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- PDB-4eot: Crystal structure of the MafA homodimer bound to the consensus MARE -

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Basic information

Entry
Database: PDB / ID: 4eot
TitleCrystal structure of the MafA homodimer bound to the consensus MARE
Components
  • 5'-D(*CP*CP*CP*TP*GP*CP*TP*GP*AP*CP*TP*CP*AP*GP*CP*AP*CP*CP*G)-3'
  • 5'-D(*CP*CP*GP*GP*TP*GP*CP*TP*GP*AP*GP*TP*CP*AP*GP*CP*AP*GP*G)-3'
  • Transcription factor MafA
KeywordsTRANSCRIPTION/DNA / leucine zipper / transcription factor / DNA binding / nucleus / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


chromatin => GO:0000785 / insulin secretion / Regulation of gene expression in beta cells / nitric oxide mediated signal transduction / response to glucose / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...chromatin => GO:0000785 / insulin secretion / Regulation of gene expression in beta cells / nitric oxide mediated signal transduction / response to glucose / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / host cell nucleus / regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function
Transcription factor MafA / 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 ...Transcription factor MafA / 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 / 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 MafA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.855 Å
AuthorsLu, X. / Guanga, G. / Wan, C. / Rose, R.B.
CitationJournal: Biochemistry / Year: 2012
Title: A Novel DNA Binding Mechanism for maf Basic Region-Leucine Zipper Factors Inferred from a MafA-DNA Complex Structure and Binding Specificities.
Authors: Lu, X. / Guanga, G.P. / Wan, C. / Rose, R.B.
History
DepositionApr 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 MafA
B: Transcription factor MafA
C: 5'-D(*CP*CP*GP*GP*TP*GP*CP*TP*GP*AP*GP*TP*CP*AP*GP*CP*AP*GP*G)-3'
D: 5'-D(*CP*CP*CP*TP*GP*CP*TP*GP*AP*CP*TP*CP*AP*GP*CP*AP*CP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8087
Polymers34,5204
Non-polymers2883
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-98 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.100, 116.100, 85.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Transcription factor MafA / Pancreatic beta-cell-specific transcriptional activator / Transcription factor RIPE3b1 / V-maf ...Pancreatic beta-cell-specific transcriptional activator / Transcription factor RIPE3b1 / V-maf musculoaponeurotic fibrosarcoma oncogene homolog A


Mass: 11453.238 Da / Num. of mol.: 2 / Fragment: DNA-binding domain (UNP residues 226-318)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAFA / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NHW3
#2: DNA chain 5'-D(*CP*CP*GP*GP*TP*GP*CP*TP*GP*AP*GP*TP*CP*AP*GP*CP*AP*GP*G)-3'


Mass: 5886.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Maf-response element (MARE) upper strand
#3: DNA chain 5'-D(*CP*CP*CP*TP*GP*CP*TP*GP*AP*CP*TP*CP*AP*GP*CP*AP*CP*CP*G)-3'


Mass: 5726.701 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Maf-response element (MARE) bottom strand
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 4.8 Å3/Da / Density % sol: 74.35 % / Description: RMEASURE = 0.073 (0.798)
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.2 M ammonium sulfate, 100 mM sodium acetate, pH 4.5, one week of growth, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 22, 2008
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.855→20 Å / Num. all: 15399 / Num. obs: 15793 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Net I/σ(I): 22.55
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsDiffraction-ID% possible all
2.855-39.43.03185.1
3-3.3199.9
3.3-3.61100
3.6-41100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A5T

3a5t


Resolution: 2.855→19.972 Å / SU ML: 0.44 / σ(F): 2.02 / Phase error: 25.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2595 768 5.02 %RANDOM
Rwork0.2208 ---
obs0.2227 15288 97.54 %-
all-15793 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.996 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2782 Å20 Å2-0 Å2
2--0.2782 Å20 Å2
3----0.5564 Å2
Refinement stepCycle: LAST / Resolution: 2.855→19.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1360 770 15 4 2149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022266
X-RAY DIFFRACTIONf_angle_d0.6963211
X-RAY DIFFRACTIONf_dihedral_angle_d22.463888
X-RAY DIFFRACTIONf_chiral_restr0.036364
X-RAY DIFFRACTIONf_plane_restr0.001280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.855-3.07520.39571420.31242697X-RAY DIFFRACTION91
3.0752-3.38330.22691530.19722889X-RAY DIFFRACTION99
3.3833-3.86980.29561550.21112899X-RAY DIFFRACTION98
3.8698-4.86380.2421560.2022964X-RAY DIFFRACTION100
4.8638-19.9720.24911620.23033071X-RAY DIFFRACTION100
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)
10.3736-0.1938-0.03183.85774.17745.7450.10670.12620.1692-0.587-0.41580.1731-0.49460.05650.25990.7526-0.0068-0.07410.28760.06440.3744-46.483517.7656-19.4154
21.32630.1033-1.16380.60450.8026.27830.1158-0.1978-0.13520.0576-0.28670.01830.35950.7220.30480.74640.0804-0.01210.33760.07360.2815-42.20170.9015-11.4022
32.2790.25630.05614.0795-0.53651.2085-0.0827-0.06990.1786-0.149-0.0072-0.265-0.1720.2315-0.01120.8824-0.51220.09690.3999-0.23130.7192-48.778417.7927-0.5718
41.0739-0.24520.32671.80351.1121.6085-0.01-0.16590.50030.0953-0.2086-0.118-0.24420.1022-0.19230.5695-0.3896-0.01490.1278-0.13550.5885-48.373415.8863-0.1199
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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