIONr_mcbond_other1.3721.24382
X-RAY DIFFRACTIONr_mcangle_it1.8351.85598
X-RAY DIFFRACTIONr_mcangle_other1.8261.88399
X-RAY DIFFRACTIONr_scbond_it1.8931.2971688
X-RAY DIFFRACTIONr_scbond_other1.8911.2961688
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7251.9552578
X-RAY DIFFRACTIONr_long_range_B_refined2.97812.7912481
X-RAY DIFFRACTIONr_long_range_B_other2.7311.692390
X-RAY DIFFRACTIONr_rigid_bond_restr1.81532767
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.178 147 -
Rwork0.15 2816 -
obs--99.66 %
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)
10.0136-0.0108-0.01190.03070.04420.09070.003-0.0009-0.0017-0.004-0.0007-0.00280.0015-0.0062-0.00230.00880.00060.00030.00890.00060.001441.6295-48.621795.5181
20.0010.00620.00810.04320.05630.0737-0.00040-0.00030.0001-0.00170.00170.0017-0.00280.0020.011900.00110.0110.00050.002541.8762-50.366195.2052
30.0323-0.02440.05220.0191-0.04450.13510.00220.0007-0.0036-0.0005-0.00020.00240.0024-0.0026-0.0020.0111-0.0009-0.00030.0099-0.00020.001966.9141-35.9245100.3894
40.0094-0.00230.02920.001-0.00950.10610.0012-0.0037-0.00080.00050.00090.00010.0004-0.0067-0.0020.0103-0.0004-0.00040.0105-0.00040.001466.4028-33.87399.3913
50.0095-0.00680.04150.0049-0.02990.1828-0.00280.00040.0010.0017-0.0004-0.0005-0.01050.00520.00320.0098-0.0008-0.00020.0108-0.00090.001744.0109-23.062599.6947
60.02430.0061-0.0060.00580.00130.00330.00210.00380.0032-0.0019-0.0007-0.0006-0.0026-0.0014-0.00140.0104-0.0011-0.00080.01020.00080.002641.8591-24.2922100.4135
70.46790.0158-0.07170.0357-0.04650.0668-0.0007-0.00660.0002-0.00370.00310.00180.0042-0.0006-0.00230.0097-0.0005-0.00080.0102-0.00070.000249.7328-32.570796.9307
80.20870.119-0.19330.1613-0.10520.17980.0016-0.0019-0.00380.0001-0.0070.0019-0.00190.00110.00530.0105-0.0011-0.00040.0102-0.00080.003146.4602-40.891199.9339
90.5163-0.14560.66050.0849-0.23651.2982-0.0464-0.0188-0.0106-0.01160.01670.0096-0.0068-0.03140.02970.0198-0.0029-00.00930.00160.008143.1696-39.033487.75
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 12
2X-RAY DIFFRACTION2B2 - 12
3X-RAY DIFFRACTION3C2 - 12
4X-RAY DIFFRACTION4D1 - 12
5X-RAY DIFFRACTION5E1 - 12
6X-RAY DIFFRACTION6F1 - 12
7X-RAY DIFFRACTION7G22 - 31
8X-RAY DIFFRACTION8H22 - 28
9X-RAY DIFFRACTION9I27 - 31

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