PDB-5ao3: Crystal structure of human SAMHD1 (amino acid residues 115-626) b...

ID or keywords:

Entry

Database: PDB / ID: 5ao3

Title

Crystal structure of human SAMHD1 (amino acid residues 115-626) bound to GTP

Components

DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1

Keywords

HYDROLASE / DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE / HIV RESTRICTION FACTOR

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 ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.004 Å

Authors

Schwefel, D. / Taylor, I.A.

Citation

Journal: Plos Pathog. / Year: 2015
Title: Phospho-Dependent Regulation of Samhd1 Oligomerisation Couples Catalysis and Restriction.
Authors: Arnold, L.H. / Groom, H.C.T. / Kunzelmann, S. / Schwefel, D. / Caswell, S.J. / Ordonez, P. / Mann, M.C. / Rueschenbaum, S. / Goldstone, D.C. / Pennell, S. / Howell, S.A. / Stoye, J.P. / ...

History

Deposition	Sep 9, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 20, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ao3.cif.gz	705.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5ao3.ent.gz	579.4 KB	Display	PDB format
PDBx/mmJSON format	5ao3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ao/5ao3 ftp://data.pdbj.org/pub/pdb/validation_reports/ao/5ao3	HTTPS FTP

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Related structure data

Related structure data	5ao0C 5ao1C 5ao2C 5ao4C 3u1nS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6u6z-d 6nd1-d 3u1n-d 2yw9-d 5ao2-d 1ooz-1 0280 6u6x-d Search similar-shape structures by Omokage search (details) 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

A: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1

B: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1

C: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1

D: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	81.919, 95.733, 97.592
Angle α, β, γ (deg.)	91.37, 108.97, 115.33
Int Tables number	1
Space group name H-M	P1

#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 / SAMHD1 Mass: 62274.141 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 115-626 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases
#2: Chemical	ChemComp-FE / FE (III) ION / Iron Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#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-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.71 Å³/Da / Density % sol: 54.61 % / Description: NONE
Crystal grow	Details: 0.2 M AMMONIUM SULPHATE, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
Detector	Type: DECTRIS PILATUS / Detector: PIXEL
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 3→30 Å / Num. obs: 45153 / % possible obs: 90.9 % / Observed criterion σ(I): -3 / Redundancy: 1.73 % / R_merge(I) obs: 0.06 / Net I/σ(I): 10.52
Reflection shell	Resolution: 3→3.18 Å / Redundancy: 1.69 % / R_merge(I) obs: 0.41 / Mean I/σ(I) obs: 1.9 / % possible all: 83.1

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.8.4_1496)	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U1N

3u1n

Resolution: 3.004→29.657 Å / SU ML: 0.47 / σ(F): 1.99 / Phase error: 27.73 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2473	2274	5 %
R_work	0.1771	-	-
obs	0.1807	45128	91.11 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.004→29.657 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13781	0	187	5	13973

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	14923
X-RAY DIFFRACTION	f_angle_d	1.338	20167
X-RAY DIFFRACTION	f_dihedral_angle_d	15.814	5643
X-RAY DIFFRACTION	f_chiral_restr	0.059	2127
X-RAY DIFFRACTION	f_plane_restr	0.007	2575

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 (%)
3.0037-3.069	0.3888	102	0.2843	1924	X-RAY DIFFRACTION	67
3.069-3.1403	0.3404	171	0.2692	2729	X-RAY DIFFRACTION	93
3.1403-3.2187	0.3569	151	0.2644	2753	X-RAY DIFFRACTION	95
3.2187-3.3056	0.3542	151	0.2331	2780	X-RAY DIFFRACTION	94
3.3056-3.4028	0.2992	159	0.2085	2793	X-RAY DIFFRACTION	95
3.4028-3.5125	0.314	109	0.2054	2772	X-RAY DIFFRACTION	93
3.5125-3.6378	0.2797	152	0.1974	2769	X-RAY DIFFRACTION	94
3.6378-3.7832	0.244	150	0.1843	2684	X-RAY DIFFRACTION	92
3.7832-3.955	0.2366	137	0.1705	2736	X-RAY DIFFRACTION	92
3.955-4.1629	0.2363	135	0.156	2719	X-RAY DIFFRACTION	92
4.1629-4.423	0.2087	158	0.1443	2622	X-RAY DIFFRACTION	90
4.423-4.7632	0.1923	128	0.1491	2696	X-RAY DIFFRACTION	91
4.7632-5.2401	0.2545	151	0.146	2694	X-RAY DIFFRACTION	92
5.2401-5.993	0.2374	134	0.1714	2762	X-RAY DIFFRACTION	93
5.993-7.53	0.2356	148	0.1849	2715	X-RAY DIFFRACTION	93
7.53-29.6589	0.1946	138	0.1542	2706	X-RAY DIFFRACTION	92

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	0.2637	0.132	-0.1778	0.1453	-0.0715	0.5953	0.0893	-0.0708	-0.1341	0.0606	-0.0977	-0.0624	0.1981	-0.0465	-0	0.2925	-0.0386	-0.0011	0.1514	0.0436	0.2345	-18.8583	10.4266	19.1779
2	0.5284	0.1739	-0.161	0.1036	-0.0928	0.076	-0.0287	-0.0896	-0.1992	-0.0628	-0.1068	-0.0896	0.0852	-0.0614	-0.0456	0.4186	0.0052	0.0213	0.3179	-0.059	0.3657	-11.188	2.4587	3.1164
3	0.0389	0.0646	-0.047	0.1127	-0.0902	0.0729	-0.0332	0.0272	-0.1475	0.2065	-0.0156	0.0036	0.0347	0.1072	-0.0152	0.293	0.0166	0.0309	0.254	-0.0887	0.2734	-10.7544	24.6086	7.1182
4	-0.0007	0.0024	-0.0007	0.0065	0.0134	0.0302	-0.0044	-0.0299	0.004	0.1396	0.0143	-0.0215	-0.0529	0.0662	0.0153	0.4446	-0.1073	0.019	0.396	0.0117	0.1648	-19.8783	27.8961	35.4674
5	0.0687	0.109	-0.0311	0.1657	-0.0639	0.1418	-0.0916	-0.3838	0.0562	0.0541	0.0168	-0.0681	-0.1847	0.0799	0	0.2635	0.0153	0.0233	0.3057	-0.0156	0.232	-10.7352	38.886	21.1188
6	-0.0008	0.0219	-0.0195	0.019	-0.0544	0.1811	-0.1157	0.0267	-0.3808	0.0667	-0.0087	-0.0394	0.02	0.2975	-0.0246	0.2138	0.0287	0.0521	0.2551	-0.0616	0.4236	-0.9378	27.6806	11.0572
7	0.0027	-0.0046	-0.0316	0.0251	0.0476	0.3712	0.0335	0.1302	0.0481	-0.0238	-0.0179	-0.062	-0.0683	0.0403	-0.0631	0.2601	-0.0517	0.0387	0.4916	-0.0414	0.3571	5.5996	43.5308	11.8257
8	0.3915	-0.0139	0.0334	0.0263	0.0689	0.4872	-0.0442	0.1641	0.2045	-0.0407	0.0721	-0.0863	-0.2536	0.0374	0.0039	0.387	-0.0118	-0.0257	0.1938	0.0907	0.3106	-20.2704	8.8241	-36.6249
9	0.3372	-0.0344	0.0015	0.0982	-0.0567	0.0469	0.024	-0.14	-0.0845	0.0813	0.0282	-0.0115	-0.2374	0.093	0.0079	0.3124	-0.0458	-0.0039	0.1042	-0.0192	0.1961	-11.4902	11.3407	-21.0738
10	-0.0101	-0.0018	-0.0044	0.058	-0.0385	0.0314	0.0013	0.1343	-0.1371	-0.2157	0.0065	-0.0946	0.0321	0.0275	0.0009	0.3147	-0.0358	-0.0165	0.3231	-0.0603	0.1828	-15.8598	-13.7686	-41.9179
11	0.2346	-0.0229	0.0913	0.0451	-0.0592	0.2479	-0.1592	0.29	-0.0634	-0.0854	0.0726	-0.0883	-0.0262	0.112	-0.0013	0.3048	-0.007	-0.0003	0.3609	0.0289	0.2283	-12.5002	-16.5511	-38.5349
12	0.016	0.0171	-0.024	0.0178	-0.0297	0.0525	-0.1406	0.1415	-0.0616	-0.1158	0.0144	-0.1435	0.2579	0.0725	-0.0082	0.3163	0.1031	0.0251	0.2489	-0.0461	0.3139	2.656	-26.531	-34.2026
13	0.0864	0.056	0.0233	0.1025	-0.0178	0.1117	-0.0026	-0.0137	0.1145	0.0624	-0.1677	-0.0033	-0.1029	0.1736	-0.1115	0.1469	-0.1056	-0.1208	0.2178	0.0015	0.3098	-3.3783	3.2654	-22.4048
14	0.0407	0.0563	0.0115	0.1271	0.1073	0.1675	0.0714	-0.2205	-0.0581	0.0851	0.0832	-0.0222	0.0743	-0.0066	0.0234	0.2908	-0.0102	-0.0167	0.4958	0.0361	0.4466	5.6175	-24.0569	-27.405
15	0.1704	0.0483	0.0823	0.1974	0.0934	0.0775	-0.0041	-0.0789	0.0787	-0.1029	0.0073	0.1385	0.0262	0.034	-0	0.2655	0.003	-0.021	0.2977	-0.0169	0.3776	-35.0064	41.1647	4.8479
16	0.0151	0.0242	-0.0175	0.0355	-0.0238	0.0421	-0.0601	-0.1322	0.0365	0.128	0.1383	-0.0611	-0.0953	-0.1258	0.0365	0.3143	0.0699	-0.0437	0.3206	0.0464	0.4519	-43.5302	42.6613	-2.9034
17	0.0059	0.0012	0.0308	0.0303	0.0364	0.1053	-0.0674	0.0538	0.0916	-0.1631	0.0814	0.1448	-0.0185	-0.1633	0.0533	0.334	0.0551	-0.1299	0.301	-0.0097	0.3362	-43.1233	29.1691	-11.9414
18	0.1201	0.1349	0.0426	0.263	0.0132	0.1712	0.0135	-0.2651	0.1043	0.1124	-0.0819	0.2619	-0.0474	-0.2047	-0.0205	0.2205	-0.0177	0.0246	0.3856	-0.0169	0.2307	-45.322	29.2644	23.6674
19	0.1182	-0.0643	0.1075	0.2118	0.1001	0.3073	-0.0054	-0.1432	-0.0849	0.0309	-0.1051	0.2902	0.102	-0.2298	-0.329	-0.1056	-0.2143	-0.0483	0.2445	0.0751	0.3017	-55.6625	23.1221	9.1459
20	0.0083	-0.0128	-0.0097	0.0157	0.0054	0.0339	0.0123	-0.0672	-0.0198	0.0355	0.0076	0.002	0.0493	-0.0041	0.0332	0.3634	0.0242	0.0667	0.562	0.099	0.5583	-63.1171	13.5404	19.5379
21	0.1716	-0.0175	-0.0807	0.0567	-0.039	0.1081	-0.0151	-0.0301	0.0215	0.0468	-0.035	0.0206	-0.0196	-0.1363	0	0.2691	0.0404	0.01	0.2258	-0.0213	0.2444	-35.0308	-18.8632	-19.847
22	0.0597	0.0598	0.0052	0.0716	-0.0014	0.2189	0.0692	0.1617	0.0633	0.032	-0.013	0.0003	0.1185	-0.2012	0.0045	0.3156	-0.0347	0.0456	0.3124	0.0122	0.3519	-40.8724	-26.0929	-15.7176
23	0.0078	0.0032	-0.0012	0.1925	-0.0656	0.025	0.1293	0.0412	0.0353	0.2367	-0.0459	0.1346	-0.0414	-0.1045	0.0012	0.2318	-0.0165	0.1028	0.1598	-0.0316	0.2182	-43.1779	-9.4991	-3.7024
24	0.1892	0.0635	0.0292	0.0894	-0.0601	0.0664	-0.0154	0.1459	0.0278	-0.1528	-0.0348	0.119	0.068	-0.2152	-0.0006	0.2494	-0.0298	-0.0137	0.3533	-0.0079	0.1634	-40.6263	-12.4299	-41.6501
25	0.122	-0.0824	-0.0158	0.0643	0.0449	0.1387	-0.0427	0.0535	0.0538	-0.0295	-0.0535	0.0103	-0.0542	0.0177	-0.1727	0.1443	0.06	-0.0068	0.3792	0.0902	0.4211	-57.0153	-3.5029	-33.6669
26	0.4345	0.1159	-0.0639	0.6449	-0.0527	0.6273	0.0455	0.2224	0.1601	0.1886	-0.0311	0.3257	0.0284	-0.181	-0.245	-0.2199	0.337	-0.0122	0.2312	0.0886	0.283	-55.6548	-3.5388	-24.2697
27	0.0365	-0.0348	-0.051	0.0308	0.046	0.0752	0.1278	0.1716	0.1218	-0.0835	-0.0682	-0.0207	-0.0341	0.0107	0.18	0.4311	0.1666	-0.2102	0.5672	0.0752	0.7825	-63.5277	6.1229	-35.2456

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 115 THROUGH 323 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 324 THROUGH 352 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 353 THROUGH 392 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 393 THROUGH 423 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 424 THROUGH 482 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 483 THROUGH 558 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 559 THROUGH 583 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 115 THROUGH 291 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 292 THROUGH 372 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 373 THROUGH 411 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 412 THROUGH 481 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 482 THROUGH 504 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 505 THROUGH 558 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 559 THROUGH 583 )
15	X-RAY DIFFRACTION	15	CHAIN 'C' AND (RESID 114 THROUGH 260 )
16	X-RAY DIFFRACTION	16	CHAIN 'C' AND (RESID 261 THROUGH 323 )
17	X-RAY DIFFRACTION	17	CHAIN 'C' AND (RESID 324 THROUGH 372 )
18	X-RAY DIFFRACTION	18	CHAIN 'C' AND (RESID 373 THROUGH 481 )
19	X-RAY DIFFRACTION	19	CHAIN 'C' AND (RESID 482 THROUGH 558 )
20	X-RAY DIFFRACTION	20	CHAIN 'C' AND (RESID 559 THROUGH 583 )
21	X-RAY DIFFRACTION	21	CHAIN 'D' AND (RESID 114 THROUGH 232 )
22	X-RAY DIFFRACTION	22	CHAIN 'D' AND (RESID 233 THROUGH 323 )
23	X-RAY DIFFRACTION	23	CHAIN 'D' AND (RESID 324 THROUGH 372 )
24	X-RAY DIFFRACTION	24	CHAIN 'D' AND (RESID 373 THROUGH 449 )
25	X-RAY DIFFRACTION	25	CHAIN 'D' AND (RESID 450 THROUGH 482 )
26	X-RAY DIFFRACTION	26	CHAIN 'D' AND (RESID 483 THROUGH 558 )
27	X-RAY DIFFRACTION	27	CHAIN 'D' AND (RESID 559 THROUGH 583 )

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