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- PDB-1nlw: Crystal structure of Mad-Max recognizing DNA -

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Basic information

Entry
Database: PDB / ID: 1nlw
TitleCrystal structure of Mad-Max recognizing DNA
Components
  • 5'-D(*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
  • MAD PROTEIN
  • MAX PROTEIN
KeywordsTRANSCRIPTION/DNA / transcription factor / DNA / bHLHZ / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


Mad-Max complex / Myc-Max complex / Transcription of E2F targets under negative control by DREAM complex / Transcriptional Regulation by E2F6 / E-box binding / MLL1 complex / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / protein-DNA complex / DNA-binding transcription repressor activity, RNA polymerase II-specific ...Mad-Max complex / Myc-Max complex / Transcription of E2F targets under negative control by DREAM complex / Transcriptional Regulation by E2F6 / E-box binding / MLL1 complex / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / protein-DNA complex / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / dendrite / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Max dimerization protein 1 / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Helix-loop-helix DNA-binding domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein max / Max dimerization protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNair, S.K. / Burley, S.K.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: X-ray structures of Myc-Max and Mad-Max recognizing DNA: Molecular bases of regulation by proto-oncogenic transcription factors
Authors: Nair, S.K. / Burley, S.K.
History
DepositionJan 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: 5'-D(*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
G: 5'-D(*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
H: 5'-D(*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
J: 5'-D(*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
A: MAD PROTEIN
B: MAX PROTEIN
D: MAD PROTEIN
E: MAX PROTEIN


Theoretical massNumber of molelcules
Total (without water)59,2018
Polymers59,2018
Non-polymers00
Water4,522251
1
F: 5'-D(*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
G: 5'-D(*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
A: MAD PROTEIN
B: MAX PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,6004
Polymers29,6004
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: 5'-D(*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
J: 5'-D(*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
D: MAD PROTEIN
E: MAX PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,6004
Polymers29,6004
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.346, 56.020, 65.602
Angle α, β, γ (deg.)88.82, 79.08, 67.11
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain
5'-D(*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'


Mass: 5516.579 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein MAD PROTEIN / MAX DIMERIZER


Mass: 9445.983 Da / Num. of mol.: 2 / Fragment: bHLHZ region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Mad / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q05195
#3: Protein MAX PROTEIN


Mass: 9121.248 Da / Num. of mol.: 2 / Fragment: bHLHZ region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Max / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61244
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.61 Å3/Da / Density % sol: 52.95 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% MPD, 5mM magnesium chloride, 50 mM sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Components of the solutions
IDNameCrystal-IDSol-ID
120% methyl pentane diol11
25MM magnesium chloride11
350MM sodium cacodylate pH 6.011
4methyl pentane diol12
5magnesium chloride12
6sodium cacodylate pH 6.012
Crystal grow
*PLUS
Temperature: 15 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 %MPD1reservoir
25 mM1reservoirMgCl2
350 mMsodium cacodylate1reservoirpH6.0
410 mg/mlprotein1drop
51
61

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.92 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 35483 / % possible obs: 88.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.052
Reflection
*PLUS
Num. measured all: 214612
Reflection shell
*PLUS
% possible obs: 59.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NKP

1nkp


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.324 3376 Random
Rwork0.264 --
obs0.264 33720 -
all-35483 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.612 Å212.525 Å2-1.434 Å2
2---10.682 Å24.315 Å2
3---11.294 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 1464 0 251 4212
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg0.94
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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