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- PDB-7knx: Crystal structure of SND1 in complex with C-26-A6 -

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Basic information

Entry
Database: PDB / ID: 7knx
TitleCrystal structure of SND1 in complex with C-26-A6
ComponentsStaphylococcal nuclease domain-containing protein 1
KeywordsHYDROLASE/INHIBITOR / Inhibitor / Endonuclease / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


RNAi effector complex / miRNA catabolic process / regulation of cell cycle process / RISC complex binding / dense body / nuclease activity / regulatory ncRNA-mediated gene silencing / micrococcal nuclease / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / mRNA catabolic process ...RNAi effector complex / miRNA catabolic process / regulation of cell cycle process / RISC complex binding / dense body / nuclease activity / regulatory ncRNA-mediated gene silencing / micrococcal nuclease / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / mRNA catabolic process / RNA endonuclease activity / transcription coregulator activity / osteoblast differentiation / Signaling by BRAF and RAF1 fusions / melanosome / endonuclease activity / cadherin binding / RNA binding / extracellular exosome / membrane / nucleus / cytosol
Similarity search - Function
RNA-induced silencing complex, nuclease component Tudor-SN / : / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue ...RNA-induced silencing complex, nuclease component Tudor-SN / : / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily
Similarity search - Domain/homology
Chem-QOV / TYROSINE / Staphylococcal nuclease domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsKang, Y.
CitationJournal: Nat Cancer / Year: 2022
Title: Small-molecule inhibitors that disrupt the MTDH-SND1 complex suppress breast cancer progression and metastasis.
Authors: Shen, M. / Wei, Y. / Kim, H. / Wan, L. / Jiang, Y.Z. / Hang, X. / Raba, M. / Remiszewski, S. / Rowicki, M. / Wu, C.G. / Wu, S. / Zhang, L. / Lu, X. / Yuan, M. / Smith, H.A. / Zheng, A. / ...Authors: Shen, M. / Wei, Y. / Kim, H. / Wan, L. / Jiang, Y.Z. / Hang, X. / Raba, M. / Remiszewski, S. / Rowicki, M. / Wu, C.G. / Wu, S. / Zhang, L. / Lu, X. / Yuan, M. / Smith, H.A. / Zheng, A. / Bertino, J. / Jin, J.F. / Xing, Y. / Shao, Z.M. / Kang, Y.
History
DepositionNov 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 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: Staphylococcal nuclease domain-containing protein 1
B: Staphylococcal nuclease domain-containing protein 1
C: Staphylococcal nuclease domain-containing protein 1
D: Staphylococcal nuclease domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,87210
Polymers147,1884
Non-polymers1,6846
Water10,088560
1
A: Staphylococcal nuclease domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3313
Polymers36,7971
Non-polymers5342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Staphylococcal nuclease domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1502
Polymers36,7971
Non-polymers3531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Staphylococcal nuclease domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1502
Polymers36,7971
Non-polymers3531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Staphylococcal nuclease domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2423
Polymers36,7971
Non-polymers4452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.127, 81.880, 81.882
Angle α, β, γ (deg.)83.770, 70.890, 70.910
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPAA18 - 32823 - 322
21ASPASPBB18 - 32823 - 322
12ASPASPAA18 - 32823 - 322
22ASPASPCC18 - 32823 - 322
13ASPASPAA18 - 32823 - 322
23ASPASPDD18 - 32823 - 322
14ASPASPBB18 - 32823 - 322
24ASPASPCC18 - 32823 - 322
15VALVALBB18 - 33023 - 324
25VALVALDD18 - 33023 - 324
16ASPASPCC18 - 32823 - 322
26ASPASPDD18 - 32823 - 322

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Staphylococcal nuclease domain-containing protein 1 / 100 kDa coactivator / EBNA2 coactivator p100 / Tudor domain-containing protein 11 / p100 co-activator


Mass: 36796.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Contains the deletions 65-70 and 235-239 / Source: (gene. exp.) Homo sapiens (human) / Gene: SND1, TDRD11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): RIL / References: UniProt: Q7KZF4, micrococcal nuclease
#2: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Chemical
ChemComp-QOV / 5-chloro-2-methoxy-N-(2-methyl[1,2,4]triazolo[1,5-a]pyridin-8-yl)benzene-1-sulfonamide


Mass: 352.796 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H13ClN4O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 0.1 MES-NaOH pH 6.2, 0.9 M trisodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Dec 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 37571 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 1 / Net I/σ(I): 5.5
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 1.8 % / Rmerge(I) obs: 1 / Num. unique obs: 2776 / % possible all: 95.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.787 / SU B: 35.2 / SU ML: 0.418 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.484 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.329 1849 4.9 %RANDOM
Rwork0.2596 ---
obs0.2632 35722 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 113.94 Å2 / Biso mean: 55.537 Å2 / Biso min: 11.02 Å2
Baniso -1Baniso -2Baniso -3
1--3.3 Å20.48 Å2-1.53 Å2
2--0.64 Å20.64 Å2
3---1.31 Å2
Refinement stepCycle: final / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9317 0 110 560 9987
Biso mean--52.41 36.16 -
Num. residues----1168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199616
X-RAY DIFFRACTIONr_bond_other_d0.0020.029124
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.97112970
X-RAY DIFFRACTIONr_angle_other_deg1.018321077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78751154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33322.839465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.92151715
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.415111
X-RAY DIFFRACTIONr_chiral_restr0.0870.21403
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110559
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022028
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A182360.05
12B182360.05
21A179720.06
22C179720.06
31A178460.05
32D178460.05
41B181180.05
42C181180.05
51B179620.06
52D179620.06
61C177660.06
62D177660.06
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 86 -
Rwork0.32 2678 -
all-2764 -
obs--95.74 %
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)
13.44740.0677-1.06051.5406-0.48953.05290.0986-0.028-0.1047-0.12570.09320.03590.0668-0.2234-0.19180.3251-0.09540.00930.04370.01450.022949.91753.361-39.413
22.99220.94520.24582.78190.31951.33290.14150.1167-0.068-0.1479-0.16280.2442-0.0927-0.03050.02130.3945-0.0310.01610.0291-0.03050.035436.70537.457-72.73
33.8335-0.92410.06132.515-0.01491.68340.0471-0.1345-0.08810.0999-0.10560.1810.1918-0.01330.05860.3482-0.12750.08310.0564-0.03170.048836.3619.463-55.191
43.0996-0.31821.15221.4826-0.59712.92860.0431-0.01640.16560.18420.12760.0144-0.1848-0.2241-0.17070.4201-0.05160.07480.05750.0160.042723.37570.564-88.833
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 328
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION2B18 - 330
4X-RAY DIFFRACTION2B2001
5X-RAY DIFFRACTION3C18 - 328
6X-RAY DIFFRACTION3C2001
7X-RAY DIFFRACTION4D18 - 330
8X-RAY DIFFRACTION4D1001 - 1002

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