[English] 日本語
Yorodumi
- PDB-1nkp: Crystal structure of Myc-Max recognizing DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nkp
TitleCrystal structure of Myc-Max recognizing DNA
Components
  • 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
  • Max protein
  • Myc proto-oncogene protein
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION / DNA / bHLHZ / oncogene / heterodimer / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


Mad-Max complex / positive regulation of metanephric cap mesenchymal cell proliferation / SCF ubiquitin ligase complex binding / Myc-Max complex / negative regulation of transcription initiation by RNA polymerase II / regulation of somatic stem cell population maintenance / regulation of cell cycle process / Binding of TCF/LEF:CTNNB1 to target gene promoters / RNA polymerase II transcription repressor complex / RUNX3 regulates WNT signaling ...Mad-Max complex / positive regulation of metanephric cap mesenchymal cell proliferation / SCF ubiquitin ligase complex binding / Myc-Max complex / negative regulation of transcription initiation by RNA polymerase II / regulation of somatic stem cell population maintenance / regulation of cell cycle process / Binding of TCF/LEF:CTNNB1 to target gene promoters / RNA polymerase II transcription repressor complex / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors / negative regulation of cell division / negative regulation of monocyte differentiation / response to growth factor / transcription regulator activator activity / protein-DNA complex disassembly / Transcription of E2F targets under negative control by DREAM complex / negative regulation of stress-activated MAPK cascade / fibroblast apoptotic process / Regulation of NFE2L2 gene expression / regulation of telomere maintenance / cellular response to peptide hormone stimulus / positive regulation of mesenchymal cell proliferation / Signaling by ALK / branching involved in ureteric bud morphogenesis / negative regulation of gene expression via chromosomal CpG island methylation / rRNA metabolic process / E-box binding / Transcriptional Regulation by E2F6 / positive regulation of telomere maintenance / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / MLL1 complex / response to axon injury / chromosome organization / core promoter sequence-specific DNA binding / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of fibroblast proliferation / ERK1 and ERK2 cascade / transcription coregulator binding / positive regulation of epithelial cell proliferation / cellular response to starvation / response to insulin / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / MAPK6/MAPK4 signaling / protein-DNA complex / PML body / positive regulation of miRNA transcription / NOTCH1 Intracellular Domain Regulates Transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / G1/S transition of mitotic cell cycle / RNA polymerase II transcription regulator complex / Transcriptional regulation of granulopoiesis / positive regulation of fibroblast proliferation / sequence-specific double-stranded DNA binding / cellular response to UV / MAPK cascade / cellular response to xenobiotic stimulus / regulation of gene expression / retina development in camera-type eye / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / Interleukin-4 and Interleukin-13 signaling / neuron apoptotic process / DNA-binding transcription factor binding / cellular response to hypoxia / Estrogen-dependent gene expression / intracellular iron ion homeostasis / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / Ub-specific processing proteases / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / negative regulation of gene expression / positive regulation of cell population proliferation / dendrite / DNA damage response / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein-containing complex binding / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / : / Myc amino-terminal region / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Helix-loop-helix DNA-binding domain / helix loop helix domain ...Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / : / Myc amino-terminal region / 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) / Myc proto-oncogene protein / Protein max
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Phased translation search / Resolution: 1.8 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 3, 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 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
G: 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
H: 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
J: 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
A: Myc proto-oncogene protein
B: Max protein
D: Myc proto-oncogene protein
E: Max protein


Theoretical massNumber of molelcules
Total (without water)63,7498
Polymers63,7498
Non-polymers00
Water10,467581
1
F: 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
G: 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
A: Myc proto-oncogene protein
B: Max protein


Theoretical massNumber of molelcules
Total (without water)31,8754
Polymers31,8754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
J: 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
D: Myc proto-oncogene protein
E: Max protein


Theoretical massNumber of molelcules
Total (without water)31,8754
Polymers31,8754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.244, 45.128, 86.484
Angle α, β, γ (deg.)87.91, 84.61, 71.50
Int Tables number1
Space group name H-MP1

-
Components

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


Mass: 5805.760 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein Myc proto-oncogene protein / c-myc


Mass: 10468.156 Da / Num. of mol.: 2 / Fragment: bHLHZ region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Myc / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01106
#3: Protein Max protein


Mass: 9795.012 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.: 581 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.95 %
Components of the solutions
IDNameCrystal-IDSol-ID
13-7% PEG 400011
230% methyl pentane diol11
31MM cobalt hexamine chloride11
450MM sodium cacodylate pH 6.511
5PEG 400012
6methyl pentane diol12
7cobalt hexamine chloride12
8sodium cacodylate pH 6.512
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13-7 %PEG40001reservoir
230 %MPD1reservoir
31 mMcobalt hexammine chloride1reservoir
450 mMsodium cacodylate1reservoirpH6.5
510 mg/mlprotein1drop
61
71
81

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 49228 / % possible obs: 95.9 % / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.053
Reflection
*PLUS
Num. measured all: 276421
Reflection shell
*PLUS
% possible obs: 90.9 %

-
Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
HKL-2000data reduction
X-PLORphasing
RefinementMethod to determine structure: Phased translation search
Starting model: PDB ENTRY 1AN2

1an2


Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.263 4123 Random
Rwork0.219 --
obs0.219 40874 -
all-49228 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.674 Å2-1.363 Å2-2.839 Å2
2--6.3 Å2-7.378 Å2
3----5.627 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 1540 0 581 4906
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0048
X-RAY DIFFRACTIONc_angle_d0.94736
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg0.95

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more