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- PDB-4to5: Structure basis of cellular dNTP regulation, SAMHD1-GTP-dTTP-dCTP... -

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Basic information

Entry
Database: PDB / ID: 4to5
TitleStructure basis of cellular dNTP regulation, SAMHD1-GTP-dTTP-dCTP 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
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / THYMIDINE-5'-TRIPHOSPHATE / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 2.0Mar 30, 2022Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
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_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn
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_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
Revision 2.1Sep 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
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,40420
Polymers238,4174
Non-polymers5,98716
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28520 Å2
ΔGint-69 kcal/mol
Surface area67850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.459, 145.121, 98.233
Angle α, β, γ (deg.)90.000, 114.130, 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

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Protein , 1 types, 4 molecules ACDB

#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, 20 molecules

#2: Chemical
ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxycytidine triphosphate


Mass: 467.157 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#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-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
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: 2.8→50 Å / Num. obs: 56679 / % possible obs: 99.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.188 / Χ2: 1.563 / Net I/av σ(I): 6.897 / Net I/σ(I): 6.9 / Num. measured all: 253013
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
2.8-2.854.328241.50499.8
2.85-2.94.328341.47799.9
2.9-2.964.428021.49699.8
2.96-3.024.428641.50199.8
3.02-3.084.528191.54899.80.942
3.08-3.154.527701.60499.80.89
3.15-3.234.528841.64599.80.721
3.23-3.324.528091.65299.90.625
3.32-3.424.528221.799.90.496
3.42-3.534.528401.76899.80.406
3.53-3.654.528611.77199.90.325
3.65-3.84.528191.69899.90.273
3.8-3.974.528261.75599.70.233
3.97-4.184.528191.7899.60.201
4.18-4.444.428101.7799.50.184
4.44-4.794.528521.70199.10.167
4.79-5.274.528211.44599.40.158
5.27-6.034.528531.33599.70.153
6.03-7.594.528491.12199.70.127
7.59-504.729011.03399.30.098

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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: 2.8→50 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.902 / SU B: 104.168 / SU ML: 0.776 / Cross valid method: THROUGHOUT / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2846 2852 5.1 %RANDOM
Rwork0.271 53620 --
obs0.2717 56472 96.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.85 Å2 / Biso mean: 13.232 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-11.14 Å2-0 Å29.23 Å2
2---16.33 Å20 Å2
3----2.2 Å2
Refinement stepCycle: final / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15679 0 360 4 16043
Biso mean--67.67 74.36 -
Num. residues----1919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01916453
X-RAY DIFFRACTIONr_bond_other_d0.0060.0215617
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.98422296
X-RAY DIFFRACTIONr_angle_other_deg1.239335966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.93851919
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.08323.938805
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94152920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.62815112
X-RAY DIFFRACTIONr_chiral_restr0.0790.22351
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02118221
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023859
X-RAY DIFFRACTIONr_mcbond_it0.8561.2137688
X-RAY DIFFRACTIONr_mcbond_other0.8561.2127687
X-RAY DIFFRACTIONr_mcangle_it1.5181.8179603
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A305380.1
12C305380.1
21A303940.1
22D303940.1
31A304870.09
32B304870.09
41C306400.09
42D306400.09
51C306600.09
52B306600.09
61D306530.09
62B306530.09
LS refinement shellHighest resolution: 2.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 116 -
Rwork0.407 2568 -
all-2684 -
obs--62 %
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)
10.90020.01480.02671.4353-0.03841.3430.05070.23690.0353-0.11340.0156-0.2731-0.0510.3053-0.06630.5713-0.0412-0.48661.3421-0.01520.5326-6.370914.4358-33.8045
21.1477-0.1636-0.55371.38090.10052.2625-0.0362-0.09950.05410.03250.00060.2397-0.0695-0.51940.03570.60220.0052-0.58511.4953-0.01090.6245-44.593319.8167-1.4343
31.29190.4719-0.74522.07410.16111.5522-0.0233-0.2091-0.11530.088-0.0815-0.15450.0280.24190.10480.6510.0102-0.5821.2850.02970.5383-10.196610.68425.2793
40.6563-0.7166-0.04671.8760.87651.63-0.15220.4388-0.12140.1354-0.18180.32530.3388-0.69220.3340.824-0.3268-0.59781.8728-0.140.8097-39.2364-0.7464-34.5738
516.23433.22628.37810.64771.66064.3796-0.25910.43-0.0973-0.0480.1465-0.033-0.22660.22470.11260.3820.0133-0.13380.62190.03120.5557-7.666714.043-32.2628
61.89491.8268-3.51061.8923-3.68897.3813-0.05570.2289-0.0395-0.01120.134-0.00010.0412-0.1585-0.07830.16010.0202-0.0770.3525-0.0930.1446-10.8051-4.9915-26.3975
750.5602-7.185913.11541.0327-1.85523.4332-0.04431.0139-0.00660.0033-0.08010.0301-0.04190.26280.12450.2642-0.0013-0.05850.4874-0.06170.5391-43.076618.6925-2.3588
80.3056-1.7549-1.177710.66077.14924.8252-0.0094-0.0165-0.0315-0.11080.02060.1277-0.0363-0.0347-0.01110.2844-0.2284-0.13270.37240.21890.366-37.6858-0.03150.7467
930.202-6.6477-26.55741.50145.930923.5821-0.20470.0242-0.5961-0.0831-0.05940.0468-0.1632-0.03140.26410.8594-0.08010.1510.4213-0.01670.5032-11.009210.68253.3073
100.2020.0545-1.380.0318-0.717217.63250.19050.03420.03020.02080.0481-0.0007-0.9766-0.9554-0.23860.3275-0.06080.04140.11570.02420.2319-16.26828.962-3.433
1116.69846.4549-13.63730.1576-28.991631.4790.20430.47980.3953-0.25560.09210.13850.1216-0.3467-0.29640.2999-0.0186-0.09560.5133-0.11290.3701-38.26780.4149-32.9293
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A114 - 598
2X-RAY DIFFRACTION2B114 - 599
3X-RAY DIFFRACTION3C114 - 599
4X-RAY DIFFRACTION4D114 - 599
5X-RAY DIFFRACTION5A701
6X-RAY DIFFRACTION6A702
7X-RAY DIFFRACTION6C701
8X-RAY DIFFRACTION6D701
9X-RAY DIFFRACTION7B703
10X-RAY DIFFRACTION8B704
11X-RAY DIFFRACTION8C703
12X-RAY DIFFRACTION8D704
13X-RAY DIFFRACTION9C702
14X-RAY DIFFRACTION10A703 - 704
15X-RAY DIFFRACTION10B701
16X-RAY DIFFRACTION11D702

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