PDB-5aja: Crystal structure of mandrill SAMHD1 (amino acid residues 1-114) ...

ID or keywords:

Entry

Database: PDB / ID: 5aja

Title

Crystal structure of mandrill SAMHD1 (amino acid residues 1-114) bound to Vpx isolated from mandrill and human DCAF1 (amino acid residues 1058-1396)

Components

PROTEIN VPRBP
SAM DOMAIN AND HD DOMAIN-CONTAINING PROTEIN
VPX PROTEIN

Keywords

VIRAL PROTEIN / SIV / ACCESSORY PROTEIN / RETROVIRAL RESTRICTION FACTOR / UBIQUITYLATION / PROTEASOMAL DEGRADATION

Function / homology

Function and homology information

cell competition in a multicellular organism / histone H2AT120 kinase activity / dGTPase activity / dGTP catabolic process / V(D)J recombination / regulation of innate immune response / Cul4-RING E3 ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / post-translational protein modification / B cell differentiation ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

SIMIAN IMMUNODEFICIENCY VIRUS

MANDRILLUS SPHINX (mandrill)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.649 Å

Authors

Schwefel, D. / Boucherit, V.C. / Christodoulou, E. / Walker, P.A. / Stoye, J.P. / Bishop, K.N. / Taylor, I.A.

Citation

Journal: Cell Host Microbe. / Year: 2015
Title: Molecular Determinants for Recognition of Divergent Samhd1 Proteins by the Lentiviral Accessory Protein Vpx.
Authors: Schwefel, D. / Boucherit, V.C. / Christodoulou, E. / Walker, P.A. / Stoye, J.P. / Bishop, K.N. / Taylor, I.A.

History

Deposition	Feb 20, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 22, 2015	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 / 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 / _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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PDBx/mmCIF format	5aja.cif.gz	210.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5aja.ent.gz	167.9 KB	Display	PDB format
PDBx/mmJSON format	5aja.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5aja_validation.pdf.gz	450.6 KB	Display	wwPDB validaton report
Full document	5aja_full_validation.pdf.gz	455.6 KB	Display
Data in XML	5aja_validation.xml.gz	18.3 KB	Display
Data in CIF	5aja_validation.cif.gz	24.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/aj/5aja ftp://data.pdbj.org/pub/pdb/validation_reports/aj/5aja	HTTPS FTP

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Related structure data

Related structure data	4cc9S S: Starting model for refinement
Similar structure data	5hvf-d 2y9x-1 6uhu-d 3khk-2 2y9w-2 4xze-4 4z8l-2 6tbk-7 5a97-2 3a31-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: PROTEIN VPRBP

B: VPX PROTEIN

C: SAM DOMAIN AND HD DOMAIN-CONTAINING PROTEIN

hetero molecules

66 kDa, 3 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)	102.021, 102.021, 265.001
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein	PROTEIN VPRBP / DCAF1 / DDB1- AND CUL4-ASSOCIATED FACTOR 1 / HIV-1 VPR-BINDING PROTEIN / VPRBP / SERINE/THREONINE- ...DCAF1 / DDB1- AND CUL4-ASSOCIATED FACTOR 1 / HIV-1 VPR-BINDING PROTEIN / VPRBP / SERINE/THREONINE-PROTEIN KINASE VPRBP / VPR-INTERACTING PROTEIN Mass: 41073.129 Da / Num. of mol.: 1 / Fragment: WD40-REPEAT DOMAIN, RESIDUES 1058-1396 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTRIEX-6 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: Q9Y4B6, non-specific serine/threonine protein kinase
#2: Protein	VPX PROTEIN Mass: 11940.628 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SIMIAN IMMUNODEFICIENCY VIRUS / Strain: MND-2 / Variant: 5440 / Plasmid: PET49B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: Q7ZB17
#3: Protein	SAM DOMAIN AND HD DOMAIN-CONTAINING PROTEIN / SAMHD1 / SAM DOMAIN AND HD DOMAIN-CONTAINING PROTEIN 1 Mass: 12914.393 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, UNP 1-114 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MANDRILLUS SPHINX (mandrill) / Plasmid: PET52B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: H6WEA4
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: 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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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.04 Å³/Da / Density % sol: 60 % / Description: NONE
Crystal grow	Details: 0.16 M TRISODIUM CITRATE-HCL PH 5.2, 4% PEG 6000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97965
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97965 Å / Relative weight: 1
Reflection	Resolution: 2.65→30 Å / Num. obs: 24555 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / B_iso Wilson estimate: 76.78 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 20.7
Reflection shell	Resolution: 2.65→2.81 Å / Redundancy: 9.7 % / R_merge(I) obs: 1.45 / Mean I/σ(I) obs: 1.63 / % possible all: 99.3

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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 4CC9

4cc9

Resolution: 2.649→29.82 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 24.27 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.227	1197	4.9 %
R_work	0.1735	-	-
obs	0.1761	24554	99.7 %

Solvent computation

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

Displacement parameters

B_iso mean: 87.6 Å²

Refinement step

Cycle: LAST / Resolution: 2.649→29.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3797	0	1	3	3801

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3893
X-RAY DIFFRACTION	f_angle_d	1.118	5283
X-RAY DIFFRACTION	f_dihedral_angle_d	15.657	1375
X-RAY DIFFRACTION	f_chiral_restr	0.045	574
X-RAY DIFFRACTION	f_plane_restr	0.006	689

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 (%)
2.6485-2.7545	0.3301	112	0.2705	2541	X-RAY DIFFRACTION	99
2.7545-2.8797	0.337	108	0.2632	2529	X-RAY DIFFRACTION	100
2.8797-3.0314	0.2861	150	0.2421	2535	X-RAY DIFFRACTION	100
3.0314-3.2212	0.272	118	0.2215	2569	X-RAY DIFFRACTION	100
3.2212-3.4695	0.2263	137	0.2093	2560	X-RAY DIFFRACTION	100
3.4695-3.818	0.2545	154	0.1706	2551	X-RAY DIFFRACTION	100
3.818-4.369	0.1935	145	0.1436	2600	X-RAY DIFFRACTION	100
4.369-5.4989	0.1724	143	0.1385	2637	X-RAY DIFFRACTION	100
5.4989-29.822	0.2441	130	0.1698	2835	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	0.6449	0.1587	0.6423	1.3166	0.1169	1.0043	0.2118	-0.2609	0.5317	-0.2599	-0.1357	0.4225	0.1606	-0.2743	0.0831	0.4078	0.1004	0.0383	0.6473	-0.0491	0.7424	-16.295	-37.4008	-6.8883
2	1.2283	0.8821	-0.1346	0.7413	0.2737	0.8377	0.1366	0.4194	0.0225	-0.1655	-0.027	0.0025	0.095	0.1069	0.0002	0.554	0.0857	0.0195	0.7687	-0.0279	0.5385	-6.4625	-43.208	-13.291
3	0.488	0.2636	0.3547	0.3639	0.0405	0.4338	-0.0338	0.3603	-0.2584	0.0371	-0.1078	-0.607	-0.3446	0.045	-0.0043	0.5713	0.0499	0.107	0.7468	-0.103	0.5725	6.5838	-40.8758	-9.3005
4	2.4558	2.1444	1.1232	0.916	1.0323	1.2817	0.3025	-0.2705	0.0626	0.036	-0.3025	0.0304	-0.009	0.0124	0.0001	0.5203	-0.0523	0.1107	0.6407	-0.0423	0.5694	9.0014	-35.3981	5.4786
5	0.0116	-0.1325	0.0359	0.1567	-0.0839	0.3891	0.1446	-0.9597	0.6123	0.3092	0.0295	1.2396	0.241	-0.1747	0.0077	0.7447	-0.0901	0.1561	0.9942	-0.3408	1.0355	-8.9301	-34.0475	9.9725
6	0.0976	0.0608	0.134	1.833	-1.3997	1.1716	0.2249	-0.6889	0.5267	-0.676	-0.0256	0.1957	0.6474	0.4046	0.0932	0.5093	-0.0144	0.1608	0.6263	-0.2216	0.9124	-15.0184	-34.2872	2.0657
7	0.0746	0.0143	0.0667	0.3966	-0.0211	0.0175	0.477	-0.2783	0.6945	0.096	-0.519	0.2644	0.0496	-0.2158	-0.0087	0.5681	0.0332	-0.0656	0.6227	-0.2483	0.9276	-21.1443	-42.0668	1.2268
8	0.3592	-0.0004	0.265	0.0634	-0.1029	0.1082	0.2226	0.8811	0.018	-0.7214	-0.5694	0.4842	-0.0066	0.7912	0.0015	0.9525	0.079	-0.0507	0.9809	0.0138	0.7251	-9.7464	-45.6725	-23.697
9	0.0656	0.0525	-0.1107	0.3326	-0.0416	0.2231	-0.0257	0.0017	-0.3945	0.2891	-0.3626	-0.8595	0.398	0.6236	0.0014	0.713	-0.0179	-0.1402	0.7166	-0.0189	0.8215	-7.1666	-64.302	-7.5874
10	0.4239	0.281	-0.5562	0.5887	-0.0997	0.7361	0.1736	-0.248	0.2581	0.2385	-0.3538	0.095	0.4455	-0.0011	-0.0006	0.6626	-0.0138	-0.1945	0.6951	0.0208	0.67	-19.5361	-65.262	1.483
11	0.3133	0.1389	-0.4705	0.292	-0.2597	0.4474	0.786	-0.3271	0.2411	0.874	-0.5176	-0.1001	0.6242	0.0298	-0.0007	0.5761	0.0292	-0.1475	0.6726	-0.0294	0.6208	-11.0198	-57.1433	-1.0329
12	0.0209	0.0643	-0.0723	0.378	-0.038	0.1414	0.2287	0.6261	0.6408	-0.4649	0.0626	-0.0292	-0.3011	-0.4366	0.0002	0.877	0.1844	-0.0775	0.8248	-0.0357	0.6874	-10.9978	-55.2642	-18.1833
13	0.6771	0.3636	-0.5352	0.3619	0.2294	0.5646	-0.6131	-0.0807	0.1096	0.0052	0.115	0.1075	0.0469	-0.0678	0.0004	0.7316	0.2592	-0.0645	0.728	-0.0769	0.6015	-19.2505	-70.1448	-3.7892
14	0.577	-0.4789	-0.7877	0.9471	-0.0444	0.9943	0.4329	-0.0092	0.2549	0.0989	-0.0222	-0.1091	1.7533	-0.192	0.0391	1.2019	-0.0789	-0.2539	0.5412	0.0506	0.5567	-22.3161	-78.0738	12.258

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 1075 THROUGH 1112 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 1113 THROUGH 1170 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 1171 THROUGH 1196 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 1197 THROUGH 1306 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 1307 THROUGH 1343 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 1344 THROUGH 1371 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 1372 THROUGH 1392 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 2 THROUGH 16 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 17 THROUGH 34 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 35 THROUGH 59 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 60 THROUGH 85 )
12	X-RAY DIFFRACTION	12	CHAIN 'C' AND (RESID 1 THROUGH 14 )
13	X-RAY DIFFRACTION	13	CHAIN 'C' AND (RESID 15 THROUGH 41 )
14	X-RAY DIFFRACTION	14	CHAIN 'C' AND (RESID 42 THROUGH 109 )

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