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- PDB-8x8s: Crystal structure of Cypovirus Polyhedra mutant fused with c-Myc ... -

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Basic information

Entry
Database: PDB / ID: 8x8s
TitleCrystal structure of Cypovirus Polyhedra mutant fused with c-Myc fragment
ComponentsPolyhedrin,Myc proto-oncogene protein
KeywordsVIRAL PROTEIN / Polyhedra
Function / homology
Function and homology information


positive regulation of metanephric cap mesenchymal cell proliferation / SCF ubiquitin ligase complex binding / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / viral occlusion body / 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 ...positive regulation of metanephric cap mesenchymal cell proliferation / SCF ubiquitin ligase complex binding / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / viral occlusion body / 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 / 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 / positive regulation of mesenchymal cell proliferation / protein-DNA complex disassembly / branching involved in ureteric bud morphogenesis / negative regulation of gene expression via chromosomal CpG island methylation / Signaling by ALK / : / E-box binding / : / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / chromosome organization / Cyclin E associated events during G1/S transition / core promoter sequence-specific DNA binding / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of fibroblast proliferation / ERK1 and ERK2 cascade / positive regulation of epithelial cell proliferation / transcription coregulator binding / response to gamma radiation / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / MAPK6/MAPK4 signaling / NOTCH1 Intracellular Domain Regulates Transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Transcriptional regulation of granulopoiesis / G1/S transition of mitotic cell cycle / cellular response to UV / positive regulation of fibroblast proliferation / MAPK cascade / cellular response to xenobiotic stimulus / cellular response to hypoxia / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / intracellular iron ion homeostasis / Estrogen-dependent gene expression / host cell cytoplasm / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / chromatin remodeling / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA damage response / positive regulation of cell population proliferation / positive regulation of gene expression / protein-containing complex binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / nucleolus / positive regulation of DNA-templated transcription / 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 / Cypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein / 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 / Cypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein / 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
Similarity search - Domain/homology
Myc proto-oncogene protein / Polyhedrin
Similarity search - Component
Biological speciesBombyx mori cypovirus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsKojima, M. / Ueno, T. / Abe, S. / Hirata, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: High-throughput structure determination of an intrinsically disordered protein using cell-free protein crystallization.
Authors: Kojima, M. / Abe, S. / Furuta, T. / Hirata, K. / Yao, X. / Kobayashi, A. / Kobayashi, R. / Ueno, T.
History
DepositionNov 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyhedrin,Myc proto-oncogene protein


Theoretical massNumber of molelcules
Total (without water)28,3011
Polymers28,3011
Non-polymers00
Water41423
1
A: Polyhedrin,Myc proto-oncogene protein

A: Polyhedrin,Myc proto-oncogene protein

A: Polyhedrin,Myc proto-oncogene protein


Theoretical massNumber of molelcules
Total (without water)84,9043
Polymers84,9043
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6440 Å2
ΔGint-44 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.530, 106.530, 106.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 28301.340 Da / Num. of mol.: 1 / Mutation: R151K
Source method: isolated from a genetically manipulated source
Details: cell-free synthesis
Source: (gene. exp.) Bombyx mori cypovirus 1, (gene. exp.) Homo sapiens (human)
Gene: MYC, BHLHE39 / Production host: Triticum aestivum (bread wheat) / References: UniProt: P11041, UniProt: P01106
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 1.78 Å3/Da / Density % sol: 30.9 %
Crystal growTemperature: 293 K / Method: small tubes / Details: cell-free crystallization

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 12981 / % possible obs: 99.9 % / Redundancy: 58 % / Biso Wilson estimate: 33.27 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.4
Reflection shellResolution: 2.04→2.11 Å / Num. unique obs: 2027 / CC1/2: 0.658

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XSCALEdata scaling
MOLREPphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→43.49 Å / SU ML: 0.3037 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.1416
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2652 1298 10 %
Rwork0.2216 11682 -
obs0.226 12980 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.84 Å2
Refinement stepCycle: LAST / Resolution: 2.04→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1394 0 0 24 1418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821426
X-RAY DIFFRACTIONf_angle_d0.91781936
X-RAY DIFFRACTIONf_chiral_restr0.0571213
X-RAY DIFFRACTIONf_plane_restr0.0059246
X-RAY DIFFRACTIONf_dihedral_angle_d5.7298194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.120.34111440.31581287X-RAY DIFFRACTION100
2.12-2.220.3251460.26831306X-RAY DIFFRACTION100
2.22-2.330.34471420.30441249X-RAY DIFFRACTION99.36
2.34-2.480.3051440.23751296X-RAY DIFFRACTION100
2.48-2.670.32371370.2661288X-RAY DIFFRACTION100
2.67-2.940.29491450.24351290X-RAY DIFFRACTION100
2.94-3.370.26391430.21021291X-RAY DIFFRACTION100
3.37-4.240.24121470.19061309X-RAY DIFFRACTION100
4.24-43.490.21291500.19061366X-RAY DIFFRACTION99.93

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