PDB-5ao4: Crystal structure of in vitro phosphorylated human SAMHD1 (amino ...

ID or keywords:

Entry

Database: PDB / ID: 5ao4

Title

Crystal structure of in vitro phosphorylated 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 / 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: 3.7 Å

Authors

Arnold, L.H. / 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	Oct 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2017	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2	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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ao4.cif.gz	622.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5ao4.ent.gz	509.8 KB	Display	PDB format
PDBx/mmJSON format	5ao4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ao/5ao4 ftp://data.pdbj.org/pub/pdb/validation_reports/ao/5ao4	HTTPS FTP

-
Related structure data

Related structure data	5ao0C 5ao1C 5ao2C 5ao3C 3u1nS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4a2m-1 4a2m-2 4a2l-2 5ao0-1 2pyj-d 1gjw-1 4q7h-d 4i8d-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

-
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

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	197.545, 80.817, 147.665
Angle α, β, γ (deg.)	90.00, 114.93, 90.00
Int Tables number	5
Space group name H-M	C121

#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 PR OTEIN 1 / DNTPASE / DENDRITIC CELL-DERIVED IFNG-INDUCED PROTEIN / DCI P / MONOCYTE PROTEIN 5 / MOP-5 / SAM DOMAIN AND HD DOMAIN-CONTAINING PR OTEIN 1 / SAMHD1 Mass: 62274.141 Da / Num. of mol.: 4 / Fragment: 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): ROSETTA PLYSS 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: 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
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.46 % / Description: NONE
Crystal grow	Details: 0.2 M SODIUM FORMATE, 20% PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
Detector	Type: DECTRIS PILATUS 6M-F / 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: 3.7→50 Å / Num. obs: 23521 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 2.85 % / B_iso Wilson estimate: 93.98 Å² / R_merge(I) obs: 0.11 / Net I/σ(I): 9.76
Reflection shell	Resolution: 3.7→3.92 Å / Redundancy: 2.75 % / R_merge(I) obs: 0.42 / Mean I/σ(I) obs: 3.23 / % possible all: 92.8

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U1N

3u1n

Resolution: 3.7→49.046 Å / SU ML: 0.56 / σ(F): 1.37 / Phase error: 34.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3082	1071	4.9 %
R_work	0.2439	-	-
obs	0.2471	22017	96.43 %

Solvent computation

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

Displacement parameters

B_iso mean: 76.3 Å²

Refinement step

Cycle: LAST / Resolution: 3.7→49.046 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12090	0	132	0	12222

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	12528
X-RAY DIFFRACTION	f_angle_d	1.05	17107
X-RAY DIFFRACTION	f_dihedral_angle_d	16.181	4196
X-RAY DIFFRACTION	f_chiral_restr	0.046	1907
X-RAY DIFFRACTION	f_plane_restr	0.004	2213

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 (%)
3.7-3.8683	0.3875	141	0.3241	2581	X-RAY DIFFRACTION	97
3.8683-4.0722	0.3187	123	0.284	2600	X-RAY DIFFRACTION	97
4.0722-4.3272	0.335	136	0.2653	2629	X-RAY DIFFRACTION	97
4.3272-4.6611	0.3072	136	0.2465	2626	X-RAY DIFFRACTION	97
4.6611-5.1297	0.3053	130	0.2271	2610	X-RAY DIFFRACTION	97
5.1297-5.8709	0.3163	135	0.2466	2621	X-RAY DIFFRACTION	97
5.8709-7.3926	0.3276	136	0.2615	2646	X-RAY DIFFRACTION	96
7.3926-49.0502	0.2602	134	0.1963	2633	X-RAY DIFFRACTION	94

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	1.548	0.1546	0.2886	1.177	-0.365	0.7286	-0.0889	0.3762	-0.1311	-0.3483	0.0547	0.2019	0.1401	0.1893	0	0.8267	0.0344	-0.064	0.7046	-0.0198	0.7214	10.2921	22.7551	16.9531
2	0.9907	0.484	-0.0968	1.0888	-0.3619	2.1354	0.1595	-0.0756	-0.101	-0.1616	0.0066	0.0729	0.423	0.015	0	0.7896	0.0456	-0.0482	0.6941	-0.0131	0.797	6.9301	12.8693	35.7621
3	1.145	0.0012	-0.6113	1.0303	1.4011	1.0172	-0.0294	-0.2042	-0.2567	0.4023	-0.072	0.1599	-0.0247	-0.2885	-0.0001	0.6364	0.0006	-0.0201	0.6879	-0.0012	0.6021	14.6056	34.0175	47.4864
4	0.9448	0.0675	0.4639	0.8162	1.0986	0.2015	0.171	-0.5705	0.0301	0.0182	-0.0658	0.2481	-0.333	-0.2551	-0.0001	0.7772	-0.0733	0.0922	0.7104	-0.0966	0.8197	8.2015	43.6894	54.0343
5	1.8074	1.3757	0.8772	1.3132	0.353	0.6722	-0.2203	-0.2789	-0	-0.1325	-0.1063	0.2251	-0.5846	0.1908	0	0.7167	0.0192	-0.0551	0.7031	-0.0607	0.7647	20.5039	45.4753	53.1291
6	0.5805	0.3827	0.4263	0.4852	-1.2189	1.836	0.0162	0.2446	0.7255	0.1329	-0.1364	0.0728	-0.1037	0.2512	0	0.8783	0.0214	-0.0684	0.6553	-0.1806	0.8384	14.0179	48.2001	40.9276
7	0.2785	-0.4855	-0.0496	1.2484	-0.3977	0.1454	-0.0948	-0.5171	0.463	-0.2886	-0.0796	0.6619	-0.6408	-0.0184	0.0001	0.8382	-0.1019	-0.1005	0.8019	-0.0098	0.9754	-1.968	44.1458	30.1318
8	0.4256	0.0655	-0.2481	0.0658	0.1539	0.2292	-0.073	-0.2098	-0.5685	0.1304	0.0286	0.2143	-0.355	-0.3636	0.0001	1.2738	-0.0281	-0.1165	0.7307	-0.1345	1.0179	3.0999	63.2001	28.5701
9	0.7452	-0.3968	-0.5643	1.0549	0.0472	0.1631	-1.0614	0.6927	0.5411	0.1469	0.359	-0.2967	-0.9485	1.0635	-0.0007	0.9493	-0.0925	-0.1004	0.6686	-0.1079	0.9106	23.7056	55.2145	40.7354
10	2.6574	1.5497	1.4083	0.8619	0.8028	0.904	-1.3451	1.938	1.0247	0.0123	0.4092	-0.1449	-2.26	1.1505	-0.0814	1.7169	0.0605	-0.4054	0.5894	0.0614	1.0758	8.6928	67.4606	20.4777
11	0.8906	-1.0533	1.4151	2.2122	0.0504	1.2487	0.0867	0.2395	0.0859	0.2762	0.1152	-0.0269	0.2167	-0.3244	0.0001	0.7336	-0.163	0.0523	0.8729	-0.0709	0.7844	52.8569	31.3317	45.1388
12	2.3937	-0.4175	1.6519	1.6619	-0.656	0.7684	0.1997	-0.3966	-0.263	-0.0305	-0.1473	-0.2275	0.0708	0.2898	0	0.7254	-0.0545	-0.0441	0.5959	-0.023	0.6657	59.8212	20.4698	53.7581
13	0.5824	0.1978	1.5377	0.4727	0.8499	1.7631	0.0557	-0.2204	-0.6388	0.0656	-0.0578	-0.2238	0.4975	0.2594	0.0001	0.9667	-0.0799	-0.0067	1.0732	0.0467	0.9408	53.5783	19.528	38.7074
14	0.0198	0.0646	-0.0759	0.3	-0.2478	0.1919	0.5941	0.1197	-0.3367	-0.4899	-0.8612	-0.78	-0.2569	-0.8603	-0.0001	0.8474	-0.1911	0.4152	1.4	0.0215	1.4017	74.4152	31.8212	24.3496
15	0.1979	0.2786	0.5782	0.4276	-0.3827	0.4911	-0.1317	0.4558	0.2488	0.1074	-0.1569	-0.098	0.1378	0.0683	-0.0002	1.0948	0.1846	0.117	1.4705	-0.101	1.081	68.315	12.1844	23.616
16	0.6528	0.8943	-0.2508	0.9757	0.1338	0.14	-0.2196	0.3783	-0.4516	0.0493	-0.1792	-0.1887	0.6047	0.0979	0.0003	1.146	0.1141	0.0319	1.3257	-0.0392	1.0458	62.1349	5.4985	22.8564
17	0.9207	-0.986	-0.0296	0.2428	0.3011	0.0181	0.09	1.2255	0.0575	-0.4263	-0.0914	-0.3107	0.48	-0.3141	0	0.7563	-0.1026	0.1061	1.421	0.1262	0.8478	54.3122	36.2033	22.9252
18	0.5072	0.0263	-0.4934	0.6582	0.4399	0.5091	0.8289	0.8982	-0.031	-0.4341	-0.3768	-0.1124	0.7268	0.199	-0.0003	0.9702	0.1348	0.0463	1.4563	0.1286	0.6258	44.8869	41.1421	10.3657
19	-0.1272	0.0622	-0.0665	0.0688	0.1081	0.1232	-0.3905	0.7013	0.6428	0.276	-0.5696	-0.1362	-0.8209	0.7039	0.0005	1.514	-0.226	0.1425	1.5942	0.5182	1.6782	61.9617	53.7454	26.6287
20	0.9538	-0.1102	-0.0007	1.0807	0.5618	-0.2389	0.3455	0.5461	0.1981	-0.4882	-0.2101	-0.2643	0.2504	-0.0328	-0	1.0368	0.141	0.1635	1.3755	0.2799	0.9641	49.3542	45.8387	13.4045
21	1.1673	-1.1673	0.1212	0.0952	-0.0661	1.3533	-0.1014	0.4015	0.5756	-0.161	0.0374	-0.3537	-0.1899	0.0494	-0	0.9079	-0.2058	-0.07	0.8657	0.1485	1.1623	55.2674	53.6891	33.4466

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 115 THROUGH 309 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 310 THROUGH 583 )
3	X-RAY DIFFRACTION	3	CHAIN 'B' AND (RESID 115 THROUGH 185 )
4	X-RAY DIFFRACTION	4	CHAIN 'B' AND (RESID 186 THROUGH 260 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 261 THROUGH 336 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 337 THROUGH 411 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 412 THROUGH 461 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 462 THROUGH 504 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 505 THROUGH 558 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 559 THROUGH 581 )
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESID 114 THROUGH 185 )
12	X-RAY DIFFRACTION	12	CHAIN 'C' AND (RESID 186 THROUGH 309 )
13	X-RAY DIFFRACTION	13	CHAIN 'C' AND (RESID 310 THROUGH 423 )
14	X-RAY DIFFRACTION	14	CHAIN 'C' AND (RESID 424 THROUGH 449 )
15	X-RAY DIFFRACTION	15	CHAIN 'C' AND (RESID 450 THROUGH 504 )
16	X-RAY DIFFRACTION	16	CHAIN 'C' AND (RESID 505 THROUGH 580 )
17	X-RAY DIFFRACTION	17	CHAIN 'D' AND (RESID 117 THROUGH 163 )
18	X-RAY DIFFRACTION	18	CHAIN 'D' AND (RESID 164 THROUGH 204 )
19	X-RAY DIFFRACTION	19	CHAIN 'D' AND (RESID 205 THROUGH 232 )
20	X-RAY DIFFRACTION	20	CHAIN 'D' AND (RESID 233 THROUGH 336 )
21	X-RAY DIFFRACTION	21	CHAIN 'D' AND (RESID 337 THROUGH 581 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi