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- PDB-8y77: Crystal structure of the complex of SAMD1-SAM and L3MBTL3-SAM domains -

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Basic information

Entry
Database: PDB / ID: 8y77
TitleCrystal structure of the complex of SAMD1-SAM and L3MBTL3-SAM domains
Components
  • Lethal(3)malignant brain tumor-like protein 3
  • Sterile alpha motif domain-containing protein 1
KeywordsGENE REGULATION / epigenetics / complex / polymer / CpG islands
Function / homology
Function and homology information


lipoprotein lipid oxidation / foam cell differentiation / negative regulation of transcription initiation-coupled chromatin remodeling / methylation-dependent protein binding / granulocyte differentiation / : / low-density lipoprotein particle binding / positive regulation of ubiquitin-dependent protein catabolic process / erythrocyte maturation / macrophage differentiation ...lipoprotein lipid oxidation / foam cell differentiation / negative regulation of transcription initiation-coupled chromatin remodeling / methylation-dependent protein binding / granulocyte differentiation / : / low-density lipoprotein particle binding / positive regulation of ubiquitin-dependent protein catabolic process / erythrocyte maturation / macrophage differentiation / protein homooligomerization / chromatin organization / chromosome / histone binding / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular space / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / Zinc finger, C2H2C-type / Zinc finger CCHHC-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / : / mbt repeat ...: / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / Zinc finger, C2H2C-type / Zinc finger CCHHC-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / : / mbt repeat / 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 / Lethal(3)malignant brain tumor-like protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCao, Y. / Wang, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071204 China
National Natural Science Foundation of China (NSFC)32125008 China
CitationJournal: To Be Published
Title: Crystal structure of the complex of SAMD1-SAM and L3MBTL3-SAM domains
Authors: Cao, Y. / Wang, Z.
History
DepositionFeb 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sterile alpha motif domain-containing protein 1
B: Lethal(3)malignant brain tumor-like protein 3


Theoretical massNumber of molelcules
Total (without water)15,7032
Polymers15,7032
Non-polymers00
Water3,207178
1
A: Sterile alpha motif domain-containing protein 1
B: Lethal(3)malignant brain tumor-like protein 3

A: Sterile alpha motif domain-containing protein 1
B: Lethal(3)malignant brain tumor-like protein 3


Theoretical massNumber of molelcules
Total (without water)31,4064
Polymers31,4064
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area3220 Å2
ΔGint-22 kcal/mol
Surface area13870 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-5 kcal/mol
Surface area7460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.981, 95.515, 65.926
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-631-

HOH

21A-641-

HOH

31A-659-

HOH

41A-662-

HOH

51B-850-

HOH

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Components

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


Mass: 7541.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAMD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6SPF0
#2: Protein Lethal(3)malignant brain tumor-like protein 3 / H-l(3)mbt-like protein 3 / L(3)mbt-like protein 3 / L3mbt-like 3 / MBT-1


Mass: 8161.290 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: L3MBTL3, KIAA1798, MBT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96JM7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.01 M Magnesium acetate tetrahydrate, 0.05 M MES monohydrate pH 5.6 and 2.63 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 22635 / % possible obs: 99.8 % / Redundancy: 12.6 % / Biso Wilson estimate: 15.21 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 23.2
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.859 / Num. unique obs: 1092

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→24.02 Å / SU ML: 0.1687 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.5752 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2078 1094 4.84 %
Rwork0.1835 21506 -
obs0.1846 22600 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.75 Å2
Refinement stepCycle: LAST / Resolution: 1.5→24.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 0 178 1262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00491104
X-RAY DIFFRACTIONf_angle_d0.7491488
X-RAY DIFFRACTIONf_chiral_restr0.0676168
X-RAY DIFFRACTIONf_plane_restr0.0053190
X-RAY DIFFRACTIONf_dihedral_angle_d2.758411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.570.25891550.22222614X-RAY DIFFRACTION98.68
1.57-1.650.22131300.20062635X-RAY DIFFRACTION99.5
1.65-1.750.26471500.19162649X-RAY DIFFRACTION99.64
1.75-1.890.18961320.18212650X-RAY DIFFRACTION99.82
1.89-2.080.20241390.17142677X-RAY DIFFRACTION100
2.08-2.380.19511180.16792717X-RAY DIFFRACTION100
2.38-30.21371300.19172729X-RAY DIFFRACTION100
3-24.020.19491400.18182835X-RAY DIFFRACTION99.77

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