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- PDB-6luj: Crystal structure of the SAMD1 SAM domain -

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Basic information

Entry
Database: PDB / ID: 6luj
TitleCrystal structure of the SAMD1 SAM domain
ComponentsAtherin
KeywordsDNA BINDING PROTEIN / CpG-islands / transcription / pentamer
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 / chromosome / chromatin organization / 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 / chromosome / chromatin organization / 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
Sterile alpha motif domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsCao, Y. / Zhou, 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
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Atherin
B: Atherin
C: Atherin
D: Atherin
E: Atherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,02521
Polymers37,4885
Non-polymers1,53716
Water12,881715
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-240 kcal/mol
Surface area16030 Å2
Unit cell
Length a, b, c (Å)69.336, 69.336, 181.887
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-711-

HOH

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Components

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


Mass: 7497.573 Da / Num. of mol.: 5 / Fragment: SAM 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 715 / 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: 3.37 Å3/Da / Density % sol: 63.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 2.1M ammonium sulfatesulphate, 0.2M magnesium chloride hexahydrate

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 1.12→50 Å / Num. obs: 190708 / % possible obs: 97.9 % / Redundancy: 12.5 % / Biso Wilson estimate: 9.37 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 49.7
Reflection shellResolution: 1.12→1.14 Å / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 7808

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A model solved by Se-Met labelled sample

Resolution: 1.12→23.847 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1784 9297 4.88 %
Rwork0.1747 181347 -
obs0.1749 190644 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 41.03 Å2 / Biso mean: 13.9187 Å2 / Biso min: 6.43 Å2
Refinement stepCycle: final / Resolution: 1.12→23.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2640 0 80 715 3435
Biso mean--23.25 22.31 -
Num. residues----330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.1203-1.1330.32632250.2932490580
1.133-1.14640.24672830.2568517486
1.1464-1.16040.22192840.2319564592
1.1604-1.1750.21592570.2115587895
1.175-1.19050.19312920.1919590296
1.1905-1.20680.18372890.1873590497
1.2068-1.2240.20992760.186611399
1.224-1.24230.19633270.1875602999
1.2423-1.26170.19743240.1877603399
1.2617-1.28240.19453530.1835604699
1.2824-1.30450.19612800.1734609299
1.3045-1.32820.17982920.1717603499
1.3282-1.35380.17043140.1679611099
1.3538-1.38140.17993560.1669608399
1.3814-1.41150.16362940.1643614299
1.4115-1.44430.17183470.16646093100
1.4443-1.48040.182890.1566100100
1.4804-1.52040.15483210.15866142100
1.5204-1.56510.17243140.1556134100
1.5651-1.61570.15483160.15656169100
1.6157-1.67340.1753100.16066164100
1.6734-1.74040.17653020.16726203100
1.7404-1.81950.17572990.17046234100
1.8195-1.91540.17193090.17086160100
1.9154-2.03540.18252970.17236272100
2.0354-2.19240.16963370.16896188100
2.1924-2.41290.16953410.1726236100
2.4129-2.76160.1793810.18576220100
2.7616-3.47760.17893350.17936359100
3.4776-23.8470.17413530.16986583100

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