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- PDB-2wt7: Crystal structure of the bZIP heterodimeric complex MafB:cFos bou... -

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Basic information

Entry
Database: PDB / ID: 2wt7
TitleCrystal structure of the bZIP heterodimeric complex MafB:cFos bound to DNA
Components
  • (MODIFIED T-MARE ...) x 2
  • PROTO-ONCOGENE PROTEIN C-FOS
  • TRANSCRIPTION FACTOR MAFB
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATION / NUCLEUS / ACTIVATOR / REPRESSOR / DNA-BINDING / PHOSPHOPROTEIN / DIFFERENTIATION / TUMOR SUPPRESSOR / PROLIFERATION / PROTO-ONCOGENE
Function / homology
Function and homology information


rhombomere 6 development / abducens nerve formation / rhombomere 5 development / brain segmentation / cornified envelope assembly / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / regulation of myeloid cell differentiation / : / transcription factor AP-1 complex / negative regulation of erythrocyte differentiation ...rhombomere 6 development / abducens nerve formation / rhombomere 5 development / brain segmentation / cornified envelope assembly / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / regulation of myeloid cell differentiation / : / transcription factor AP-1 complex / negative regulation of erythrocyte differentiation / FCERI mediated MAPK activation / segment specification / : / response to gravity / response to xenobiotic stimulus => GO:0009410 / Activation of the AP-1 family of transcription factors / : / Oxidative Stress Induced Senescence / respiratory gaseous exchange by respiratory system / conditioned taste aversion / SMAD protein signal transduction / sleep / positive regulation of osteoclast differentiation / inner ear morphogenesis / response to corticosterone / negative regulation of osteoclast differentiation / skeletal muscle cell differentiation / R-SMAD binding / transcription factor binding / response to immobilization stress / response to light stimulus / RNA polymerase II core promoter sequence-specific DNA binding / keratinocyte differentiation / cellular response to hormone stimulus / response to cAMP / cellular response to cadmium ion / cellular response to calcium ion / response to muscle stretch / response to cold / transforming growth factor beta receptor signaling pathway / thymus development / response to cytokine / response to progesterone / female pregnancy / protein-DNA complex / protein processing / response to toxic substance / positive regulation of miRNA transcription / cellular response to reactive oxygen species / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / nervous system development / gene expression / T cell differentiation in thymus / regulation of gene expression / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / response to lipopolysaccharide / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / neuron projection / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / protein-containing complex binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
c-Fos/v-Fos / Maf transcription factor, N-terminal / Maf N-terminal region / Transcription factor Maf family / AP-1 transcription factor / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / bZIP transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 ...c-Fos/v-Fos / Maf transcription factor, N-terminal / Maf N-terminal region / Transcription factor Maf family / AP-1 transcription factor / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / bZIP 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 signature. / 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
PHOSPHATE ION / DNA / DNA (> 10) / Proto-oncogene c-Fos / Transcription factor MafB
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsPogenberg, V. / Holton, S. / Wilmanns, M.
CitationJournal: Structure / Year: 2014
Title: Design of a bZIP Transcription Factor with Homo/Heterodimer-Induced DNA-Binding Preference.
Authors: Pogenberg, V. / Consani Textor, L. / Vanhille, L. / Holton, S.J. / Sieweke, M.H. / Wilmanns, M.
History
DepositionSep 11, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references / Source and taxonomy / Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Mar 19, 2014Group: Database references
Revision 1.4Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5May 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTO-ONCOGENE PROTEIN C-FOS
B: TRANSCRIPTION FACTOR MAFB
C: MODIFIED T-MARE MOTIF
D: MODIFIED T-MARE MOTIF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3305
Polymers28,2354
Non-polymers951
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-58.7 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.676, 146.676, 51.117
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-2034-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein PROTO-ONCOGENE PROTEIN C-FOS / CFOS / CELLULAR ONCOGENE FOS


Mass: 7524.621 Da / Num. of mol.: 1 / Fragment: RESIDUES 138-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS RIL / References: UniProt: P01101
#2: Protein TRANSCRIPTION FACTOR MAFB / MAFB / MAF-B / V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG B / TRANSCRIPTION FACTOR MAF- ...MAFB / MAF-B / V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG B / TRANSCRIPTION FACTOR MAF-1 / SEGMENTATION PROTEIN KR / KREISLER


Mass: 10915.589 Da / Num. of mol.: 1 / Fragment: RESIDUES 214-303 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS RIL / References: UniProt: P54841

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MODIFIED T-MARE ... , 2 types, 2 molecules CD

#3: DNA chain MODIFIED T-MARE MOTIF


Mass: 4897.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: DNA chain MODIFIED T-MARE MOTIF


Mass: 4897.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 2 types, 173 molecules

#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN B, CYS 298 TO SER

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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: 2.24 Å3/Da / Density % sol: 51.3 % / Description: NONE

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONEMBL/DESY, HAMBURG X1110.8162
SYNCHROTRONEMBL/DESY, HAMBURG BW7A21.501
Detector
TypeIDDetectorDate
MAR555 FLAT PANEL1IMAGE PLATEJun 5, 2006
MARESEARCH2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.81621
21.5011
ReflectionResolution: 2.3→47.4 Å / Num. obs: 28122 / % possible obs: 99.5 % / Observed criterion σ(I): 2.4 / Redundancy: 11.9 % / Biso Wilson estimate: 57.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.4 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.4.0069refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.3→127 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.433 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25579 1415 5 %RANDOM
Rwork0.22826 ---
obs0.22967 26707 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.611 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.3→127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1290 650 5 172 2117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212094
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3912.3622946
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.155165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.77123.33381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.99415307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9591522
X-RAY DIFFRACTIONr_chiral_restr0.0660.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021366
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_it0.6861.5796
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36621285
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.81431298
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8564.51658
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 102 -
Rwork0.293 1962 -
obs--98.9 %
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)
10.4351-1.0811-0.22577.68390.41930.12110.06770.0833-0.0734-0.3980.0364-0.33810.05210.0016-0.1042-0.1627-0.04910.0039-0.1296-0.01920.080341.35-39.304-6.19
21.5458-0.58691.41643.00480.119710.0205-0.0288-0.0575-0.01890.19650.05210.0441-0.0852-0.1527-0.0234-0.1501-0.0516-0.007-0.25150.0002-0.20534.909-18.186-1.694
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A138 - 200
2X-RAY DIFFRACTION1B214 - 303
3X-RAY DIFFRACTION2C1 - 16
4X-RAY DIFFRACTION2D1 - 16

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