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- PDB-4zwg: Crystal structure of the GTP-dATP-bound catalytic core of SAMHD1 ... -

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Basic information

Entry
Database: PDB / ID: 4zwg
TitleCrystal structure of the GTP-dATP-bound catalytic core of SAMHD1 phosphomimetic T592E 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 / triphosphoric monoester hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / DNA strand resection involved in replication fork processing / deoxyribonucleotide catabolic process ...Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / triphosphoric monoester hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / DNA strand resection involved in replication fork processing / deoxyribonucleotide catabolic process / dGTP catabolic process / negative regulation of type I interferon-mediated signaling pathway / regulation of innate immune response / somatic hypermutation of immunoglobulin genes / RNA nuclease activity / double-strand break repair via homologous recombination / Interferon alpha/beta signaling / site of double-strand break / single-stranded DNA binding / 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'-DEOXYADENOSINE 5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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_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 / _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_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)244,64820
Polymers238,5294
Non-polymers6,11916
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26790 Å2
ΔGint-48 kcal/mol
Surface area64710 Å2
MethodPISA
2
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,34811
Polymers119,2642
Non-polymers3,0849
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-29 kcal/mol
Surface area37070 Å2
MethodPISA
3
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,3009
Polymers119,2642
Non-polymers3,0357
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8720 Å2
ΔGint-28 kcal/mol
Surface area37140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.720, 136.970, 95.843
Angle α, β, γ (deg.)90.000, 113.960, 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: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRPROPROAA114 - 5812 - 469
21THRTHRPROPROBB114 - 5812 - 469
12THRTHRLYSLYSAA114 - 5802 - 468
22THRTHRLYSLYSCC114 - 5802 - 468
13THRTHRTHRTHRAA114 - 5792 - 467
23THRTHRTHRTHRDD114 - 5792 - 467
14ASPASPLYSLYSBB113 - 5801 - 468
24ASPASPLYSLYSCC113 - 5801 - 468
15ASPASPTHRTHRBB113 - 5791 - 467
25ASPASPTHRTHRDD113 - 5791 - 467
16ASPASPTHRTHRCC113 - 5791 - 467
26ASPASPTHRTHRDD113 - 5791 - 467

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: 59632.188 Da / Num. of mol.: 4 / Fragment: residues 113-626 / Mutation: H206R, D207N, T592E
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-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.02 Å3/Da / Density % sol: 39.14 %
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: Jun 7, 2014
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: 82062 / % possible obs: 98.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.119 / Rrim(I) all: 0.188 / Χ2: 1.2 / Net I/av σ(I): 8.375 / Net I/σ(I): 5.2 / Num. measured all: 277496
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.3-2.343.240720.2220.7111.15697.6
2.34-2.383.540580.3450.6641.1498.9
2.38-2.433.541550.3280.6171.13799.30.99
2.43-2.483.441210.3890.5871.172990.939
2.48-2.533.441260.4880.511.17990.8140.963
2.53-2.593.441250.4930.4831.17499.10.7680.91
2.59-2.663.340990.5620.4381.18898.50.6890.819
2.66-2.733.340430.640.3771.18997.80.5870.7
2.73-2.81339980.6790.3461.19996.40.5130.622
2.81-2.93.340720.7730.2831.20998.10.4430.528
2.9-33.541530.8630.2191.21499.40.3560.419
3-3.123.541510.8980.1931.2399.30.3120.368
3.12-3.263.541090.9350.1521.29198.90.2430.288
3.26-3.443.441280.9560.1191.35998.70.1870.223
3.44-3.653.239800.9650.11.50495.90.1530.184
3.65-3.933.440850.9230.0971.09797.60.1520.181
3.93-4.333.641480.9870.0561.10199.40.0920.108
4.33-4.953.541620.9870.0511.15698.90.080.095
4.95-6.243.340840.9870.0531.15297.20.0830.099
6.24-503.441930.9960.0351.1998.20.0560.067

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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: 2.3→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / SU B: 21.467 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.491 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.246 4052 4.9 %RANDOM
Rwork0.205 ---
obs0.2085 77952 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.69 Å2 / Biso mean: 39.809 Å2 / Biso min: 11.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å2-1.29 Å2
2--2.73 Å20 Å2
3----0.66 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15051 0 372 206 15629
Biso mean--40.93 33.9 -
Num. residues----1840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01915818
X-RAY DIFFRACTIONr_bond_other_d0.0070.0214936
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.98521426
X-RAY DIFFRACTIONr_angle_other_deg1.374334372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.51651836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56623.827784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.457152793
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.23315112
X-RAY DIFFRACTIONr_chiral_restr0.0870.22247
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02117522
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023762
X-RAY DIFFRACTIONr_mcbond_it2.4643.3217365
X-RAY DIFFRACTIONr_mcbond_other2.4633.327364
X-RAY DIFFRACTIONr_mcangle_it3.8594.9659191
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A287150.11
12B287150.11
21A283960.12
22C283960.12
31A278340.12
32D278340.12
41B287460.11
42C287460.11
51B281940.11
52D281940.11
61C283010.11
62D283010.11
LS refinement shellResolution: 2.296→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 293 -
Rwork0.319 5405 -
all-5698 -
obs--92.08 %
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)
10.0895-0.0115-0.11060.13040.12070.2552-0.0281-0.03950.00250.01750.0202-0.02080.06480.07410.00790.02310.02390.00620.02670.00180.052763.9504-5.905130.237
20.2188-0.0313-0.03810.067-0.03630.1217-0.02660.0438-0.0073-0.00730.01550.00760.0297-0.06520.01120.0105-0.0182-0.00690.0376-0.00460.05726.98561.17798.1325
30.2057-0.0866-0.07750.09160.0670.3174-0.01110.04040.0552-0.01280.00230.0092-0.0170.06410.00880.012-0.015-0.00310.03460.01550.056659.12315.871797.262
40.1313-0.103-0.03950.15320.050.1678-0.0028-0.00660.02490.0219-0.00780.02590.0188-0.02180.01060.0065-0.00510.01260.0069-0.00380.063232.44748.4877137.9658
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A114 - 900
2X-RAY DIFFRACTION2B113 - 900
3X-RAY DIFFRACTION3C113 - 900
4X-RAY DIFFRACTION4D113 - 900

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