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- PDB-4tnx: Structure basis of cellular dNTP regulation, SAMHD1-GTP-dGTP complex -

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Basic information

Entry
Database: PDB / ID: 4tnx
TitleStructure basis of cellular dNTP regulation, SAMHD1-GTP-dGTP 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
TRIPHOSPHATE / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 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 1.3Mar 30, 2022Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / database_2 ...citation / database_2 / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _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 / _pdbx_struct_oper_list.symmetry_operation / _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 / _struct_keywords.text
Revision 1.4Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)242,89317
Polymers238,4174
Non-polymers4,47713
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26020 Å2
ΔGint-64 kcal/mol
Surface area68480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.886, 140.734, 97.603
Angle α, β, γ (deg.)90.000, 114.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#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 / Fragment: UNP residues 113-626
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

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Non-polymers , 5 types, 262 molecules

#2: Chemical
ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#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: Chemical ChemComp-3PO / TRIPHOSPHATE


Mass: 257.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O10P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.13 Å3/Da / Density % sol: 42.37 %
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: Aug 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 86382 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.136 / Χ2: 1.326 / Net I/av σ(I): 13.232 / Net I/σ(I): 6.3 / Num. measured all: 619894
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Num. unique allΧ2Rmerge(I) obs
2.3-2.346.342761.043
2.34-2.386.842931.038
2.38-2.43743331.045
2.43-2.48742971.068
2.48-2.53743041.073
2.53-2.597.143001.078
2.59-2.667.143081.1160.867
2.66-2.737.142871.1370.699
2.73-2.817.242991.1870.595
2.81-2.97.243211.2420.48
2.9-37.243171.320.386
3-3.127.343131.3950.313
3.12-3.267.343271.5080.247
3.26-3.447.343171.4970.185
3.44-3.657.443081.570.146
3.65-3.937.443541.6850.115
3.93-4.337.543051.7030.099
4.33-4.957.543471.7460.088
4.95-6.247.343591.4960.082
6.24-507.544171.4030.065

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0071refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZB

4bzb


Resolution: 2.31→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 20.793 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.437 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 4335 5 %RANDOM
Rwork0.1879 82017 --
obs0.1898 86352 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.69 Å2 / Biso mean: 53.473 Å2 / Biso min: 22.22 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å20 Å20.03 Å2
2---3.31 Å20 Å2
3---0.83 Å2
Refinement stepCycle: final / Resolution: 2.31→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15730 0 269 249 16248
Biso mean--40.31 44.26 -
Num. residues----1924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01916462
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215634
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.97722303
X-RAY DIFFRACTIONr_angle_other_deg0.831336009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.61651936
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.68824.027817
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.805152936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.71815112
X-RAY DIFFRACTIONr_chiral_restr0.0860.22350
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02118374
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023882
X-RAY DIFFRACTIONr_mcbond_it2.1692.5597738
X-RAY DIFFRACTIONr_mcbond_other2.1692.5587737
X-RAY DIFFRACTIONr_mcangle_it3.5743.8249676
LS refinement shellResolution: 2.31→2.368 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 320 -
Rwork0.319 5395 -
all-5715 -
obs--89.26 %
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)
10.173-0.02620.07830.24280.03640.10070.0379-0.036-0.06270.0444-0.0797-0.1142-0.0283-0.02110.04180.2361-0.0062-0.06980.38030.04150.278929.4484-4.09745.4803
20.2083-0.06560.17650.1195-0.16710.2958-0.05440.0961-0.0235-0.15920.08710.01990.1322-0.129-0.03280.4169-0.1001-0.04750.5241-0.02660.01750.1672-11.0663-34.8318
30.16660.0045-0.00110.0209-0.06150.2679-0.05380.16010.0382-0.0406-0.0619-0.0310.00940.1320.11560.31060.04640.06220.48970.0540.113234.09450.3408-33.1921
40.3853-0.03040.19810.379-0.20420.2035-0.0221-0.07010.00030.03360.01930.025-0.0651-0.07390.00290.25540.0653-0.02730.45150.00990.1702-3.8228.0701-1.0334
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A113 - 599
2X-RAY DIFFRACTION2B114 - 598
3X-RAY DIFFRACTION3C113 - 599
4X-RAY DIFFRACTION4D113 - 599

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