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- PDB-6cm2: SAMHD1 HD domain bound to decitabine triphosphate -

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Basic information

Entry
Database: PDB / ID: 6cm2
TitleSAMHD1 HD domain bound to decitabine triphosphate
ComponentsDeoxynucleoside triphosphate triphosphohydrolase SAMHD1
KeywordsHYDROLASE / SAMHD1 / analogues / decitabine
Function / homology
Function and homology information


Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / dGTP catabolic process / DNA strand resection involved in replication fork processing ...Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / dGTP catabolic process / DNA strand resection involved in replication fork processing / negative regulation of type I interferon-mediated signaling pathway / regulation of innate immune response / somatic hypermutation of immunoglobulin genes / RNA nuclease activity / double-strand break repair via homologous recombination / Interferon alpha/beta signaling / site of double-strand break / single-stranded DNA binding / defense response to virus / protein homotetramerization / nucleic acid binding / immune response / innate immune response / DNA damage response / GTP binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane
Similarity search - Function
: / HD domain profile. / HD domain / HD domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / Sterile alpha motif. / HD/PDEase domain / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily
Similarity search - Domain/homology
Chem-F6G / GUANOSINE-5'-TRIPHOSPHATE / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsOellerich, T. / Schneider, C. / Thomas, D. / Knecht, K.M. / Buzovetsky, O. / Kaderali, L. / Schliemann, C. / Bohnenberger, H. / Angenendt, L. / Hartmann, W. ...Oellerich, T. / Schneider, C. / Thomas, D. / Knecht, K.M. / Buzovetsky, O. / Kaderali, L. / Schliemann, C. / Bohnenberger, H. / Angenendt, L. / Hartmann, W. / Wardelmann, E. / Rothenburger, T. / Mohr, S. / Scheich, S. / Comoglio, F. / Wilke, A. / Strobel, P. / Serve, H. / Michaelis, M. / Ferreiros, N. / Geisslinger, G. / Xiong, Y. / Keppler, O.T. / Cinatl, J.
CitationJournal: Nat Commun / Year: 2019
Title: Selective inactivation of hypomethylating agents by SAMHD1 provides a rationale for therapeutic stratification in AML.
Authors: Oellerich, T. / Schneider, C. / Thomas, D. / Knecht, K.M. / Buzovetsky, O. / Kaderali, L. / Schliemann, C. / Bohnenberger, H. / Angenendt, L. / Hartmann, W. / Wardelmann, E. / Rothenburger, ...Authors: Oellerich, T. / Schneider, C. / Thomas, D. / Knecht, K.M. / Buzovetsky, O. / Kaderali, L. / Schliemann, C. / Bohnenberger, H. / Angenendt, L. / Hartmann, W. / Wardelmann, E. / Rothenburger, T. / Mohr, S. / Scheich, S. / Comoglio, F. / Wilke, A. / Strobel, P. / Serve, H. / Michaelis, M. / Ferreiros, N. / Geisslinger, G. / Xiong, Y. / Keppler, O.T. / Cinatl Jr., J.
History
DepositionMar 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,36820
Polymers238,4174
Non-polymers5,95116
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23710 Å2
ΔGint-69 kcal/mol
Surface area69560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.492, 146.536, 98.552
Angle α, β, γ (deg.)90.00, 114.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 / dNTPase / Dendritic cell-derived IFNG-induced protein / DCIP / Monocyte protein 5 / MOP-5 / SAM ...dNTPase / Dendritic cell-derived IFNG-induced protein / DCIP / Monocyte protein 5 / MOP-5 / SAM domain and HD domain-containing protein 1


Mass: 59604.172 Da / Num. of mol.: 4 / Mutation: H94R, D95N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAMHD1, MOP5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases
#2: Chemical
ChemComp-F6G / 6-amino-3-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-3,4-dihydro-1,3,5-triazin-2(1H)-one


Mass: 470.161 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H17N4O13P3
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 298 K / Method: batch mode / Details: SPG buffer, PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 125515 / % possible obs: 98.9 % / Redundancy: 4.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.132 / Net I/σ(I): 9.3
Reflection shellResolution: 2.14→2.18 Å / Mean I/σ(I) obs: 0.88 / CC1/2: 0.175

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZB

4bzb


Resolution: 2.14→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.059 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.182 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22534 6373 5.1 %RANDOM
Rwork0.17354 ---
obs0.17614 119197 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.374 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20.31 Å2
2---1.28 Å20 Å2
3---0.28 Å2
Refinement stepCycle: 1 / Resolution: 2.14→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15724 0 356 368 16448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01916515
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215149
X-RAY DIFFRACTIONr_angle_refined_deg1.861.98322383
X-RAY DIFFRACTIONr_angle_other_deg1.034335230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15251929
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.37124.012815
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.84152931
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.04915112
X-RAY DIFFRACTIONr_chiral_restr0.1010.22358
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02117968
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023372
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0553.887716
X-RAY DIFFRACTIONr_mcbond_other3.0543.887715
X-RAY DIFFRACTIONr_mcangle_it4.5765.8079642
X-RAY DIFFRACTIONr_mcangle_other4.5765.8089643
X-RAY DIFFRACTIONr_scbond_it4.0694.3378799
X-RAY DIFFRACTIONr_scbond_other4.0714.3398787
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.386.30212721
X-RAY DIFFRACTIONr_long_range_B_refined8.04143.97618234
X-RAY DIFFRACTIONr_long_range_B_other8.04243.94918161
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.117→2.172 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 360 -
Rwork0.337 7560 -
obs--83.75 %

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