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- PDB-1hlo: THE CRYSTAL STRUCTURE OF AN INTACT HUMAN MAX-DNA COMPLEX: NEW INS... -

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Basic information

Entry
Database: PDB / ID: 1hlo
TitleTHE CRYSTAL STRUCTURE OF AN INTACT HUMAN MAX-DNA COMPLEX: NEW INSIGHTS INTO MECHANISMS OF TRANSCRIPTIONAL CONTROL
Components
  • DNA (5'-D(*AP*CP*CP*AP*CP*GP*TP*GP*GP*TP*G)-3')
  • DNA (5'-D(*CP*AP*CP*CP*AP*CP*GP*TP*GP*GP*T)-3')
  • PROTEIN (TRANSCRIPTION FACTOR MAX)
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTIONAL REGULATION / DNA BINDING / COMPLEX (TRANSCRIPTION FACTOR MAX-DNA) / 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 / cellular response to peptide hormone stimulus / E-box binding / Transcriptional Regulation by E2F6 / MLL1 complex / response to axon injury / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry ...Mad-Max complex / Myc-Max complex / Transcription of E2F targets under negative control by DREAM complex / cellular response to peptide hormone stimulus / E-box binding / Transcriptional Regulation by E2F6 / MLL1 complex / response to axon injury / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / cellular response to starvation / response to insulin / protein-DNA complex / PML body / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / retina development in camera-type eye / protein-containing complex assembly / neuron apoptotic process / DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of gene expression / dendrite / regulation of transcription by RNA polymerase II / protein-containing complex binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsBrownlie, P. / Ceska, T.A. / Lamers, M. / Romier, C. / Theo, H. / Suck, D.
CitationJournal: Structure / Year: 1997
Title: The crystal structure of an intact human Max-DNA complex: new insights into mechanisms of transcriptional control.
Authors: Brownlie, P. / Ceska, T. / Lamers, M. / Romier, C. / Stier, G. / Teo, H. / Suck, D.
History
DepositionSep 10, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Oct 27, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*CP*AP*CP*CP*AP*CP*GP*TP*GP*GP*T)-3')
D: DNA (5'-D(*AP*CP*CP*AP*CP*GP*TP*GP*GP*TP*G)-3')
A: PROTEIN (TRANSCRIPTION FACTOR MAX)
B: PROTEIN (TRANSCRIPTION FACTOR MAX)


Theoretical massNumber of molelcules
Total (without water)25,7934
Polymers25,7934
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.000, 108.000, 127.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: DNA chain DNA (5'-D(*CP*AP*CP*CP*AP*CP*GP*TP*GP*GP*T)-3')


Mass: 3334.186 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*CP*CP*AP*CP*GP*TP*GP*GP*TP*G)-3')


Mass: 3374.210 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (TRANSCRIPTION FACTOR MAX)


Mass: 9542.478 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P61244
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.14 Å3/Da / Density % sol: 70.32 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CITRATE11
Crystal
*PLUS
Density % sol: 53 %
Crystal grow
*PLUS
PH range low: 4 / PH range high: 3.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 mg/mlprotein1drop
221 %1reservoir
3100 mMsodium citrate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.8 Å / % possible obs: 96 % / Rsym value: 0.098
Reflection
*PLUS
Highest resolution: 2.8 Å / Rmerge(I) obs: 0.098

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Processing

Software
NameClassification
X-PLORrefinement
XDSdata reduction
RefinementResolution: 2.8→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.273 -
Rwork0.213 -
obs0.213 9496
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 445 0 18 1746
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / Num. reflection all: 10256 / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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