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- PDB-7ksp: Crystal structure of hSAMD9_DBD with DNA -

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Basic information

Entry
Database: PDB / ID: 7ksp
TitleCrystal structure of hSAMD9_DBD with DNA
Components
  • (DNA) x 2
  • Sterile alpha motif domain-containing protein 9
KeywordsDNA BINDING PROTEIN/DNA / SAMD9 / Alba domain / DNA binding / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


endosomal vesicle fusion / innate immune response / intracellular membrane-bounded organelle / cytoplasm / cytosol
Similarity search - Function
SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / Sterile alpha motif domain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsPeng, S. / Pathak, P. / Xiang, Y. / Deng, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structure and function of an effector domain in antiviral factors and tumor suppressors SAMD9 and SAMD9L.
Authors: Peng, S. / Meng, X. / Zhang, F. / Pathak, P.K. / Chaturvedi, J. / Coronado, J. / Morales, M. / Mao, Y. / Qian, S.B. / Deng, J. / Xiang, Y.
History
DepositionNov 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Apr 27, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3May 22, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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 9
B: Sterile alpha motif domain-containing protein 9
C: DNA
D: DNA


Theoretical massNumber of molelcules
Total (without water)67,0174
Polymers67,0174
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.796, 59.022, 88.383
Angle α, β, γ (deg.)90.000, 97.470, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 160:172 or (resid 173 and (name...
21(chain B and (resseq 160:172 or (resid 173 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRPROPRO(chain A and (resseq 160:172 or (resid 173 and (name...AA160 - 1725 - 17
12TYRTYRTYRTYR(chain A and (resseq 160:172 or (resid 173 and (name...AA17318
13LEULEUPHEPHE(chain A and (resseq 160:172 or (resid 173 and (name...AA159 - 3804 - 225
14LEULEUPHEPHE(chain A and (resseq 160:172 or (resid 173 and (name...AA159 - 3804 - 225
15LEULEUPHEPHE(chain A and (resseq 160:172 or (resid 173 and (name...AA159 - 3804 - 225
16LEULEUPHEPHE(chain A and (resseq 160:172 or (resid 173 and (name...AA159 - 3804 - 225
17LEULEUPHEPHE(chain A and (resseq 160:172 or (resid 173 and (name...AA159 - 3804 - 225
18LEULEUPHEPHE(chain A and (resseq 160:172 or (resid 173 and (name...AA159 - 3804 - 225
19LEULEUPHEPHE(chain A and (resseq 160:172 or (resid 173 and (name...AA159 - 3804 - 225
110LEULEUPHEPHE(chain A and (resseq 160:172 or (resid 173 and (name...AA159 - 3804 - 225
111LEULEUPHEPHE(chain A and (resseq 160:172 or (resid 173 and (name...AA159 - 3804 - 225
112LEULEUPHEPHE(chain A and (resseq 160:172 or (resid 173 and (name...AA159 - 3804 - 225
21THRTHRPROPRO(chain B and (resseq 160:172 or (resid 173 and (name...BB160 - 1725 - 17
22TYRTYRTYRTYR(chain B and (resseq 160:172 or (resid 173 and (name...BB17318
23LEULEUPHEPHE(chain B and (resseq 160:172 or (resid 173 and (name...BB159 - 3804 - 225
24LEULEUPHEPHE(chain B and (resseq 160:172 or (resid 173 and (name...BB159 - 3804 - 225
25LEULEUPHEPHE(chain B and (resseq 160:172 or (resid 173 and (name...BB159 - 3804 - 225
26LEULEUPHEPHE(chain B and (resseq 160:172 or (resid 173 and (name...BB159 - 3804 - 225
27LEULEUPHEPHE(chain B and (resseq 160:172 or (resid 173 and (name...BB159 - 3804 - 225
28LEULEUPHEPHE(chain B and (resseq 160:172 or (resid 173 and (name...BB159 - 3804 - 225
29LEULEUPHEPHE(chain B and (resseq 160:172 or (resid 173 and (name...BB159 - 3804 - 225
210LEULEUPHEPHE(chain B and (resseq 160:172 or (resid 173 and (name...BB159 - 3804 - 225
211LEULEUPHEPHE(chain B and (resseq 160:172 or (resid 173 and (name...BB159 - 3804 - 225
212LEULEUPHEPHE(chain B and (resseq 160:172 or (resid 173 and (name...BB159 - 3804 - 225

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Components

#1: Protein Sterile alpha motif domain-containing protein 9 / SAM domain-containing protein 9


Mass: 26759.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAMD9, C7orf5, DRIF1, KIAA2004, OEF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5K651
#2: DNA chain DNA


Mass: 6773.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA


Mass: 6724.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium acetate, 20mM magnesium chloride, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97887 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97887 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 16022 / % possible obs: 89.3 % / Redundancy: 1.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.054 / Net I/σ(I): 6.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 1 / Num. unique obs: 1976 / CC1/2: 0.833 / % possible all: 59.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→50 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 33.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.284 1597 9.99 %
Rwork0.208 14392 -
obs0.2157 15989 92.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.62 Å2 / Biso mean: 83.5413 Å2 / Biso min: 27.31 Å2
Refinement stepCycle: final / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3496 902 0 10 4408
Biso mean---51.35 -
Num. residues----468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014584
X-RAY DIFFRACTIONf_angle_d1.2186351
X-RAY DIFFRACTIONf_chiral_restr0.065686
X-RAY DIFFRACTIONf_plane_restr0.009661
X-RAY DIFFRACTIONf_dihedral_angle_d20.8612591
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1824X-RAY DIFFRACTION12.717TORSIONAL
12B1824X-RAY DIFFRACTION12.717TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8012-2.89220.33781010.322193567
2.8922-2.99560.35031250.2863112480
2.9956-3.11550.38241410.2815127290
3.1155-3.25730.33461480.2641130895
3.2573-3.4290.32421500.2621136596
3.429-3.64370.31761540.2183137899
3.6437-3.9250.30441560.2063140799
3.925-4.31970.25931500.1777135496
4.3197-4.94430.22861580.1637142199
4.9443-6.22730.27711550.1994139298
6.2273-500.26061590.1918143697
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9308-5.73550.26159.16941.22323.1562-0.3862-1.46231.14151.3080.1761-0.4897-0.2020.40040.14460.7335-0.13160.19840.5985-0.4640.755444.17811.237180.7779
20.3154-0.3531-0.71085.3860.75751.4665-0.4120.66982.0852-0.08540.3893-1.0477-0.5943-0.16740.21650.5535-0.02980.01110.67270.49431.333546.6989.23468.6033
33.6119-1.60370.97136.1284-1.33233.6819-0.10131.0080.8726-0.5921-0.29740.1204-0.29250.2873-0.05920.2044-0.01230.23710.70570.23390.627737.71783.627261.6196
42.7071.6069-0.16850.972-0.34093.18340.24840.84641.73870.178-0.0889-0.7346-0.26330.4991-0.03070.2598-0.00120.07250.57990.05931.209344.90410.695369.2999
53.8673-0.85930.42762.3985-0.13634.1918-0.11340.04730.62970.3833-0.06270.3516-0.2643-0.40940.22020.27960.07580.06330.542-0.01570.777534.17423.945470.3266
64.76380.38530.42884.372-0.14176.7188-0.10750.74890.3301-0.53760.0221-0.03830.3327-0.326-0.00850.29620.12430.25250.71010.03720.640839.0011-6.283459.2034
73.65611.42492.70768.7321.26176.21620.09350.55280.1939-0.7401-0.1288-1.4115-0.3132.0851-0.33490.47880.20690.22031.0980.22450.643350.4375-2.052456.7749
80.90740.1392-0.76850.71370.63211.46790.10220.65560.2229-0.30010.2664-0.5099-0.03630.5956-0.09380.47020.6730.93761.4705-0.18060.834453.8638-12.231354.1701
92.1577-1.3406-0.66729.5966-0.74682.06180.1498-0.84190.38241.96320.3745-1.80620.94651.5254-0.67510.64590.0963-0.26280.7587-0.03580.818452.9682-14.13273.0703
107.592-1.8341-3.81932.62811.81667.393-0.1371.2297-1.3873-1.0314-0.0355-0.27360.7683-0.01230.1780.54090.0294-0.00680.684-0.1550.629747.74158.53885.2366
110.26510.49721.05342.78241.15544.4864-0.81710.5331-1.24450.04360.7024-1.1413-0.05421.0657-0.49210.41090.10710.13930.7902-0.15761.312359.15989.919711.4464
125.63521.5326-1.15345.09330.22117.0841-0.2239-1.1605-1.42870.0915-0.2559-0.3360.70840.43070.40790.30210.05110.04890.49520.050.5544.497512.980722.3335
135.41330.7785-1.89637.34811.15674.7316-0.2815-0.4733-1.2520.34120.0083-1.36470.7490.48150.15270.39650.02150.06570.5074-0.00920.752548.64337.988516.9256
147.44581.032-0.13732.1021.09137.13660.1569-0.0477-1.15510.152-0.31720.58760.6477-0.91610.21390.3209-0.0804-0.06390.5868-0.07370.725332.311414.799719.6517
154.2047-3.617-1.86833.12931.75875.36780.05740.212-0.6757-0.2736-0.81091.35890.2358-0.69220.560.237-0.0522-0.01620.594-0.1180.596840.457116.401815.1332
163.061-0.84940.01366.35060.64284.7944-0.1415-1.15920.43840.4058-0.0285-0.43030.41940.47190.16880.3774-0.07280.01160.9575-0.12180.459449.814626.113526.7136
179.24791.98194.06473.1863-2.70766.27391.71960.3295-0.61950.6497-0.6311-1.80181.7178-2.0987-0.46331.9471-0.06110.2910.9384-0.39181.159147.30825.407355.3679
182.3346-2.2314-0.90798.93285.93467.54180.85040.9111-0.8737-0.6217-1.0507-0.7129-0.6314-1.16930.21111.5124-0.19040.44481.1303-0.55381.634349.1203-3.565334.3631
197.0748-3.2036-3.8994.39651.42923.81421.09040.31960.2747-0.12530.5751-2.3625-1.0396-0.7225-1.44312.3535-0.20340.0061.0701-0.46991.176249.6441-6.503533.4594
205.94593.71761.11266.79861.24955.58250.5365-0.98390.62931.1987-0.6986-0.61541.5409-0.78180.00682.0338-0.0712-0.16880.6176-0.12431.176249.58511.687250.1593
218.05521.5869-6.10413.6537-2.10025.17250.9302-0.10161.82310.20530.9331-2.21441.0545-0.2509-1.91411.51820.1766-0.18590.7199-0.08380.823345.163928.924853.4646
223.81862.9132.77562.35171.3836.10891.4774-1.0481.65290.62690.1468-1.70310.22010.8233-1.79411.3951-0.00790.04120.9118-0.57591.90945.192232.67467.3321
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 159 through 178 )A159 - 178
2X-RAY DIFFRACTION2chain 'A' and (resid 179 through 207 )A179 - 207
3X-RAY DIFFRACTION3chain 'A' and (resid 208 through 228 )A208 - 228
4X-RAY DIFFRACTION4chain 'A' and (resid 229 through 253 )A229 - 253
5X-RAY DIFFRACTION5chain 'A' and (resid 254 through 309 )A254 - 309
6X-RAY DIFFRACTION6chain 'A' and (resid 310 through 341 )A310 - 341
7X-RAY DIFFRACTION7chain 'A' and (resid 342 through 355 )A342 - 355
8X-RAY DIFFRACTION8chain 'A' and (resid 356 through 365 )A356 - 365
9X-RAY DIFFRACTION9chain 'A' and (resid 366 through 380 )A366 - 380
10X-RAY DIFFRACTION10chain 'B' and (resid 159 through 178 )B159 - 178
11X-RAY DIFFRACTION11chain 'B' and (resid 179 through 188 )B179 - 188
12X-RAY DIFFRACTION12chain 'B' and (resid 189 through 228 )B189 - 228
13X-RAY DIFFRACTION13chain 'B' and (resid 229 through 253 )B229 - 253
14X-RAY DIFFRACTION14chain 'B' and (resid 254 through 271 )B254 - 271
15X-RAY DIFFRACTION15chain 'B' and (resid 272 through 309 )B272 - 309
16X-RAY DIFFRACTION16chain 'B' and (resid 310 through 380 )B310 - 380
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 10 )C1 - 10
18X-RAY DIFFRACTION18chain 'C' and (resid 11 through 22 )C11 - 22
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 10 )D1 - 10
20X-RAY DIFFRACTION20chain 'D' and (resid 11 through 15 )D11 - 15
21X-RAY DIFFRACTION21chain 'D' and (resid 16 through 20 )D16 - 20
22X-RAY DIFFRACTION22chain 'D' and (resid 21 through 22 )D21 - 22

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