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- PDB-6lui: Crystal structure of the SAMD1 WH domain and DNA complex -

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Basic information

Entry
Database: PDB / ID: 6lui
TitleCrystal structure of the SAMD1 WH domain and DNA complex
Components
  • Atherin
  • DNA (5'-D(*AP*CP*CP*TP*GP*CP*GP*CP*AP*CP*CP*AP*T)-3')
  • DNA (5'-D(*AP*TP*GP*GP*TP*GP*CP*GP*CP*AP*GP*GP*T)-3')
KeywordsDNA BINDING PROTEIN / CpG islands / transcription / polycomb
Function / homology
Function and homology information


lipoprotein lipid oxidation / foam cell differentiation / regulation of DNA methylation-dependent heterochromatin formation / low-density lipoprotein particle binding / protein homooligomerization / chromatin organization / chromosome / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding ...lipoprotein lipid oxidation / foam cell differentiation / regulation of DNA methylation-dependent heterochromatin formation / low-density lipoprotein particle binding / protein homooligomerization / chromatin organization / chromosome / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular space / nucleus
Similarity search - Function
: / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Sterile alpha motif domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.781 Å
AuthorsZhou, Y. / Cao, Y. / Wang, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870725 China
National Natural Science Foundation of China (NSFC)31570729 China
CitationJournal: Sci Adv / Year: 2021
Title: The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands.
Authors: Stielow, B. / Zhou, Y. / Cao, Y. / Simon, C. / Pogoda, H.M. / Jiang, J. / Ren, Y. / Phanor, S.K. / Rohner, I. / Nist, A. / Stiewe, T. / Hammerschmidt, M. / Shi, Y. / Bulyk, M.L. / Wang, Z. / Liefke, R.
History
DepositionJan 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _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: Atherin
B: DNA (5'-D(*AP*CP*CP*TP*GP*CP*GP*CP*AP*CP*CP*AP*T)-3')
C: DNA (5'-D(*AP*TP*GP*GP*TP*GP*CP*GP*CP*AP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)17,4783
Polymers17,4783
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-12 kcal/mol
Surface area8160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.925, 45.925, 132.638
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Atherin / Sterile alpha motif domain-containing protein 1 / SAM domain-containing protein 1


Mass: 9533.800 Da / Num. of mol.: 1 / Fragment: WH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAMD1 / Production host: Escherichia Coli BL21(DE3) (bacteria) / References: UniProt: Q6SPF0
#2: DNA chain DNA (5'-D(*AP*CP*CP*TP*GP*CP*GP*CP*AP*CP*CP*AP*T)-3')


Mass: 3896.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*TP*GP*GP*TP*GP*CP*GP*CP*AP*GP*GP*T)-3')


Mass: 4047.632 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.2M Calcium calcium acetate hydrate, 20% w/v Polyethylene polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97855 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 16308 / % possible obs: 100 % / Redundancy: 18.5 % / Biso Wilson estimate: 34.15 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 60
Reflection shellResolution: 1.78→1.81 Å / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 794

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.781→25.469 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2418 708 4.36 %
Rwork0.2024 15533 -
obs0.204 16241 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.37 Å2 / Biso mean: 39.4588 Å2 / Biso min: 24.5 Å2
Refinement stepCycle: final / Resolution: 1.781→25.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms598 527 0 103 1228
Biso mean---40.25 -
Num. residues----97
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.781-1.91790.32571600.23523003
1.9179-2.11090.26861520.22933027
2.1109-2.41610.28821080.22553135
2.4161-3.04320.31361330.24593120
3.0432-25.4690.20141550.17763248

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