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- PDB-6g6l: The crystal structures of Human MYC:MAX bHLHZip complex -

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Basic information

Entry
Database: PDB / ID: 6g6l
TitleThe crystal structures of Human MYC:MAX bHLHZip complex
Components
  • Myc proto-oncogene protein
  • Protein max
KeywordsAPOPTOSIS / Myc/Max
Function / homology
Function and homology information


Mad-Max complex / positive regulation of metanephric cap mesenchymal cell proliferation / positive regulation of acinar cell proliferation / acinar cell proliferation / negative regulation of transcription initiation by RNA polymerase II / SCF ubiquitin ligase complex binding / NK T cell proliferation / Myc-Max complex / regulation of somatic stem cell population maintenance / regulation of cell cycle process ...Mad-Max complex / positive regulation of metanephric cap mesenchymal cell proliferation / positive regulation of acinar cell proliferation / acinar cell proliferation / negative regulation of transcription initiation by RNA polymerase II / SCF ubiquitin ligase complex binding / NK T cell proliferation / Myc-Max complex / regulation of somatic stem cell population maintenance / regulation of cell cycle process / Binding of TCF/LEF:CTNNB1 to target gene promoters / cellular response to interferon-alpha / RNA polymerase II transcription repressor complex / myotube differentiation / positive regulation of B cell apoptotic process / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors / negative regulation of cell division / negative regulation of monocyte differentiation / detection of mechanical stimulus involved in sensory perception of sound / response to growth factor / response to alkaloid / B cell apoptotic process / 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 / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Regulation of NFE2L2 gene expression / regulation of telomere maintenance / positive regulation of mesenchymal cell proliferation / skeletal system morphogenesis / middle ear morphogenesis / Signaling by ALK / branching involved in ureteric bud morphogenesis / negative regulation of gene expression via chromosomal CpG island methylation / pigmentation / rRNA metabolic process / E-box binding / Transcriptional Regulation by E2F6 / positive regulation of telomere maintenance / MLL1 complex / skeletal muscle cell differentiation / chromosome organization / positive regulation of transcription initiation by RNA polymerase II / Cyclin E associated events during G1/S transition / negative regulation of fibroblast proliferation / core promoter sequence-specific DNA binding / Cyclin A:Cdk2-associated events at S phase entry / ERK1 and ERK2 cascade / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / positive regulation of epithelial cell proliferation / transcription coregulator binding / MAPK6/MAPK4 signaling / NOTCH1 Intracellular Domain Regulates Transcription / G1/S transition of mitotic cell cycle / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / euchromatin / protein-DNA complex / protein processing / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / spindle / RNA polymerase II transcription regulator complex / Wnt signaling pathway / cellular response to xenobiotic stimulus / Transcriptional regulation of granulopoiesis / positive regulation of fibroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage / sequence-specific double-stranded DNA binding / cellular response to UV / MAPK cascade / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / cellular response to hypoxia / DNA-binding transcription factor binding / Estrogen-dependent gene expression / intracellular iron ion homeostasis / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / protein dimerization activity / nuclear body / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / axon / positive regulation of cell population proliferation / ubiquitin protein ligase binding / dendrite / DNA damage response / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription
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
Myc proto-oncogene protein / Protein max
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsAllen, M.D. / Zinzalla, G.
CitationJournal: Biochemistry / Year: 2019
Title: Crystal Structures and Nuclear Magnetic Resonance Studies of the Apo Form of the c-MYC:MAX bHLHZip Complex Reveal a Helical Basic Region in the Absence of DNA.
Authors: Sammak, S. / Hamdani, N. / Gorrec, F. / Allen, M.D. / Freund, S.M.V. / Bycroft, M. / Zinzalla, G.
History
DepositionApr 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Apr 5, 2023Group: Database references / Derived calculations / Experimental preparation
Category: database_2 / exptl_crystal_grow / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal_grow.temp / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myc proto-oncogene protein
B: Protein max
C: Myc proto-oncogene protein
D: Protein max
E: Myc proto-oncogene protein
F: Protein max
G: Myc proto-oncogene protein
H: Protein max
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,98622
Polymers85,6418
Non-polymers1,34514
Water8,647480
1
A: Myc proto-oncogene protein
B: Protein max
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7956
Polymers21,4102
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-64 kcal/mol
Surface area10050 Å2
MethodPISA
2
C: Myc proto-oncogene protein
D: Protein max
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6995
Polymers21,4102
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-69 kcal/mol
Surface area10570 Å2
MethodPISA
3
E: Myc proto-oncogene protein
F: Protein max
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6995
Polymers21,4102
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-64 kcal/mol
Surface area10480 Å2
MethodPISA
4
G: Myc proto-oncogene protein
H: Protein max
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7956
Polymers21,4102
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-75 kcal/mol
Surface area10070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.680, 74.330, 80.060
Angle α, β, γ (deg.)107.12, 107.67, 90.05
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Myc proto-oncogene protein / Class E basic helix-loop-helix protein 39 / bHLHe39 / Proto-oncogene c-Myc / Transcription factor p64


Mass: 11501.192 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYC, BHLHE39 / Production host: Escherichia coli (E. coli) / References: UniProt: P01106
#2: Protein
Protein max / Class D basic helix-loop-helix protein 4 / bHLHd4 / Myc-associated factor X


Mass: 9909.151 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAX, BHLHD4 / Production host: Escherichia coli (E. coli) / References: UniProt: P61244
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 3.07 Å3/Da / Density % sol: 59.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 15% PEG 8000 15, 0.2M ammonium sulfate, pH 7
PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979507 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979507 Å / Relative weight: 1
ReflectionResolution: 2.2→72.54 Å / Num. obs: 41701 / % possible obs: 80.7 % / Redundancy: 2.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.064 / Rrim(I) all: 0.109 / Net I/σ(I): 6.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6326 / CC1/2: 0.82 / Rpim(I) all: 0.333 / Rrim(I) all: 0.557 / % possible all: 83.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.2→46.155 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.92
RfactorNum. reflection% reflection
Rfree0.2681 1979 4.77 %
Rwork0.2149 --
obs0.2173 41512 80.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4961 0 70 480 5511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035066
X-RAY DIFFRACTIONf_angle_d0.516768
X-RAY DIFFRACTIONf_dihedral_angle_d1.9783234
X-RAY DIFFRACTIONf_chiral_restr0.034729
X-RAY DIFFRACTIONf_plane_restr0.003884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.2981640.27262859X-RAY DIFFRACTION82
2.255-2.3160.30291540.26382880X-RAY DIFFRACTION82
2.316-2.38410.31271200.25622799X-RAY DIFFRACTION80
2.3841-2.46110.31441410.25122715X-RAY DIFFRACTION77
2.4611-2.5490.29561490.24122686X-RAY DIFFRACTION76
2.549-2.65110.31451570.242967X-RAY DIFFRACTION86
2.6511-2.77170.31511410.25862989X-RAY DIFFRACTION84
2.7717-2.91780.2891920.23852983X-RAY DIFFRACTION84
2.9178-3.10060.26261580.22882920X-RAY DIFFRACTION82
3.1006-3.340.23541570.21622751X-RAY DIFFRACTION80
3.34-3.67590.26961420.20122582X-RAY DIFFRACTION73
3.6759-4.20750.22621430.16932904X-RAY DIFFRACTION82
4.2075-5.29980.23641130.17352861X-RAY DIFFRACTION81
5.2998-46.16510.26721480.21692637X-RAY DIFFRACTION75

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