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- PDB-3a5t: Crystal structure of MafG-DNA complex -

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Basic information

Entry
Database: PDB / ID: 3a5t
TitleCrystal structure of MafG-DNA complex
Components
  • 5'-D(*CP*TP*GP*AP*TP*GP*AP*GP*TP*CP*AP*GP*CP*AP*C)-3'
  • 5'-D(*GP*TP*GP*CP*TP*GP*AP*CP*TP*CP*AP*TP*CP*AP*G)-3'
  • Transcription factor MafG
KeywordsTRANSCRIPTION REGULATOR/DNA / PROTEIN-DNA COMPLEX / BZIP FACTOR / Acetylation / DNA-binding / Isopeptide bond / Nucleus / Repressor / Transcription / Transcription regulation / Ubl conjugation / TRANSCRIPTION REGULATOR-DNA COMPLEX
Function / homology
Function and homology information


Factors involved in megakaryocyte development and platelet production / regulation of epidermal cell differentiation / regulation of cellular pH / adult behavior / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / transcription regulator complex ...Factors involved in megakaryocyte development and platelet production / regulation of epidermal cell differentiation / regulation of cellular pH / adult behavior / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus
Similarity search - Function
Transcription factor Maf family / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Transcription factor Maf family / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor MafG
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsKurokawa, H. / Motohashi, H. / Sueno, S. / Kimura, M. / Takagawa, H. / Kanno, Y. / Yamamoto, M. / Tanaka, T.
CitationJournal: Mol.Cell.Biol. / Year: 2009
Title: Structural Basis of Alternative DNA Recognition by Maf Transcription Factors
Authors: Kurokawa, H. / Motohashi, H. / Sueno, S. / Kimura, M. / Takagawa, H. / Kanno, Y. / Yamamoto, M. / Tanaka, T.
History
DepositionAug 11, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 14, 2023Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_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
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor MafG
B: Transcription factor MafG
C: 5'-D(*CP*TP*GP*AP*TP*GP*AP*GP*TP*CP*AP*GP*CP*AP*C)-3'
D: 5'-D(*GP*TP*GP*CP*TP*GP*AP*CP*TP*CP*AP*TP*CP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2475
Polymers34,2234
Non-polymers241
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-52 kcal/mol
Surface area16940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.364, 185.243, 230.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Transcription factor MafG / Mafg Transcription Factor / V-maf musculoaponeurotic fibrosarcoma oncogene homolog G


Mass: 12521.845 Da / Num. of mol.: 2 / Fragment: BINDING DOMAIN, RESIDUES 21-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mafg / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-CodonPlus-RIL / References: UniProt: O54790
#2: DNA chain 5'-D(*CP*TP*GP*AP*TP*GP*AP*GP*TP*CP*AP*GP*CP*AP*C)-3'


Mass: 4593.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 5'-D(*GP*TP*GP*CP*TP*GP*AP*CP*TP*CP*AP*TP*CP*AP*G)-3'


Mass: 4584.985 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 83 / 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: 6.288576 Å3/Da / Density % sol: 80.44072 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M sodium acetate, 40mM magnesium chloride hexahydrate, 8% 2-methyl-2,4-pentandiol, 4mM Tris(2-carboxyethyl)phosphine, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97939, 0.97898, 0.96416
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 14, 2006 / Details: mirrors
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979391
20.978981
30.964161
ReflectionResolution: 2.8→36.08 Å / Num. obs: 22101 / % possible obs: 98.9 % / Redundancy: 13 % / Biso Wilson estimate: -0.8 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 56.77 / Num. measured all: 284413
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 11.91 / Num. unique all: 2016 / % possible all: 92.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXDEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→36.08 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 59212.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2050 9.8 %RANDOM
Rwork0.261 ---
all-20843 --
obs-20843 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 17.7589 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 73.4 Å2
Baniso -1Baniso -2Baniso -3
1--22.72 Å20 Å20 Å2
2---31.49 Å20 Å2
3---54.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.67 Å
Refinement stepCycle: LAST / Resolution: 2.8→36.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 609 1 83 2129
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it2.22
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.445 293 9.7 %
Rwork0.432 2734 -
obs--84.2 %

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