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- PDB-4zwe: Crystal structure of the dGTP-bound catalytic core of SAMHD1 T592... -

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Basic information

Entry
Database: PDB / ID: 4zwe
TitleCrystal structure of the dGTP-bound catalytic core of SAMHD1 T592V mutant
ComponentsDeoxynucleoside triphosphate triphosphohydrolase SAMHD1
KeywordsHYDROLASE / Phosphorylation / Tetramer stability / dNTPase / HIV-1 Restriction
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 / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsTang, C. / Ji, X. / Xiong, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI102778 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Impaired dNTPase Activity of SAMHD1 by Phosphomimetic Mutation of Thr-592.
Authors: Tang, C. / Ji, X. / Wu, L. / Xiong, Y.
History
DepositionMay 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact ...pdbx_audit_support / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_ref_seq_dif
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq_dif.details
Revision 1.4Sep 27, 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 / struct_ncs_dom_lim
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_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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)244,61721
Polymers238,4094
Non-polymers6,20817
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28290 Å2
ΔGint-55 kcal/mol
Surface area68700 Å2
MethodPISA
2
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,80311
Polymers119,2042
Non-polymers3,5999
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8620 Å2
ΔGint-24 kcal/mol
Surface area39690 Å2
MethodPISA
3
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,29610
Polymers119,2042
Non-polymers3,0928
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-16 kcal/mol
Surface area39950 Å2
MethodPISA
4
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,81310
Polymers119,2042
Non-polymers2,6098
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-34 kcal/mol
Surface area39800 Å2
MethodPISA
5
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,32011
Polymers119,2042
Non-polymers3,1169
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-28 kcal/mol
Surface area39910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.083, 146.091, 98.463
Angle α, β, γ (deg.)90.000, 115.030, 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: THR / Beg label comp-ID: THR / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 114 - 599 / Label seq-ID: 2 - 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: 59602.203 Da / Num. of mol.: 4 / Fragment: residues 113-626 / Mutation: H206R, D207N, T592V
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.: 12 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 7.4 / 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: Feb 16, 2015
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: 54764 / % possible obs: 98.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.099 / Rrim(I) all: 0.199 / Χ2: 1.001 / Net I/av σ(I): 8.714 / Net I/σ(I): 3.2 / Num. measured all: 379452
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.8-2.857.127440.3330.7360.91199.7
2.85-2.97.127260.3930.6460.92398.8
2.9-2.96727640.4370.590.93499.3
2.96-3.02727220.5570.5120.92199.1
3.02-3.08727250.5750.4660.92698.8
3.08-3.156.927720.6380.3850.95198.80.94
3.15-3.236.726950.6990.3370.94299.10.8130.882
3.23-3.326.326880.7620.2850.95497.40.6690.729
3.32-3.426.826830.8650.2240.9797.30.5460.591
3.42-3.537.227860.9070.1850.96999.30.4650.501
3.53-3.657.127270.9450.1480.9999.30.3690.398
3.65-3.87.127360.9610.1161.03499.50.290.313
3.8-3.97727650.9750.0921.06399.50.2270.245
3.97-4.186.827550.9780.0781.09899.20.190.206
4.18-4.446.426710.9830.0661.124960.1560.169
4.44-4.797.227730.9870.0571.09499.70.1420.153
4.79-5.277.227490.9890.0551.06399.40.1390.149
5.27-6.03727840.9870.0581.0599.30.1420.153
6.03-7.596.827050.9910.0441.04796.90.1070.116
7.59-506.927940.9940.0331.06980.0810.088

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZB

4bzb


Resolution: 2.81→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.917 / SU B: 39.58 / SU ML: 0.334 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 2789 5.1 %RANDOM
Rwork0.208 ---
obs0.2101 51938 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 172.06 Å2 / Biso mean: 70.01 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å21.59 Å2
2---1.21 Å20 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 2.81→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15700 0 377 3 16080
Biso mean--70.62 54.97 -
Num. residues----1920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01916484
X-RAY DIFFRACTIONr_bond_other_d0.0070.0215639
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.98622342
X-RAY DIFFRACTIONr_angle_other_deg1.425336005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.90751916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08223.975810
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.365152924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.26115112
X-RAY DIFFRACTIONr_chiral_restr0.0730.22346
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02118258
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023882
X-RAY DIFFRACTIONr_mcbond_it3.1344.9057682
X-RAY DIFFRACTIONr_mcbond_other3.1334.9057681
X-RAY DIFFRACTIONr_mcangle_it4.937.3579592
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A301540.12
12B301540.12
21A304460.11
22C304460.11
31A303780.11
32D303780.11
41B302740.12
42C302740.12
51B301580.12
52D301580.12
61C304070.11
62D304070.11
LS refinement shellResolution: 2.806→2.879 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 178 -
Rwork0.308 3564 -
all-3742 -
obs--91.07 %
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)
10.48070.0869-0.1480.57890.05510.2616-0.03460.03140.02060.0245-0.00570.1336-0.0471-0.07650.04030.26590.0026-0.17220.0239-0.00010.1528-21.33133.870243.3058
20.62840.1621-0.17450.32730.23410.7329-0.06280.1598-0.0585-0.10170.1229-0.1063-0.11920.1447-0.06010.3064-0.0647-0.12030.1228-0.03640.121817.1531-0.760111.2939
30.46720.1239-0.02340.50020.16120.3692-0.11850.214-0.1049-0.08320.05090.04690.0849-0.0770.06760.3403-0.0727-0.13570.1158-0.05640.1394-15.5163-16.13310.3591
40.4537-0.0186-0.02890.76350.03340.33190.0172-0.0917-0.06140.10110.0413-0.16160.0490.1142-0.05840.28170.0054-0.20880.0556-0.00620.172713.3121-3.981250.1114
51.20821.8181.32132.7482.02121.5746-0.0632-0.00890.3214-0.0575-0.00690.44850.07510.00720.070.3664-0.0558-0.28820.1880.00341.0306-22.15093.296342.8916
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A114 - 599
2X-RAY DIFFRACTION1A700 - 900
3X-RAY DIFFRACTION2B114 - 599
4X-RAY DIFFRACTION2B700 - 900
5X-RAY DIFFRACTION3C114 - 599
6X-RAY DIFFRACTION3C700 - 900
7X-RAY DIFFRACTION4D114 - 599
8X-RAY DIFFRACTION4D700 - 900
9X-RAY DIFFRACTION5E1 - 28

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