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- PDB-1ckt: CRYSTAL STRUCTURE OF HMG1 DOMAIN A BOUND TO A CISPLATIN-MODIFIED ... -

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Basic information

Entry
Database: PDB / ID: 1ckt
TitleCRYSTAL STRUCTURE OF HMG1 DOMAIN A BOUND TO A CISPLATIN-MODIFIED DNA DUPLEX
Components
  • DNA (5'-D(*CP*CP*(5IU)P*CP*TP*CP*TP*GP*GP*AP*CP*CP*TP*TP*CP*C)-3')
  • DNA (5'-D(*GP*GP*AP*AP*GP*GP*TP*CP*CP*AP*GP*AP*GP*AP*GP*G)-3')
  • HIGH MOBILITY GROUP 1 PROTEIN
KeywordsGENE REGULATION/DNA / HIGH-MOBILITY GROUP DOMAIN / BENT DNA / PROTEIN-DRUG-DNA COMPLEX / GENE REGULATION-DNA COMPLEX
Function / homology
Function and homology information


male-specific defense response to bacterium / Apoptosis induced DNA fragmentation / open form four-way junction DNA binding / crossed form four-way junction DNA binding / positive regulation of myeloid cell apoptotic process / non-sequence-specific DNA binding, bending / Pyroptosis / TAK1-dependent IKK and NF-kappa-B activation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling ...male-specific defense response to bacterium / Apoptosis induced DNA fragmentation / open form four-way junction DNA binding / crossed form four-way junction DNA binding / positive regulation of myeloid cell apoptotic process / non-sequence-specific DNA binding, bending / Pyroptosis / TAK1-dependent IKK and NF-kappa-B activation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / Regulation of TLR by endogenous ligand / regulation of tolerance induction / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / negative regulation of apoptotic cell clearance / plasmacytoid dendritic cell activation / negative regulation of RNA polymerase II transcription preinitiation complex assembly / toll-like receptor 2 signaling pathway / T-helper 1 cell activation / T-helper 1 cell differentiation / positive regulation of myeloid cell differentiation / myeloid dendritic cell activation / positive regulation of toll-like receptor 2 signaling pathway / glycolipid binding / positive regulation of macrophage inflammatory protein 1 alpha production / positive regulation of dendritic cell differentiation / C-X-C chemokine binding / negative regulation of CD4-positive, alpha-beta T cell differentiation / bent DNA binding / positive regulation of toll-like receptor 9 signaling pathway / neutrophil clearance / positive regulation of glycogen catabolic process / 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 / induction of positive chemotaxis / bubble DNA binding / V(D)J recombination / myeloid cell differentiation / alphav-beta3 integrin-HMGB1 complex / myeloid progenitor cell differentiation / inflammatory response to antigenic stimulus / macrophage activation involved in immune response / positive regulation of monocyte chemotaxis / positive regulation of monocyte chemotactic protein-1 production / regulation of nucleotide-excision repair / positive regulation of innate immune response / endothelial cell proliferation / positive regulation of vascular endothelial cell proliferation / positive regulation of chemokine (C-X-C motif) ligand 2 production / cellular response to interleukin-7 / glycogen catabolic process / apoptotic cell clearance / positive regulation of mesenchymal cell proliferation / positive regulation of smooth muscle cell migration / MyD88-dependent toll-like receptor signaling pathway / DNA binding, bending / Neutrophil degranulation / supercoiled DNA binding / toll-like receptor 4 signaling pathway / positive regulation of wound healing / phosphatidylserine binding / positive regulation of sprouting angiogenesis / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of DNA replication / negative regulation of type II interferon production / myoblast proliferation / positive regulation of activated T cell proliferation / negative regulation of blood vessel endothelial cell migration / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / positive regulation of blood vessel endothelial cell migration / cellular response to interleukin-1 / protein kinase activator activity / response to type II interferon / positive regulation of myoblast differentiation / response to glucose / four-way junction DNA binding / condensed chromosome / DNA polymerase binding / transcription repressor complex / positive regulation of interleukin-12 production / positive regulation of autophagy / peptide binding / positive regulation of mitotic cell cycle / activation of innate immune response / lung development / positive regulation of interferon-beta production / response to glucocorticoid / cytokine activity / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / lipopolysaccharide binding / positive regulation of non-canonical NF-kappaB signal transduction
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
Cisplatin / DNA / DNA (> 10) / High mobility group protein B1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.5 Å
AuthorsOhndorf, U.-M. / Rould, M.A. / Pabo, C.O. / Lippard, S.J.
CitationJournal: Nature / Year: 1999
Title: Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins.
Authors: Ohndorf, U.M. / Rould, M.A. / He, Q. / Pabo, C.O. / Lippard, S.J.
History
DepositionApr 23, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0Jun 30, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*CP*CP*(5IU)P*CP*TP*CP*TP*GP*GP*AP*CP*CP*TP*TP*CP*C)-3')
C: DNA (5'-D(*GP*GP*AP*AP*GP*GP*TP*CP*CP*AP*GP*AP*GP*AP*GP*G)-3')
A: HIGH MOBILITY GROUP 1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7084
Polymers18,4083
Non-polymers3001
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.210, 50.410, 53.130
Angle α, β, γ (deg.)90.00, 99.82, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: DNA chain DNA (5'-D(*CP*CP*(5IU)P*CP*TP*CP*TP*GP*GP*AP*CP*CP*TP*TP*CP*C)-3')


Mass: 4872.949 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*GP*AP*AP*GP*GP*TP*CP*CP*AP*GP*AP*GP*AP*GP*G)-3')


Mass: 5037.280 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein HIGH MOBILITY GROUP 1 PROTEIN / HMG-1 / AMPHOTERIN / HEPARIN-BINDING PROTEIN P30


Mass: 8497.785 Da / Num. of mol.: 1 / Fragment: RESIDUES 8-78, DOMAIN A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: SORAGYE-DAWLEY / Tissue: LIVER / Plasmid: PT7-HMG1BA / Species (production host): Escherichia coli / Gene (production host): HMG1 DOMAIN A (M1-F89) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P63159
#4: Chemical ChemComp-CPT / Cisplatin / diammine(dichloro)platinum


Mass: 300.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 69 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: CRYSTALS WERE OBTAINED FROM A SOLUTION THAT CONTAINED HEPES, MAGNESIUM ACETATE, PEG 3350, GLYCEROL AND DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1MAGNESIUM ACETATE11
2HEPES11
3PEG 335011
4GLYCEROL11
5DTT11
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.6 mMprotein1drop
20.9 mMDNA duplex1drop
30.05 MHEPES1drop
440 mMmagnesium acetate1drop
51 %glycerol1drop
616 %PEG33501drop
72.5 mMdithiothreitol1drop
80.1 MHEPES1reservoir
980 mMmagnesium acetate1reservoir
101 %glycerol1reservoir
1116 %PEG33501reservoir
125 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 9655 / % possible obs: 97.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 84.2 % / Rmerge(I) obs: 0.334

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.5→100 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: TYR: TYR 77 C-TERMINAL OXYGEN OXT WAS NOT FOUND IN ELECTRON DENSITY MAP; C-TERMINAL RESIDUES 78-89 WERE NOT SEEN IN DENSITY MAP
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1710 10 %RANDOM
Rwork0.238 ---
obs0.238 17638 65.6 %-
Refinement stepCycle: LAST / Resolution: 2.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms562 650 3 74 1289
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d32.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg32.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6

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