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- PDB-4to2: Structure basis of cellular dNTP regulation, SAMHD1-dGTP-dGTP-dGT... -

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Basic information

Entry
Database: PDB / ID: 4to2
TitleStructure basis of cellular dNTP regulation, SAMHD1-dGTP-dGTP-dGTP/dTTP complex
ComponentsDeoxynucleoside triphosphate triphosphohydrolase SAMHD1
KeywordsHYDROLASE / SAMHD1 / HIV / restriction factor / dNTPase / dNTP regulation / host pathogen interaction
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 / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / dGTPase activity / 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 / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / dGTPase activity / 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 / RNA nuclease activity / somatic hypermutation of immunoglobulin genes / double-strand break repair via homologous recombination / Interferon alpha/beta signaling / single-stranded DNA binding / site of double-strand break / protein homotetramerization / defense response to virus / 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
Hypothetical protein af1432 / Hypothetical protein af1432 / : / 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. ...Hypothetical protein af1432 / Hypothetical protein af1432 / : / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / THYMIDINE-5'-TRIPHOSPHATE / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsJi, X. / Tang, C. / Zhao, Q. / Wang, W. / Xiong, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI097064 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis of cellular dNTP regulation by SAMHD1.
Authors: Ji, X. / Tang, C. / Zhao, Q. / Wang, W. / Xiong, Y.
History
DepositionJun 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Oct 29, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 30, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _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 / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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
Revision 1.5Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / 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: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,67224
Polymers238,4174
Non-polymers6,25620
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29670 Å2
ΔGint-72 kcal/mol
Surface area67430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.313, 145.798, 98.257
Angle α, β, γ (deg.)90.000, 114.220, 90.000
Int Tables number4
Space group name H-MP1211
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: ASP / Beg label comp-ID: ASP / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 113 - 599 / Label seq-ID: 1 - 487

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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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
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-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
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-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 99828 / % possible obs: 99.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.142 / Rsym value: 0.142 / Χ2: 1.252 / Net I/av σ(I): 7.115 / Net I/σ(I): 8.9 / Num. measured all: 489251
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.28-2.324.80.893149741.31199.9
2.32-2.364.849361.33899.9
2.36-2.414.850021.3699.9
2.41-2.464.850051.381100
2.46-2.514.849741.402100
2.51-2.574.80.89349621.45100
2.57-2.634.90.79149621.47399.9
2.63-2.74.90.6249721.555100
2.7-2.784.90.48749961.61299.9
2.78-2.874.90.41850011.73899.8
2.87-2.984.90.32849651.21999.8
2.98-3.094.90.27949751.2199.9
3.09-3.2450.23249961.17499.9
3.24-3.4150.19549841.12100
3.41-3.6250.17149991.06100
3.62-3.950.15550071.039100
3.9-4.2950.14550240.95999.9
4.29-4.914.90.12149891.02199.9
4.91-6.194.80.09750400.864100
6.19-5050.06850650.82699.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
PDB_EXTRACT3.14data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZB

4bzb


Resolution: 2.27→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 26.101 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.361 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 4941 5 %RANDOM
Rwork0.206 94221 --
obs0.2074 99162 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 160.13 Å2 / Biso mean: 68.197 Å2 / Biso min: 35.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20.34 Å2
2---4.47 Å2-0 Å2
3---3.56 Å2
Refinement stepCycle: final / Resolution: 2.27→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15732 0 378 233 16343
Biso mean--55.54 58.96 -
Num. residues----1924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01916521
X-RAY DIFFRACTIONr_bond_other_d0.0060.0215649
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.98522395
X-RAY DIFFRACTIONr_angle_other_deg1.056336039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5251924
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04223.99812
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.216152928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.99815112
X-RAY DIFFRACTIONr_chiral_restr0.0880.22352
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02118316
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023884
X-RAY DIFFRACTIONr_mcbond_it1.851.8267708
X-RAY DIFFRACTIONr_mcbond_other1.8471.8267707
X-RAY DIFFRACTIONr_mcangle_it3.0842.7289628
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A317850.04
12B317850.04
21A317850.03
22C317850.03
31A317130.04
32D317130.04
41B318530.03
42C318530.03
51B317150.05
52D317150.05
61C317060.04
62D317060.04
LS refinement shellResolution: 2.271→2.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 296 -
Rwork0.354 5947 -
all-6243 -
obs--83.47 %
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)
10.24390.29410.21440.42720.0121.2353-0.0873-0.16690.0063-0.0232-0.096-0.0646-0.1919-0.70380.18320.65210.1113-0.00880.9249-0.05280.1148-1.69714.1055-0.9704
20.1126-0.0850.15880.1725-0.11060.8065-0.03250.1907-0.0125-0.08780.04340.0472-0.09060.3222-0.01090.7242-0.05730.04760.7622-0.00240.135236.2028-1.6235-33.4667
30.22130.19160.43760.21040.42971.04270.07-0.01710.0201-0.0191-0.1033-0.0080.2724-0.4150.03330.8673-0.2509-0.08470.88550.00210.07353.2929-16.0507-34.1898
40.11610.10060.20720.14130.06490.74540.0309-0.0607-0.04420.0833-0.0153-0.05550.00070.0755-0.01560.7405-0.0116-0.02640.62760.0160.222432.4072-4.94785.4443
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A113 - 599
2X-RAY DIFFRACTION2B113 - 599
3X-RAY DIFFRACTION3C113 - 599
4X-RAY DIFFRACTION4D113 - 599

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