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- PDB-4auw: CRYSTAL STRUCTURE OF THE BZIP HOMODIMERIC MAFB IN COMPLEX WITH TH... -

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Basic information

Entry
Database: PDB / ID: 4auw
TitleCRYSTAL STRUCTURE OF THE BZIP HOMODIMERIC MAFB IN COMPLEX WITH THE C- MARE BINDING SITE
Components
  • (C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')) x 2
  • TRANSCRIPTION FACTOR MAFB
KeywordsTRANSCRIPTION / DNA / MACROPHAGE
Function / homology
Function and homology information


rhombomere 6 development / abducens nerve formation / rhombomere 5 development / brain segmentation / cornified envelope assembly / regulation of myeloid cell differentiation / negative regulation of erythrocyte differentiation / segment specification / respiratory gaseous exchange by respiratory system / inner ear morphogenesis ...rhombomere 6 development / abducens nerve formation / rhombomere 5 development / brain segmentation / cornified envelope assembly / regulation of myeloid cell differentiation / negative regulation of erythrocyte differentiation / segment specification / respiratory gaseous exchange by respiratory system / inner ear morphogenesis / negative regulation of osteoclast differentiation / keratinocyte differentiation / thymus development / protein processing / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / gene expression / T cell differentiation in thymus / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein-containing complex binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Maf transcription factor, N-terminal / Maf N-terminal region / 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 ...Maf transcription factor, N-terminal / Maf N-terminal region / 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 / Basic-leucine zipper domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / : / DNA / DNA (> 10) / Transcription factor MafB
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.9 Å
AuthorsTextor, L.C. / Holton, S. / Wilmanns, M.
CitationJournal: Acta Crystallogr Sect F Struct Biol Cryst Commun. / Year: 2007
Title: Expression, purification, crystallization and preliminary crystallographic analysis of the mouse transcription factor MafB in complex with its DNA-recognition motif Cmare
Authors: Textor, L.C. / Wilmanns, M. / Holton, S.J.
History
DepositionMay 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_source / reflns / reflns_shell
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _diffrn_source.pdbx_synchrotron_beamline / _reflns.pdbx_Rsym_value
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_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
A: TRANSCRIPTION FACTOR MAFB
B: TRANSCRIPTION FACTOR MAFB
C: C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')
D: C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')
E: TRANSCRIPTION FACTOR MAFB
F: TRANSCRIPTION FACTOR MAFB
G: C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')
H: C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,88413
Polymers71,9288
Non-polymers9575
Water00
1
A: TRANSCRIPTION FACTOR MAFB
B: TRANSCRIPTION FACTOR MAFB
C: C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')
D: C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5197
Polymers35,9644
Non-polymers5553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-114.2 kcal/mol
Surface area18650 Å2
MethodPISA
2
E: TRANSCRIPTION FACTOR MAFB
F: TRANSCRIPTION FACTOR MAFB
G: C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')
H: C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3656
Polymers35,9644
Non-polymers4012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-107.5 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.964, 94.964, 200.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
TRANSCRIPTION FACTOR MAFB / MAF-B / KREISLER / SEGMENTATION PROTEIN KR / TRANSCRIPTION FACTOR MAF-1 / V-MAF MUSCULOAPONEUROTIC ...MAF-B / KREISLER / SEGMENTATION PROTEIN KR / TRANSCRIPTION FACTOR MAF-1 / V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG B


Mass: 11540.252 Da / Num. of mol.: 4 / Fragment: RESIDUES 211-305 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P54841
#2: DNA chain C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')


Mass: 6437.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')


Mass: 6446.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#5: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.44 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Type: ESRF / Wavelength: 0.9535
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9535 Å / Relative weight: 1
ReflectionResolution: 2.9→48 Å / Num. obs: 20968 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.08 / Rsym value: 0.083 / Net I/σ(I): 7
Reflection shellResolution: 2.9→3.06 Å / Mean I/σ(I) obs: 1.8 / Rsym value: 0.218 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.5.0102 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.9→85.75 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.888 / SU B: 16.896 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R: 0.69 / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.29047 1081 5.1 %RANDOM
Rwork0.25505 ---
obs0.25684 19927 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.303 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---0.38 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.9→85.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 1710 12 0 4660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214891
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1472.4046909
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.015349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62823.136169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.71115643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9341544
X-RAY DIFFRACTIONr_chiral_restr0.0550.2759
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023094
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.462 81 -
Rwork0.492 1450 -
obs--100 %

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