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- PDB-4tnq: Structural basis of cellular dNTP regulation, SAMHD1-GTP-dTTP-dTT... -

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Basic information

Entry
Database: PDB / ID: 4tnq
TitleStructural basis of cellular dNTP regulation, SAMHD1-GTP-dTTP-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 / triphosphoric monoester hydrolase activity / dATP catabolic process / dGTPase activity / 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 / triphosphoric monoester hydrolase activity / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / dGTP catabolic process / DNA strand resection involved in replication fork processing / deoxyribonucleotide catabolic process / regulation of innate immune response / negative regulation of type I interferon-mediated signaling pathway / somatic hypermutation of immunoglobulin genes / RNA nuclease activity / 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. / HD/PDEase domain ...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
GUANOSINE-5'-TRIPHOSPHATE / THYMIDINE-5'-TRIPHOSPHATE / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 4, 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 2.0Mar 30, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site_anisotrop / citation ...atom_site_anisotrop / 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 / pdbx_validate_symm_contact / refine_hist / struct_conn / struct_keywords
Item: _atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id ..._atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _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 / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _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 2.1Sep 27, 2023Group: Data collection / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity_src_gen / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _struct_ncs_dom_lim.beg_auth_comp_id ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_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
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,46420
Polymers238,4174
Non-polymers6,04716
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28390 Å2
ΔGint-84 kcal/mol
Surface area67050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.159, 140.292, 97.268
Angle α, β, γ (deg.)90.000, 114.560, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22D
13A
23B
14C
24D
15C
25B
16D
26B

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TRPTRPAA114 - 5982 - 486
21TRPTRPCB114 - 5982 - 486
12TRPTRPAA114 - 5982 - 486
22TRPTRPDC114 - 5982 - 486
13TRPTRPAA114 - 5982 - 486
23TRPTRPBD114 - 5982 - 486
14TRPTRPCB114 - 5982 - 486
24TRPTRPDC114 - 5982 - 486
15ASNASNCB114 - 5992 - 487
25ASNASNBD114 - 5992 - 487
16ASNASNDC114 - 5992 - 487
26ASNASNBD114 - 5992 - 487

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 / 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
#2: Chemical
ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine 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 / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 42.25 %
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: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 61164 / % possible obs: 95.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.089 / Χ2: 1.105 / Net I/av σ(I): 14.595 / Net I/σ(I): 10.6 / Num. measured all: 277014
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.55-2.593.70.38322721.07372.5
2.59-2.643.90.34824941.13778.2
2.64-2.6940.31727351.14984.1
2.69-2.754.20.29328431.16889.7
2.75-2.814.30.27129771.13393.5
2.81-2.874.40.25431011.05898.1
2.87-2.944.40.2232141.1598.9
2.94-3.024.20.19131421.18598.8
3.02-3.114.50.17731911.17699.1
3.11-3.214.90.16131771.19799.8
3.21-3.334.90.13831851.02599.9
3.33-3.464.90.12231991.07699.5
3.46-3.624.80.10731761.09899.4
3.62-3.814.70.09531841.07299.4
3.81-4.054.30.0833207199
4.05-4.3650.08132001.02599.9
4.36-4.84.90.07532121.181100
4.8-5.494.80.06831781.06999.1
5.49-6.924.60.06132211.1199.3
6.92-504.70.05532561.06199.2

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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: 2.55→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 18.789 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1976 2966 4.9 %RANDOM
Rwork0.1614 58175 --
obs0.1631 61141 95.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.63 Å2 / Biso mean: 40.199 Å2 / Biso min: 16.44 Å2
Baniso -1Baniso -2Baniso -3
1-4.11 Å20 Å2-2.02 Å2
2---1.29 Å2-0 Å2
3----0.69 Å2
Refinement stepCycle: final / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15688 0 364 238 16290
Biso mean--37.62 46.26 -
Num. residues----1919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01916446
X-RAY DIFFRACTIONr_bond_other_d0.0070.0215618
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.98422286
X-RAY DIFFRACTIONr_angle_other_deg1.315335967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3951915
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.17723.945806
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.265152919
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.31615112
X-RAY DIFFRACTIONr_chiral_restr0.0860.22349
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02118199
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023845
X-RAY DIFFRACTIONr_mcbond_it2.9563.7097678
X-RAY DIFFRACTIONr_mcbond_other2.9563.7087677
X-RAY DIFFRACTIONr_mcangle_it4.5955.5569587
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A306780.09
12C306780.09
21A305430.1
22D305430.1
31A308450.09
32B308450.09
41C308890.09
42D308890.09
51C309940.09
52B309940.09
61D309260.09
62B309260.09
LS refinement shellResolution: 2.552→2.618 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 142 -
Rwork0.228 3115 -
all-3257 -
obs--69.17 %
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)
10.8484-0.04810.30190.9997-0.66970.9577-0.0338-0.17360.02480.0730.07040.1379-0.1693-0.3213-0.03670.03930.08-0.00240.1866-0.01230.060198.0661-3.6857131.6732
20.640.02270.33760.3751-0.29420.8053-0.02070.242-0.1019-0.34060.06980.08140.2703-0.1897-0.04910.3099-0.0629-0.06760.3062-0.04560.1152101.6197-22.579297.9227
30.4272-0.09270.2410.6099-0.12610.59780.041-0.0614-0.07690.0985-0.099-0.2284-0.03850.07280.0580.0297-0.0279-0.05970.09430.0580.1598131.2179-16.0713137.8923
40.63630.02030.23010.60160.02181.00340.00710.38560.0149-0.2342-0.0993-0.1954-0.00110.32390.09220.09920.04860.09480.29720.06590.1162135.6969-11.491999.4502
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A114 - 598
2X-RAY DIFFRACTION2C114 - 599
3X-RAY DIFFRACTION3D113 - 599
4X-RAY DIFFRACTION4B114 - 599

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