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- PDB-4qr9: Crystal structure of two HMGB1 Box A domains cooperating to under... -

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Basic information

Entry
Database: PDB / ID: 4qr9
TitleCrystal structure of two HMGB1 Box A domains cooperating to underwind and kink a DNA
Components
  • DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3')
  • High mobility group protein B1
KeywordsDNA BINDING PROTEIN / HMG-box / HMGB1 / Box A domain / High mobility group / DNA-binding / bend DNA / kink DNA / architectural factor / minor groove / chromatin / Nucleus
Function / homology
Function and homology information


male-specific defense response to bacterium / Apoptosis induced DNA fragmentation / open form four-way junction DNA binding / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / crossed form four-way junction DNA binding / positive regulation of myeloid cell apoptotic process / Pyroptosis / TAK1-dependent IKK and NF-kappa-B activation / TRAF6 mediated NF-kB activation ...male-specific defense response to bacterium / Apoptosis induced DNA fragmentation / open form four-way junction DNA binding / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / crossed form four-way junction DNA binding / positive regulation of myeloid cell apoptotic process / Pyroptosis / TAK1-dependent IKK and NF-kappa-B activation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / plasmacytoid dendritic cell activation / Regulation of TLR by endogenous ligand / regulation of tolerance induction / positive regulation of mismatch repair / regulation of T cell mediated immune response to tumor cell / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of myeloid cell differentiation / myeloid dendritic cell activation / positive regulation of toll-like receptor 2 signaling pathway / T-helper 1 cell activation / T-helper 1 cell differentiation / glycolipid binding / positive regulation of dendritic cell differentiation / positive regulation of macrophage inflammatory protein 1 alpha production / C-X-C chemokine binding / negative regulation of CD4-positive, alpha-beta T cell differentiation / positive regulation of toll-like receptor 9 signaling pathway / bent DNA binding / positive regulation of glycogen catabolic process / neutrophil clearance / positive regulation of toll-like receptor 4 signaling pathway / DNA geometric change / endothelial cell chemotaxis / RAGE receptor binding / eye development / positive regulation of interleukin-1 production / bubble DNA binding / induction of positive chemotaxis / V(D)J recombination / myeloid cell differentiation / alphav-beta3 integrin-HMGB1 complex / myeloid progenitor cell differentiation / regulation of nucleotide-excision repair / macrophage activation involved in immune response / inflammatory response to antigenic stimulus / positive regulation of monocyte chemotaxis / positive regulation of monocyte chemotactic protein-1 production / positive regulation of innate immune response / cellular response to interleukin-7 / endothelial cell proliferation / glycogen catabolic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / apoptotic cell clearance / myoblast proliferation / supercoiled DNA binding / positive regulation of vascular endothelial cell proliferation / DNA binding, bending / positive regulation of mesenchymal cell proliferation / Neutrophil degranulation / positive regulation of wound healing / positive regulation of smooth muscle cell migration / phosphatidylserine binding / positive regulation of sprouting angiogenesis / negative regulation of DNA replication / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of activated T cell proliferation / positive regulation of interferon-alpha production / negative regulation of type II interferon production / negative regulation of blood vessel endothelial cell migration / positive regulation of interleukin-10 production / protein kinase activator activity / cellular response to interleukin-1 / response to type II interferon / positive regulation of blood vessel endothelial cell migration / positive regulation of myoblast differentiation / response to glucose / response to glucocorticoid / four-way junction DNA binding / condensed chromosome / DNA polymerase binding / positive regulation of autophagy / transcription repressor complex / positive regulation of interleukin-12 production / positive regulation of mitotic cell cycle / activation of innate immune response / peptide binding / positive regulation of interferon-beta production / positive regulation of interleukin-1 beta production / cytokine activity / positive regulation of interleukin-8 production / response to insulin / positive regulation of JNK cascade / lipopolysaccharide binding / lung development / positive regulation of non-canonical NF-kappaB signal transduction / cell morphogenesis / base-excision repair / positive regulation of neuron projection development
Similarity search - Function
HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / : / High mobility group box domain / DNA Binding (I), subunit A / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain ...HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / : / High mobility group box domain / DNA Binding (I), subunit A / HMG-box domain / 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 / High mobility group protein B1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSanchez-Giraldo, R. / Acosta-Reyes, F.J. / Malarkey, C.S. / Saperas, N. / Churchill, M.E.A. / Campos, J.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Two high-mobility group box domains act together to underwind and kink DNA.
Authors: Sanchez-Giraldo, R. / Acosta-Reyes, F.J. / Malarkey, C.S. / Saperas, N. / Churchill, M.E. / Campos, J.L.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Jul 29, 2015Group: Database references / Experimental preparation / Source and taxonomy
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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.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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: High mobility group protein B1
B: High mobility group protein B1
C: DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3')
D: DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3')
E: DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3')
F: DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0957
Polymers30,0716
Non-polymers241
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.751, 84.170, 94.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 5 - 79 / Label seq-ID: 1 - 75

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein High mobility group protein B1 / Amphoterin / Heparin-binding protein p30 / High mobility group protein 1 / HMG-1


Mass: 8949.302 Da / Num. of mol.: 2 / Fragment: Residues 8-81
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Hmgb1, Hmg-1, Hmg1 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLySS / References: UniProt: P63159
#2: DNA chain
DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3')


Mass: 3043.029 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
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: 2.82 Å3/Da / Density % sol: 56.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.025M Sodium Cacodylate 0.020M Magnesium Chloride 2.5% MPD (equilibrated against 40% MPD), pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2013 / Details: Mirrors
RadiationMonochromator: Channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→42.12 Å / Num. all: 23702 / Num. obs: 23441 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 16.025
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2162 / % possible all: 93.5

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Processing

Software
NameVersionClassification
XalocBeamlinedata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CKT

1ckt


Resolution: 2→42.12 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.442 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23387 1176 5 %RANDOM
Rwork0.19675 ---
obs0.19868 22219 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.412 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å2-0 Å2-0 Å2
2---1.21 Å2-0 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 2→42.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1234 808 1 115 2158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0162200
X-RAY DIFFRACTIONr_bond_other_d0.0120.021676
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.6023094
X-RAY DIFFRACTIONr_angle_other_deg2.9243.0013933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4855154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95622.88159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.18715269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2291510
X-RAY DIFFRACTIONr_chiral_restr0.0980.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021872
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02466
Refine LS restraints NCS

Ens-ID: 1 / Number: 3839 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 76 -
Rwork0.279 1486 -
obs-1486 90.39 %
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)
10.40210.18510.06940.6477-0.32961.28460.09320.0263-0.08070.1243-0.0993-0.15380.09950.18940.00610.05260.0129-0.03720.09140.02040.091-8.8554-22.728820.4295
20.2471-0.10360.01750.06060.06730.3977-0.0198-0.0573-0.0202-0.0165-0.00760.0242-0.0614-0.09620.02750.04070.0139-0.03120.0927-0.00740.0648-30.7182-12.06199.8549
30.30260.29620.31420.5917-0.00030.6428-0.00820.00010.0048-0.0162-0.0008-0.01090.00650.00340.0090.03170.00410.0070.0883-0.00340.0585-18.8661-17.630811.9551
40.2850.32120.34510.8225-0.06730.8710.01-0.00090.00070.0333-0.00370.0032-0.0153-0.0007-0.00630.03080.00310.00170.0857-0.01120.0566-20.4637-16.641818.466
50.65010.2776-0.35270.1479-0.32181.20880.1732-0.07370.07040.0421-0.03990.04830.04630.1722-0.13330.1515-0.00610.06090.08220.02880.1045-12.59590.6902-8.5549
60.0176-0.01980.04990.0673-0.23310.86150.0792-0.01640.0006-0.02850.01220.04090.05040.1538-0.09140.1353-0.04270.04020.13060.03010.0959-12.7330.5379-8.7752
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 79
2X-RAY DIFFRACTION1A101 - 120
3X-RAY DIFFRACTION2B5 - 79
4X-RAY DIFFRACTION2B101 - 131
5X-RAY DIFFRACTION3C1 - 10
6X-RAY DIFFRACTION3C101 - 129
7X-RAY DIFFRACTION4D11 - 20
8X-RAY DIFFRACTION4D101
9X-RAY DIFFRACTION4D201 - 227
10X-RAY DIFFRACTION5E1 - 10
11X-RAY DIFFRACTION5E101 - 105
12X-RAY DIFFRACTION6F11 - 20
13X-RAY DIFFRACTION6F101 - 103

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