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- PDB-6c48: Crystal structure of B-Myb-LIN9-LIN52 complex -

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Basic information

Entry
Database: PDB / ID: 6c48
TitleCrystal structure of B-Myb-LIN9-LIN52 complex
Components
  • Myb-related protein BMYBL2
  • Protein lin-52 homolog
  • Protein lin-9 homolog
KeywordsCELL CYCLE/DNA Binding / Myb / B-Myb / LIN52 / LIN9 / MMB / MuvB / CELL CYCLE / CELL CYCLE-DNA Binding complex
Function / homology
Function and homology information


DRM complex / : / Myb complex / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / Transcription of E2F targets under negative control by DREAM complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Polo-like kinase mediated events / G1/S-Specific Transcription / DNA biosynthetic process / mitotic spindle assembly ...DRM complex / : / Myb complex / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / Transcription of E2F targets under negative control by DREAM complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Polo-like kinase mediated events / G1/S-Specific Transcription / DNA biosynthetic process / mitotic spindle assembly / G0 and Early G1 / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / transcription repressor complex / cellular response to leukemia inhibitory factor / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / mitotic cell cycle / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of cell cycle / DNA-binding transcription factor activity, RNA polymerase II-specific / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Myb-related protein B / Protein LIN52 / Retinal tissue protein / Protein LIN-9/Protein ALWAYS EARLY / DIRP domain / LIN-9, C-terminal / DIRP / LIN9 C-terminal / DIRP / C-myb, C-terminal ...Myb-related protein B / Protein LIN52 / Retinal tissue protein / Protein LIN-9/Protein ALWAYS EARLY / DIRP domain / LIN-9, C-terminal / DIRP / LIN9 C-terminal / DIRP / C-myb, C-terminal / C-myb, C-terminal / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Myb-related protein B / Protein lin-52 homolog / Protein lin-9 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.32 Å
AuthorsGuiley, K.Z. / Tripathi, S.M. / Rubin, S.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)F31CA206244 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA132685 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural mechanism of Myb-MuvB assembly.
Authors: Guiley, K.Z. / Iness, A.N. / Saini, S. / Tripathi, S. / Lipsick, J.S. / Litovchick, L. / Rubin, S.M.
History
DepositionJan 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein lin-9 homolog
D: Protein lin-9 homolog
F: Myb-related protein B
C: Myb-related protein B
B: Protein lin-52 homolog
E: Protein lin-52 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1368
Polymers50,9446
Non-polymers1922
Water1,49583
1
A: Protein lin-9 homolog
C: Myb-related protein B
B: Protein lin-52 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5684
Polymers25,4723
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-67 kcal/mol
Surface area10040 Å2
MethodPISA
2
D: Protein lin-9 homolog
F: Myb-related protein B
E: Protein lin-52 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5684
Polymers25,4723
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-48 kcal/mol
Surface area10030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.760, 30.770, 105.350
Angle α, β, γ (deg.)90.00, 99.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein lin-9 homolog / hLin-9 / Beta subunit-associated regulator of apoptosis / TUDOR gene similar protein / Type I ...hLin-9 / Beta subunit-associated regulator of apoptosis / TUDOR gene similar protein / Type I interferon receptor beta chain-associated protein / pRB-associated protein


Mass: 13999.179 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIN9, BARA, TGS / Production host: Escherichia coli (E. coli) / References: UniProt: Q5TKA1
#2: Protein/peptide Myb-related protein B / MYBL2 / B-Myb / Myb-like protein 2


Mass: 3649.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYBL2, BMYB / Production host: Escherichia coli (E. coli) / References: UniProt: P10244
#3: Protein Protein lin-52 homolog


Mass: 7823.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIN52, C14orf46 / Production host: Escherichia coli (E. coli) / References: UniProt: Q52LA3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.9 Å3/Da / Density % sol: 35.41 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5 / Details: 100 mM citric acid 10% PEG 6000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.32→59.86 Å / Num. obs: 16249 / % possible obs: 94.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.052 / Net I/σ(I): 9.9
Reflection shellResolution: 2.32→2.44 Å / Rmerge(I) obs: 0.528 / Num. unique all: 14701 / CC1/2: 0.89 / Rpim(I) all: 0.218

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.32→59.857 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.09
RfactorNum. reflection% reflection
Rfree0.2643 761 4.69 %
Rwork0.2171 --
obs0.2194 16234 94.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.32→59.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2732 0 10 83 2825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092770
X-RAY DIFFRACTIONf_angle_d1.1033694
X-RAY DIFFRACTIONf_dihedral_angle_d7.8411740
X-RAY DIFFRACTIONf_chiral_restr0.052418
X-RAY DIFFRACTIONf_plane_restr0.007460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.318-2.4970.34251370.2452984X-RAY DIFFRACTION92
2.497-2.74830.28781520.23493036X-RAY DIFFRACTION94
2.7483-3.1460.27931460.22753069X-RAY DIFFRACTION94
3.146-3.96350.25661690.19653144X-RAY DIFFRACTION96
3.9635-59.87740.23511570.21433240X-RAY DIFFRACTION95

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