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- PDB-3bbb: Crystal structure of the NM23-H2 transcription factor complex wit... -

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Basic information

Entry
Database: PDB / ID: 3bbb
TitleCrystal structure of the NM23-H2 transcription factor complex with dinucleotide d(AG)
Components
  • DNA (5'-D(*AP*G)-3')
  • Nucleoside diphosphate kinase B
KeywordsTRANSFERASE / transcription factor / cancer / nm23 gen / hexamer / Activator / Anti-oncogene / ATP-binding / Cell cycle / DNA-binding / Kinase / Magnesium / Metal-binding / Nucleotide metabolism / Nucleotide-binding / Nucleus / Phosphorylation / Transcription regulation
Function / homology
Function and homology information


regulation of epidermis development / nucleoside triphosphate biosynthetic process / protein histidine kinase activity / Ribavirin ADME / G-quadruplex DNA binding / nucleoside-diphosphate kinase / positive regulation of keratinocyte differentiation / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process ...regulation of epidermis development / nucleoside triphosphate biosynthetic process / protein histidine kinase activity / Ribavirin ADME / G-quadruplex DNA binding / nucleoside-diphosphate kinase / positive regulation of keratinocyte differentiation / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / Azathioprine ADME / nucleoside diphosphate kinase activity / GTP biosynthetic process / histidine kinase / ruffle / positive regulation of epithelial cell proliferation / integrin-mediated signaling pathway / cell periphery / GDP binding / lamellipodium / secretory granule lumen / regulation of apoptotic process / ficolin-1-rich granule lumen / transcription coactivator activity / cell adhesion / Neutrophil degranulation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / extracellular region / ATP binding / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits ...Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / Nucleoside diphosphate kinase B
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsWeichsel, A. / Montfort, W.R.
Citation
Journal: Mol.Cancer Ther. / Year: 2009
Title: NM23-H2 may play an indirect role in transcriptional activation of c-myc gene expression but does not cleave the nuclease hypersensitive element III1.
Authors: Dexheimer, T.S. / Carey, S.S. / Zuohe, S. / Gokhale, V.M. / Hu, X. / Murata, L.B. / Maes, E.M. / Weichsel, A. / Sun, D. / Meuillet, E.J. / Montfort, W.R. / Hurley, L.H.
#1: Journal: Structure / Year: 1995
Title: X-ray structure of human nucleoside diphosphate kinase B complexed with GDP at 2 A resolution.
Authors: Morera, S. / Lacombe, M.L. / Xu, Y. / LeBras, G. / Janin, J.
History
DepositionNov 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0May 29, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _refine.B_iso_mean / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_percent_reflns_obs / _refine.pdbx_starting_model / _refine_hist.d_res_low / _refine_ls_shell.d_res_low / _reflns.number_all / _reflns.observed_criterion_sigma_F / _reflns_shell.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase B
B: Nucleoside diphosphate kinase B
C: Nucleoside diphosphate kinase B
D: Nucleoside diphosphate kinase B
E: Nucleoside diphosphate kinase B
F: Nucleoside diphosphate kinase B
G: DNA (5'-D(*AP*G)-3')
H: DNA (5'-D(*AP*G)-3')
I: DNA (5'-D(*AP*G)-3')
J: DNA (5'-D(*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)105,54710
Polymers105,54710
Non-polymers00
Water11,548641
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.466, 118.219, 128.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Nucleoside diphosphate kinase B / NDK B / NDP kinase B / C-myc purine-binding transcription factor PUF / Histidine protein kinase NDKB / nm23-H2


Mass: 17192.859 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NME2, NM23B / Plasmid: plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P22392, nucleoside-diphosphate kinase, histidine kinase
#2: DNA chain
DNA (5'-D(*AP*G)-3')


Mass: 597.455 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 1500, 50 mM sodium citrate, 20 mM MgCl2, 5 mM DTT, Crystals soaked with 10 mM d(AG), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.3→27 Å / Num. obs: 195789 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.4
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.3 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDISPLAYFdata collection
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NUE

1nue


Resolution: 1.3→27 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.02 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 9678 5 %RANDOM
Rwork0.175 ---
obs0.177 183782 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.3→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7218 0 126 641 7985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0227703
X-RAY DIFFRACTIONr_bond_other_d0.0020.025427
X-RAY DIFFRACTIONr_angle_refined_deg1.8851.97810432
X-RAY DIFFRACTIONr_angle_other_deg1.202313194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3845938
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61223.523352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.714151380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7771556
X-RAY DIFFRACTIONr_chiral_restr0.1870.21104
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028472
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021588
X-RAY DIFFRACTIONr_nbd_refined0.2270.21563
X-RAY DIFFRACTIONr_nbd_other0.2150.25704
X-RAY DIFFRACTIONr_nbtor_refined0.1870.23718
X-RAY DIFFRACTIONr_nbtor_other0.0840.23972
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2471
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.210.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2651.55925
X-RAY DIFFRACTIONr_mcbond_other1.2371.51866
X-RAY DIFFRACTIONr_mcangle_it2.69927393
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.68833756
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7914.53025
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.39939451
X-RAY DIFFRACTIONr_sphericity_free10.7713638
X-RAY DIFFRACTIONr_sphericity_bonded5.74137374
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 674 -
Rwork0.206 13198 -
obs--96.05 %

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