PDB-8gb2: Crystal structure of Apo-SAMHD1

ID or keywords:

Entry

Database: PDB / ID: 8gb2

Title

Crystal structure of Apo-SAMHD1

Components

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

Keywords

HYDROLASE / SAMHD1 / dNTPase / dimer / dimeric

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 / dGTPase activity / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / dGTP catabolic process / DNA strand resection involved in replication fork processing ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.07 Å

Authors

Egleston, M. / Dong, L. / Howlader, A.H. / Bhat, S. / Orris, B. / Bianchet, M.A. / Greenberg, M.M. / Stivers, J.T.

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM056834	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	CA233567	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM131736	United States

Citation

Journal: Acs Chem.Biol. / Year: 2023
Title: Deoxyguanosine-Linked Bifunctional Inhibitor of SAMHD1 dNTPase Activity and Nucleic Acid Binding.
Authors: Egleston, M. / Dong, L. / Howlader, A.H. / Bhat, S. / Orris, B. / Bianchet, M.A. / Greenberg, M.M. / Stivers, J.T.

History

Deposition	Feb 24, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 7, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 1, 2023	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8gb2.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb8gb2.ent.gz	905.3 KB	Display	PDB format
PDBx/mmJSON format	8gb2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8gb2_validation.pdf.gz	477.4 KB	Display	wwPDB validaton report
Full document	8gb2_full_validation.pdf.gz	523.5 KB	Display
Data in XML	8gb2_validation.xml.gz	64.4 KB	Display
Data in CIF	8gb2_validation.cif.gz	86.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gb/8gb2 ftp://data.pdbj.org/pub/pdb/validation_reports/gb/8gb2	HTTPS FTP

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Related structure data

Related structure data	8gb1C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#152 - Aug 2012 cAMP-dependent Protein Kinase similarity (2)

Deposited unit

D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

hetero molecules

239 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

hetero molecules

defined by author&software
Evidence: assay for oligomerization
120 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

hetero molecules

defined by author&software
120 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	202.574, 81.884, 154.026
Angle α, β, γ (deg.)	90.00, 118.52, 90.00
Int Tables number	5
Space group name H-M	C121
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

#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 / hSAMHD1 Mass: 59804.383 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SAMHD1, MOP5 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.57 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 17% PEG3350, 0.15 M Ammonium citrate pH 7.3, 293 K, 5 mg/mL, 1 uL protein + 2 uL ML.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 16, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9201 Å / Relative weight: 1
Reflection	Resolution: 3.07→27.61 Å / Num. obs: 41553 / % possible obs: 99.43 % / Redundancy: 3.6 % / B_iso Wilson estimate: 81.07 Å² / CC_1/2: 1 / R_merge(I) obs: 0.13 / R_pim(I) all: 0.082 / Net I/σ(I): 99.8
Reflection shell	Resolution: 3.07→3.18 Å / Redundancy: 3.3 % / R_merge(I) obs: 2.16 / Mean I/σ(I) obs: 99.9 / Num. unique obs: 4038 / CC_1/2: 0.7 / R_pim(I) all: 1.32 / % possible all: 97.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
Coot	0.9.8	model building
MOLREP	11.9.02	phasing
DIMPLE		data reduction
DIMPLE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.07→27.61 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.26 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2503	2113	5.09 %
R_work	0.1973	-	-
obs	0.2	41532	99.37 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.07→27.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14529	0	4	1	14534

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	14868
X-RAY DIFFRACTION	f_angle_d	1.348	20052
X-RAY DIFFRACTION	f_dihedral_angle_d	4.979	1955
X-RAY DIFFRACTION	f_chiral_restr	0.064	2130
X-RAY DIFFRACTION	f_plane_restr	0.026	4356

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.07-3.14	0.3227	118	0.2947	2477	X-RAY DIFFRACTION	94
3.14-3.22	0.2999	152	0.2658	2615	X-RAY DIFFRACTION	100
3.22-3.3	0.2729	158		2610	X-RAY DIFFRACTION	100
3.3-3.4	0.293	130	0.2637	2618	X-RAY DIFFRACTION	100
3.4-3.51	0.3068	148	0.2556	2615	X-RAY DIFFRACTION	100
3.51-3.64	0.2768	126	0.2339	2638	X-RAY DIFFRACTION	100
3.64-3.78	0.3002	141	0.2162	2629	X-RAY DIFFRACTION	100
3.78-3.95	0.2726	123	0.2045	2638	X-RAY DIFFRACTION	100
3.95-4.16	0.2675	156	0.1889	2626	X-RAY DIFFRACTION	100
4.16-4.42	0.2234	155	0.1749	2612	X-RAY DIFFRACTION	100
4.42-4.76	0.2123	131	0.166	2659	X-RAY DIFFRACTION	100
4.76-5.24	0.1933	137	0.1638	2645	X-RAY DIFFRACTION	100
5.24-5.99	0.2642	126	0.19	2676	X-RAY DIFFRACTION	100
5.99-7.52	0.2783	137	0.2016	2679	X-RAY DIFFRACTION	100
7.52-27.61	0.2189	175	0.1642	2694	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	2.7668	-0.2388	1.3096	2.3811	0.0994	4.714	-0.0402	-0.4282	0.2835	0.4524	0.0049	0.1396	-0.3655	-0.3383	0.0173	0.659	0.011	0.1644	0.4756	0.0166	0.5539	8.5085	-6.0798	53.4511
2	2.2513	-0.2356	-0.4378	3.5214	3.474	3.759	-0.1472	-0.1339	0.6297	-0.3217	-0.0229	0.1484	-2.1224	0.1426	0.0718	1.0237	-0.0205	0.1275	0.4819	-0.002	0.6315	18.9807	-1.1555	50.8141
3	2.401	-0.7466	0.9702	2.4375	-0.6753	3.5078	-0.052	0.0164	0.3929	0.1659	-0.0448	-0.1209	-0.4053	0.1291	0.1227	0.7197	0.0087	0.0664	0.3716	0.014	0.6741	8.2273	0.2912	37.8842
4	4.7587	1.0188	-0.8297	6.3881	-1.1711	2.0261	0.1518	0.5094	1.239	0.601	0.3069	-0.1624	-1.6492	-0.4462	-0.5587	1.2333	0.0276	-0.078	0.6961	0.2143	1.2143	-0.4152	20.2824	24.0241
5	5.4318	-1.8192	2.1043	3.2765	-1.2366	3.4755	-0.9488	-0.0729	0.9999	0.0897	0.0075	-0.3269	-1.1538	0.1469	0.9581	1.1457	-0.0765	0.0977	0.55	0.049	0.8405	14.1574	13.5085	32.3058
6	2.9614	0.1634	-0.9117	1.9443	-0.1318	6.0535	-0.0037	0.2248	-0.2091	-0.5128	0.1583	-0.0532	0.2676	0.1275	-0.0959	0.5602	0.0083	0.0447	0.4093	0.0101	0.4973	9.0992	-21.1207	19.028
7	1.8899	0.1653	0.3787	2.201	-0.4151	6.1128	0.1244	0.4023	-0.4364	-0.5541	0.088	-0.4509	0.8955	0.9147	-0.3626	0.7683	0.0555	0.1351	0.6134	-0.1016	0.7041	18.2258	-29.9304	16.6326
8	3.7987	0.1095	0.6057	2.0802	-0.2129	3.2993	-0.0062	-0.2081	-0.3976	0.0119	0.1937	0.1288	0.152	-0.1554	-0.1976	0.5591	-0.0892	0.0454	0.3615	0.1201	0.6374	1.9695	-27.0133	32.6216
9	3.1077	-1.2497	-1.054	4.8611	1.2866	4.698	-0.1203	-0.1774	-0.5447	-0.2071	0.2189	0.7101	0.5446	-0.2376	-0.1618	0.9075	-0.1675	-0.0768	0.6614	0.2298	0.9979	-2.5164	-44.9639	44.0653
10	8.0944	2.4204	-7.4135	1.8484	-2.1838	7.1686	-0.282	-0.0399	-1.2869	-0.6282	-0.1875	-0.4894	1.0324	0.662	0.5814	1.0199	0.1584	0.0363	1.1188	0.0011	0.9899	17.3891	-39.6713	28.4396
11	1.8779	1.3269	0.5965	4.1134	-1.1978	2.3143	0.0281	-0.2463	-0.9559	0.1832	0.2203	-0.3028	0.9916	-0.069	-0.0729	0.9304	-0.053	-0.2045	0.5699	0.1078	0.8323	4.6178	-45.0821	44.2694
12	4.274	-0.3138	2.4911	4.0087	-0.0219	4.5544	0.1168	0.4274	-0.2563	0.5163	-0.1943	-0.5481	-0.0262	0.2225	-0.0298	0.6835	-0.0106	-0.0927	0.8826	0.067	1.0725	51.1708	-19.0551	47.0238
13	4.3281	-0.1551	1.4888	3.7623	-0.4958	2.9855	0.1998	0.9542	-0.9732	0.281	0.0525	-1.1952	0.4816	1.1586	-0.1192	0.6779	0.026	-0.2321	1.1252	-0.079	1.5787	64.7279	-25.09	48.4203
14	2.5498	-4.9628	1.7056	9.7945	-2.76	4.1115	1.1119	0.6531	-1.6237	-0.0994	-0.2664	-0.5803	1.6989	0.8801	-0.5397	1.2656	0.1721	-0.1999	1.103	-0.0529	1.6212	53.502	-38.2936	50.7504
15	5.2994	1.9514	0.0124	5.0015	0.261	5.2377	0.5804	0.9647	-1.1371	0.4544	0.0073	-0.5586	0.4496	0.4954	-0.5014	0.7209	0.1212	-0.1557	0.9739	-0.0367	1.0597	42.8298	-29.7724	40.0546
16	3.213	-0.6222	-0.0446	1.4626	0.7358	1.6359	0.2392	1.2806	-0.13	-0.1167	0.004	-0.685	0.1326	1.1041	-0.1801	0.8229	0.0106	0.1723	1.9182	0.0249	1.2878	67.0296	-21.0245	29.1699
17	0.7079	-0.5223	0.8431	1.5382	0.9303	2.7573	0.2543	0.1928	-0.3059	-0.5338	0.0209	-0.2691	0.2135	1.5658	-0.0733	1.0087	0.2208	0.0625	1.7319	-0.2676	1.522	65.4665	-35.042	19.8004
18	0.3838	-0.0872	-0.4374	3.4166	0.1859	0.7154	0.2642	1.5195	0.2185	-0.8303	-0.7714	-0.5975	-0.3057	0.3627	0.4732	0.9787	-0.0495	0.1148	2.7399	0.4796	1.1626	52.5913	-4.7103	21.3813
19	0.8732	-0.4918	0.4022	0.7434	0.0823	0.3335	-0.0593	1.2755	0.8659	-0.7918	-0.4628	-0.8243	-0.7549	0.9936	0.5149	1.403	-0.2269	0.2688	2.4137	0.8408	1.7758	58.2259	7.2829	18.1584
20	1.085	1.392	0.4824	3.0811	0.0014	0.4749	-0.4446	1.9406	1.7377	-1.0131	0.2329	-0.7682	-0.2189	0.5933	0.3426	1.814	0.1337	0.1753	3.0861	1.2026	1.7891	48.3042	14.3805	13.366
21	2.836	-1.5874	-0.2329	3.9498	0.241	2.3406	-0.2755	2.244	0.6208	-0.7796	-0.2284	0.0612	-0.3982	0.2665	0.4452	1.0123	-0.1996	-0.1302	1.7345	0.3931	1.0362	36.5769	3.0714	24.7724
22	2.6125	0.4222	1.0803	2.9704	1.2015	4.1621	-0.1487	1.0425	0.4961	-0.3863	-0.1753	-0.9895	-0.597	1.0891	0.2629	0.9597	-0.3243	-0.1691	1.3613	0.405	1.6006	65.082	5.1344	41.0993
23	2.5203	0.2204	1.9559	1.9435	0.2983	4.6858	-1.1202	0.3795	1.3192	-0.2236	-0.1674	-0.567	-1.654	0.1642	1.2172	1.6712	-0.2124	-0.5155	1.0707	0.3148	1.9187	49.1584	15.8601	45.7412

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'D' and (resid 114 through 291 )
2	X-RAY DIFFRACTION	2	chain 'D' and (resid 292 through 323 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 324 through 469 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 470 through 494 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 495 through 582 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 114 through 260 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 261 through 343 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 344 through 450 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 451 through 494 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 495 through 526 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 527 through 582 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 115 through 204 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 205 through 273 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 274 through 309 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 310 through 352 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 353 through 469 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 470 through 582 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 115 through 185 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 186 through 262 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 263 through 310 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 311 through 372 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 373 through 469 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 470 through 582 )

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+
Jul 12, 2017. Major update of PDB

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Yorodumi