PDB-8q1k: Structural analysis of PLD3 reveals insights into the mechanism o...

ID or keywords:

Entry

Database: PDB / ID: 8q1k

Title

Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation

Components

5'-3' exonuclease PLD3

Keywords

DNA BINDING PROTEIN / PLD3 / structural biology / lysosome / DNA/RNA degradation / phospholipase D / 5' exonuclease

Function / homology

Function and homology information

spleen exonuclease / Synthesis of PG / single-stranded DNA 5'-3' DNA exonuclease activity / myotube differentiation / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phospholipase D activity / regulation of cytokine production involved in inflammatory response / immune system process / Role of phospholipids in phagocytosis / lysosomal lumen ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.51 Å

Authors

Roske, Y. / Daumke, O. / Damme, M.

Funding support

Germany, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2024
Title: Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation.
Authors: Roske, Y. / Cappel, C. / Cremer, N. / Hoffmann, P. / Koudelka, T. / Tholey, A. / Heinemann, U. / Daumke, O. / Damme, M.

History

Deposition	Jul 31, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 6, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8q1k.cif.gz	418.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8q1k_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	8q1k_full_validation.pdf.gz	2 MB	Display
Data in XML	8q1k_validation.xml.gz	46.5 KB	Display
Data in CIF	8q1k_validation.cif.gz	71.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q1/8q1k ftp://data.pdbj.org/pub/pdb/validation_reports/q1/8q1k	HTTPS FTP

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Related structure data

Related structure data	8q1xC 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	#214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1)

Deposited unit

A: 5'-3' exonuclease PLD3

B: 5'-3' exonuclease PLD3

hetero molecules

98.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	60.251, 115.304, 101.082
Angle α, β, γ (deg.)	90.00, 106.64, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	5'-3' exonuclease PLD3 Mass: 46945.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLD3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IV08

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Sugars , 3 types, 4 molecules

#2: Polysaccharide

alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...

Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}	LINUCS	PDB-CARE

#3: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

#4: Polysaccharide

alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...

Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1 / Source method: obtained synthetically

Descriptor	Type	Program
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{}}}}}	LINUCS	PDB-CARE

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Non-polymers , 4 types, 1243 molecules

#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO₄
#7: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mn
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1224 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 17% PEG 4000, 0.02 M NaI, 0.6 M Ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.51→44.65 Å / Num. obs: 200406 / % possible obs: 97.8 % / Redundancy: 3.77 % / CC_1/2: 0.99 / R_rim(I) all: 0.0074 / Net I/σ(I): 10.71
Reflection shell	Resolution: 1.51→1.61 Å / Num. unique obs: 31270 / CC_1/2: 0.26 / R_rim(I) all: 0.228 / % possible all: 94.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XSCALE		data scaling
XDS		data reduction
HKL2Map		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.51→44.65 Å / Cor.coef. F_o:F_c: 0.978 / Cor.coef. F_o:F_c free: 0.969 / SU B: 1.719 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.012 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18632	2105	1.1 %	RANDOM
R_work	0.15389	-	-	-
obs	0.15423	198247	97.84 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 30.94 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	9.16 Å²	0 Å²	-3.84 Å²
2-	-	-9.31 Å²	-0 Å²
3-	-	-	0.15 Å²

Refinement step

Cycle: 1 / Resolution: 1.51→44.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6576	0	294	1224	8094

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	7173
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.014	6494
X-RAY DIFFRACTION	r_angle_refined_deg	1.297	1.691	9833
X-RAY DIFFRACTION	r_angle_other_deg	1.258	1.611	15010
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.585	5	875
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.22	21.793	368
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.498	15	1066
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.722	15	49
X-RAY DIFFRACTION	r_chiral_restr	0.057	0.2	982
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	9069
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1673
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.931	2.65	3401
X-RAY DIFFRACTION	r_mcbond_other	1.918	2.649	3400
X-RAY DIFFRACTION	r_mcangle_it	2.389	3.994	4254
X-RAY DIFFRACTION	r_mcangle_other	2.389	3.995	4255
X-RAY DIFFRACTION	r_scbond_it	2.263	3.211	3772
X-RAY DIFFRACTION	r_scbond_other	2.26	3.211	3772
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.839	4.69	5560
X-RAY DIFFRACTION	r_long_range_B_refined	5.028	36.608	8382
X-RAY DIFFRACTION	r_long_range_B_other	5.028	36.605	8382
X-RAY DIFFRACTION	r_rigid_bond_restr	1.015	3	13667
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.515→1.554 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.423	143	-
R_work	0.356	13413	-
obs	-	-	89.71 %

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	1.272	-0.5146	0.6136	0.5435	-1.2872	3.9013	0.0721	-0.0496	-0.1369	-0.0467	0.0432	0.0776	0.1521	-0.0797	-0.1153	0.0156	-0.0024	-0.0055	0.0087	0.0091	0.0358	-23.8233	99.7954	42.8339
2	0.3227	-0.0219	-0.3852	0.3339	-0.1199	0.6028	0.011	0.0371	0.0459	-0.0265	-0.0044	-0.0072	-0.0042	-0.0402	-0.0067	0.0183	0.0025	-0.002	0.0124	0.0055	0.034	-6.9933	112.4907	18.228
3	0.1363	0.0187	0.0003	0.041	-0.055	0.1408	-0.0006	-0.0028	0.0004	0.0021	-0.0104	-0.0077	-0.0076	0.0105	0.011	0.0168	-0.0003	0.0013	0.0109	-0.0026	0.0275	-1.7744	110.7861	32.2506
4	0.0871	-0.0668	-0.0138	0.1633	0.0757	0.0883	0.0062	0.0052	0.0234	0.0075	0.0016	-0.0204	0.0097	0.0024	-0.0077	0.0146	-0.0019	-0.0015	0.0159	0.0015	0.0263	-7.5044	88.8514	30.5281
5	0.0992	-0.0211	-0.0731	0.1879	-0.0836	0.1149	0.0011	0.0006	0.0268	-0.0165	0.01	0.0024	0.0083	-0.0072	-0.0111	0.0144	-0.002	-0.0011	0.0142	0.0021	0.0318	-3.3525	91.0482	14.961
6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.0024	0	0	0.0024	0	0.0024	0	0	0
7	0.2999	0.0144	0.1901	0.0954	0.1517	0.449	0.01	0.0392	-0.0179	-0.0081	-0.0012	-0.0073	0.0042	0.0211	-0.0088	0.0146	0.0029	0.0023	0.013	0.0043	0.0134	11.3196	40.9433	24.8094
8	0.2923	0.033	0.0489	0.1032	0.0486	0.1293	0.0092	-0.0023	-0.0117	0.009	-0.0073	0.0099	0.0078	-0.0059	-0.0019	0.0173	-0.0004	-0.0008	0.011	0.0052	0.0193	4.0618	40.4499	32.7029
9	0.5378	0.2571	-0.0872	0.1248	-0.0338	0.0797	0.0077	-0.0246	0.008	0.0024	-0.0098	0.0098	-0.0038	0.0154	0.0022	0.014	0.0019	-0.0014	0.015	0.0035	0.0373	9.1201	52.7626	43.545
10	0.0944	-0.0404	0.1048	0.084	-0.018	0.1342	-0.0067	-0.0101	-0.0104	0.0006	0.0039	0.0125	-0.0084	-0.01	0.0028	0.0156	-0.0016	0.0015	0.0166	-0.0013	0.0233	4.7611	66.254	24.132
11	0.0566	0.0003	0.0844	0.05	0.026	0.1489	0.0049	-0.0036	-0.015	-0.0095	0.0072	-0.0101	-0.0046	-0.0005	-0.0121	0.0178	-0.0001	-0.0008	0.0166	-0.0006	0.0384	7.5059	57.5181	16.7397

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	15 - 81
2	X-RAY DIFFRACTION	2	A	82 - 146
3	X-RAY DIFFRACTION	3	A	147 - 269
4	X-RAY DIFFRACTION	4	A	270 - 360
5	X-RAY DIFFRACTION	5	A	361 - 436
6	X-RAY DIFFRACTION	6	B	15 - 67
7	X-RAY DIFFRACTION	7	B	68 - 146
8	X-RAY DIFFRACTION	8	B	147 - 249
9	X-RAY DIFFRACTION	9	B	250 - 299
10	X-RAY DIFFRACTION	10	B	300 - 385
11	X-RAY DIFFRACTION	11	B	386 - 434

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