PDB-8v07: Crystal structure of mouse PLD3 co-crystallized with 5'Pi-ssDNA f...

ID or keywords:

Entry

Database: PDB / ID: 8v07

Title

Crystal structure of mouse PLD3 co-crystallized with 5'Pi-ssDNA for 30 days

Components

5'-3' exonuclease PLD3

Keywords

HYDROLASE / PLD3 / phospholipase / phosphohistidine / nuclease

Function / homology

Function and homology information

spleen exonuclease / single-stranded DNA 5'-3' DNA exonuclease activity / myotube differentiation / Role of phospholipids in phagocytosis / phospholipase D activity / regulation of cytokine production involved in inflammatory response / lysosomal lumen / late endosome membrane / early endosome membrane / inflammatory response ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.99 Å

Authors

Yuan, M. / Wilson, I.A.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI142945	United States
National Institutes of Health/National Institute on Aging (NIH/NIA)	AG070775	United States

Citation

Journal: Structure / Year: 2024
Title: Structural and mechanistic insights into disease-associated endolysosomal exonucleases PLD3 and PLD4.
Authors: Yuan, M. / Peng, L. / Huang, D. / Gavin, A. / Luan, F. / Tran, J. / Feng, Z. / Zhu, X. / Matteson, J. / Wilson, I.A. / Nemazee, D.

History

Deposition	Nov 17, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 13, 2024	Provider: repository / Type: Initial release
Revision 1.1	Apr 17, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jun 19, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8v07.cif.gz	353.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8v07.ent.gz	282.1 KB	Display	PDB format
PDBx/mmJSON format	8v07.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8v07_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	8v07_full_validation.pdf.gz	2.8 MB	Display
Data in XML	8v07_validation.xml.gz	66.3 KB	Display
Data in CIF	8v07_validation.cif.gz	92.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v0/8v07 ftp://data.pdbj.org/pub/pdb/validation_reports/v0/8v07	HTTPS FTP

-
Related structure data

Related structure data	8v05C 8v06C 8v08C C: citing same article (ref.)
Similar structure data	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	#21 - Sep 2001 Antibodies similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #76 - Apr 2006 Hemagglutinin similarity (1)

Deposited unit

B: 5'-3' exonuclease PLD3

A: 5'-3' exonuclease PLD3

C: 5'-3' exonuclease PLD3

D: 5'-3' exonuclease PLD3

hetero molecules

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

1

B: 5'-3' exonuclease PLD3

A: 5'-3' exonuclease PLD3

hetero molecules

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

2

C: 5'-3' exonuclease PLD3

D: 5'-3' exonuclease PLD3

hetero molecules

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

Unit cell

Length a, b, c (Å)	54.523, 54.789, 203.574
Angle α, β, γ (deg.)	83.65, 89.10, 89.90
Int Tables number	1
Space group name H-M	P1

-
Protein , 1 types, 4 molecules BACD

#1: Protein	5'-3' exonuclease PLD3 Mass: 51856.188 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pld3 / Production host: Homo sapiens (human) / References: UniProt: O35405

-
Sugars , 4 types, 8 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.: 2
Source method: isolated from a genetically manipulated source

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)][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.: 4
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-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...

Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}	LINUCS	PDB-CARE

#9: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

-
Non-polymers , 5 types, 570 molecules

#5: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Chemical	ChemComp-ACE / ACETYL GROUP Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₄O
#8: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#10: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 558 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.91 Å³/Da / Density % sol: 57.78 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 1.6 M ammonium sulfate, 0.5 mM magnesium chloride, 0.1 M citric acid, pH 4.0

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-B / Wavelength: 1.0332 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.0332 Å / Relative weight: 1

Reflection

Resolution: 1.99→50 Å / Num. obs: 131978 / % possible obs: 83.1 % / Redundancy: 2.3 % / R_merge(I) obs: 0.091 / Net I/σ(I): 6.9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2-2.03	1.9	0.701	5605	0.529	0.832	0.587	0.919	0.738	69.3
2.03-2.07	2	0.65	6107	0.603	0.868	0.536	0.847	0.763	78.7
2.07-2.11	2.1	0.601	6898	0.657	0.89	0.492	0.78	0.804	85.4
2.11-2.15	2.2	0.501	7180	0.74	0.922	0.405	0.648	0.764	91.3
2.15-2.2	2.2	0.492	7463	0.76	0.929	0.395	0.634	0.757	93.6
2.2-2.25	2	0.488	5024	0.704	0.909	0.395	0.631	0.75	63.9
2.25-2.31	1.8	0.35	4089	0.722	0.916	0.292	0.458	1.299	51.3
2.31-2.37	2.2	0.319	7484	0.853	0.959	0.256	0.412	0.859	93.6
2.37-2.44	2.2	0.265	7440	0.883	0.968	0.211	0.341	0.894	94.5
2.44-2.52	2.1	0.225	7419	0.883	0.969	0.183	0.291	0.974	93.7
2.52-2.61	2.3	0.189	7656	0.934	0.983	0.148	0.241	0.948	95.3
2.61-2.71	2.4	0.164	7494	0.944	0.986	0.126	0.208	1.036	95
2.71-2.84	2.3	0.135	7407	0.956	0.989	0.104	0.171	1.145	93.7
2.84-2.99	2.5	0.109	7556	0.972	0.993	0.081	0.137	1.321	95
2.99-3.17	2.6	0.089	7364	0.98	0.995	0.064	0.11	1.57	93.2
3.17-3.42	2.6	0.075	7328	0.985	0.996	0.054	0.092	1.828	91.6
3.42-3.76	2.2	0.066	4609	0.985	0.996	0.05	0.084	2.239	58.6
3.76-4.31	2.3	0.056	5331	0.988	0.997	0.042	0.071	2.711	66.8
4.31-5.43	2.4	0.048	5880	0.992	0.998	0.035	0.06	2.705	74.1
5.43-50	2.6	0.045	6644	0.994	0.999	0.032	0.056	2.35	83.7

-
Processing

Software

Name	Version	Classification
PHENIX	(1.19.2_4158: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.99→37.12 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2638	6469	4.9 %
R_work	0.2236	-	-
obs	0.2256	131925	82.21 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.99→37.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12777	0	414	558	13749

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.017	13536
X-RAY DIFFRACTION	f_angle_d	1.781	18450
X-RAY DIFFRACTION	f_dihedral_angle_d	9.181	2008
X-RAY DIFFRACTION	f_chiral_restr	0.159	2126
X-RAY DIFFRACTION	f_plane_restr	0.014	2333

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 (%)
1.99-2.01	0.3442	105	0.3349	2235	X-RAY DIFFRACTION	43
2.01-2.04	0.3875	212	0.3276	3747	X-RAY DIFFRACTION	73
2.04-2.06	0.3598	212	0.3116	3893	X-RAY DIFFRACTION	79
2.06-2.09	0.3385	237	0.3099	4273	X-RAY DIFFRACTION	82
2.09-2.12	0.3241	253	0.3182	4436	X-RAY DIFFRACTION	88
2.12-2.14	0.3465	228	0.2882	4679	X-RAY DIFFRACTION	92
2.14-2.18	0.3561	232	0.2904	4730	X-RAY DIFFRACTION	93
2.18-2.21	0.3511	263	0.2974	4752	X-RAY DIFFRACTION	94
2.21-2.24	0.3299	163	0.3119	3408	X-RAY DIFFRACTION	68
2.24-2.28	0.4113	150	0.37	2693	X-RAY DIFFRACTION	52
2.28-2.32	0.3759	165	0.3001	2616	X-RAY DIFFRACTION	54
2.32-2.36	0.3111	255	0.2567	4829	X-RAY DIFFRACTION	94
2.36-2.41	0.3119	255	0.2556	4808	X-RAY DIFFRACTION	95
2.41-2.45	0.282	258	0.2482	4721	X-RAY DIFFRACTION	94
2.45-2.51	0.3085	272	0.2472	4791	X-RAY DIFFRACTION	94
2.51-2.57	0.2861	256	0.2404	4795	X-RAY DIFFRACTION	95
2.57-2.63	0.3419	228	0.2421	4883	X-RAY DIFFRACTION	96
2.63-2.7	0.3251	229	0.2376	4848	X-RAY DIFFRACTION	95
2.7-2.78	0.2655	238	0.2297	4822	X-RAY DIFFRACTION	94
2.78-2.87	0.291	235	0.2308	4844	X-RAY DIFFRACTION	94
2.87-2.97	0.2884	233	0.223	4799	X-RAY DIFFRACTION	95
2.97-3.09	0.2868	199	0.2139	4817	X-RAY DIFFRACTION	94
3.09-3.23	0.2519	217	0.2147	4785	X-RAY DIFFRACTION	93
3.23-3.4	0.2656	206	0.2139	4674	X-RAY DIFFRACTION	91
3.4-3.62	0.2405	166	0.2126	3585	X-RAY DIFFRACTION	71
3.62-3.9	0.2027	138	0.1897	2682	X-RAY DIFFRACTION	52
3.9-4.29	0.2104	220	0.1755	3290	X-RAY DIFFRACTION	66
4.29-4.91	0.1821	201	0.1618	3686	X-RAY DIFFRACTION	72
4.91-6.18	0.2102	184	0.1855	4111	X-RAY DIFFRACTION	81
6.18-37.12	0.2263	259	0.2025	4224	X-RAY DIFFRACTION	84

-
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://pdbjlvh1.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

-
Protein , 1 types, 4 molecules BACD

-
Sugars , 4 types, 8 molecules

-
Non-polymers , 5 types, 570 molecules

-
Details

-
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

-Protein , 1 types, 4 molecules BACD

-Sugars , 4 types, 8 molecules

-Non-polymers , 5 types, 570 molecules

-Details

-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

-
Protein , 1 types, 4 molecules BACD

-
Sugars , 4 types, 8 molecules

-
Non-polymers , 5 types, 570 molecules

-
Details

-
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