PDB-6eua: The fibrinogen-like domain of human Angptl3

ID or keywords:

Entry

Database: PDB / ID: 6eua

Title

The fibrinogen-like domain of human Angptl3

Components

Angiopoietin-related protein 3

Keywords

SIGNALING PROTEIN /

lipid metabolism / plasma triglyceride /

angiopoietin-like /

coronary artery disease

Function / homology

Function and homology information

regulation of lipoprotein lipase activity / acylglycerol homeostasis / negative regulation of phospholipase activity / negative regulation of lipoprotein lipase activity / phospholipase inhibitor activity / Assembly of active LPL and LIPC lipase complexes / positive regulation of lipid catabolic process / glycerol metabolic process / phospholipid catabolic process /

lipid storage ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.095 Å

Authors

Biterova, E.I. / Esmaeeli, M.E. / Alanen, H.I. / Saaranen, M. / Ruddock, L.W.

Funding support

Finland, 1items

Citation

Journal: Sci Rep / Year: 2018
Title: Structures of Angptl3 and Angptl4, modulators of triglyceride levels and coronary artery disease.
Authors: Biterova, E. / Esmaeeli, M. / Alanen, H.I. / Saaranen, M. / Ruddock, L.W.

History

Deposition	Oct 30, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 9, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6eua.cif.gz	264.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6eua.ent.gz	214.1 KB	Display	PDB format
PDBx/mmJSON format	6eua.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eu/6eua ftp://data.pdbj.org/pub/pdb/validation_reports/eu/6eua	HTTPS FTP

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Related structure data

Related structure data	6eubC 1z3sS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2j64-d 2j5z-d 2j2p-1 2j60-d 2j2p-2 5tzo-d 5ap8-d 4cbg-2 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	#83 - Nov 2006 Fibrin similarity (5) #134 - Feb 2011 Integrin similarity (5) #209 - May 2017 Tissue Transglutaminase and Celiac Disease similarity (5) #155 - Nov 2012 Vitamin D Receptor similarity (1)

Deposited unit

A: Angiopoietin-related protein 3

B: Angiopoietin-related protein 3

C: Angiopoietin-related protein 3

80.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	60.050, 63.650, 169.430
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Angiopoietin-related protein 3 / Angiopoietin-5 / ANG-5 / Angiopoietin-like protein 3 Mass: 26706.746 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANGPTL3, ANGPT5, UNQ153/PRO179 / Production host: Escherichia coli (E. coli) / Strain (production host): MDS42 / References: UniProt: Q9Y5C1
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Angiopoietin-related protein 3 / Angiopoietin-5 / ANG-5 / Angiopoietin-like protein 3

Mass: 26706.746 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: ANGPTL3, ANGPT5, UNQ153/PRO179 / Production host:

Escherichia coli (E. coli) / Strain (production host): MDS42 / References: UniProt: Q9Y5C1

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.02 Å³/Da / Density % sol: 35.14 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-Tris pH 5.5, 25 % (w/v) PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: MASSIF-1 / Wavelength: 0.966 Å

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 25, 2016

Radiation

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

Radiation wavelength

Wavelength: 0.966 Å / Relative weight: 1

Reflection

Resolution: 2.1→48.99 Å / Num. obs: 38790 / % possible obs: 99.3 % / Redundancy: 3.833 % / B_iso Wilson estimate: 35.38 Å² / CC_1/2: 0.994 / R_merge(I) obs: 0.129 / R_rim(I) all: 0.15 / Χ²: 0.93 / Net I/σ(I): 7.16 / Num. measured all: 148692 / Scaling rejects: 13

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.1-2.15	3.786	1.284	1	10382	2854	2742	0.334	1.488	96.1
2.15-2.21	3.921	0.98	1.34	10829	2767	2762	0.476	1.133	99.8
2.21-2.27	3.825	0.859	1.53	10300	2698	2693	0.557	0.996	99.8
2.27-2.34	3.557	0.709	1.74	9298	2628	2614	0.638	0.833	99.5
2.34-2.42	3.673	0.599	2.1	9318	2541	2537	0.737	0.701	99.8
2.42-2.5	3.994	0.514	2.64	9874	2481	2472	0.775	0.593	99.6
2.5-2.6	4.043	0.389	3.44	9490	2355	2347	0.867	0.448	99.7
2.6-2.71	4.038	0.32	4.19	9198	2283	2278	0.902	0.368	99.8
2.71-2.83	4.017	0.247	5.2	8906	2228	2217	0.944	0.285	99.5
2.83-2.96	3.959	0.176	6.95	8210	2086	2074	0.968	0.203	99.4
2.96-3.12	3.885	0.148	8.07	7934	2046	2042	0.975	0.172	99.8
3.12-3.31	3.593	0.113	9.53	6784	1903	1888	0.983	0.132	99.2
3.31-3.54	3.55	0.083	12.52	6425	1815	1810	0.989	0.097	99.7
3.54-3.83	4.012	0.073	15.34	6664	1669	1661	0.992	0.084	99.5
3.83-4.19	4.015	0.062	17.49	6219	1555	1549	0.994	0.071	99.6
4.19-4.69	3.92	0.054	19.62	5601	1431	1429	0.995	0.062	99.9
4.69-5.41	3.75	0.055	18.97	4691	1260	1251	0.995	0.064	99.3
5.41-6.63	3.426	0.061	16.31	3666	1082	1070	0.993	0.073	98.9
6.63-9.37	3.693	0.052	19.4	3165	861	857	0.995	0.06	99.5
9.37-48.99	3.497	0.049	23.32	1738	515	497	0.995	0.058	96.5

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Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
XSCALE		data scaling
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1Z3S

1z3s

Resolution: 2.095→48.99 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2537	1940	5 %
R_work	0.1938	36847	-
obs	0.1968	38787	99.32 %

Solvent computation

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

Displacement parameters

B_iso max: 168.01 Å² / B_iso mean: 46.8072 Å² / B_iso min: 17.74 Å²

Refinement step

Cycle: final / Resolution: 2.095→48.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4964	0	0	161	5125
B_iso mean	-	-	-	40.47	-
Num. residues	-	-	-	-	601

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5142
X-RAY DIFFRACTION	f_angle_d	0.774	6986
X-RAY DIFFRACTION	f_chiral_restr	0.051	693
X-RAY DIFFRACTION	f_plane_restr	0.004	891
X-RAY DIFFRACTION	f_dihedral_angle_d	2.903	3302

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.0953-2.1477	0.3161	133	0.2764	2523	2656	96
2.1477-2.2057	0.3288	135	0.2693	2576	2711	100
2.2057-2.2706	0.3131	137	0.268	2601	2738	100
2.2706-2.3439	0.3315	138	0.2696	2612	2750	99
2.3439-2.4277	0.3621	137	0.2555	2613	2750	100
2.4277-2.5249	0.35	137	0.2393	2597	2734	100
2.5249-2.6398	0.2622	138	0.2192	2617	2755	100
2.6398-2.779	0.3168	138	0.2239	2624	2762	100
2.779-2.9531	0.3023	137	0.2118	2600	2737	99
2.9531-3.181	0.2688	140	0.2032	2669	2809	100
3.181-3.5011	0.2669	139	0.1809	2642	2781	99
3.5011-4.0075	0.2254	141	0.1595	2674	2815	100
4.0075-5.0482	0.1647	142	0.1339	2692	2834	100
5.0482-49.0038	0.2244	148	0.1898	2807	2955	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	4.7937	-2.1711	-1.4078	3.5104	0.7984	3.6535	0.0274	-0.0621	-0.1733	-0.0449	-0.1227	0.1245	0.1447	-0.0602	0.0755	0.3214	-0.0332	0.009	0.2242	-0.0078	0.1991	-25.588	-3.5571	14.1052
2	3.1264	-1.2858	-0.0838	1.501	0.068	2.9289	0.1574	0.4796	0.0096	-0.5352	-0.1077	-0.012	0.2694	0.0446	0.0069	0.496	-0.0008	0.0464	0.2765	-0.0371	0.2537	-24.3529	-7.0918	-1.1949
3	5.9403	1.9141	-3.0306	2.9525	-1.7228	5.2298	0.032	0.5502	0.1576	-0.4125	-0.049	-0.1169	-0.3034	0.1598	0.0393	0.4956	0.0152	0.0672	0.3052	0.0305	0.3017	-18.9367	1.756	-1.9078
4	2.4595	-0.2958	1.3489	2.7745	-0.3372	3.0481	0.0479	-0.065	-0.2384	-0.3438	0.0511	-0.1097	0.0958	-0.0786	-0.0482	0.3284	0.016	0.0369	0.1673	-0.0307	0.2286	-28.1488	12.268	27.3048
5	4.7952	0.7741	-0.8088	5.3998	0.8036	3.6817	0.0332	-0.0962	0.212	0.123	-0.1522	-0.1326	-0.2918	-0.0253	0.0993	0.3143	0.0659	-0.045	0.1699	0.0064	0.1957	-29.5327	25.8007	31.6201
6	1.8983	1.8102	0.0517	2.8871	-0.3534	1.5532	-0.2678	0.1796	0.4014	-0.5874	0.0303	0.1111	-0.4612	0.019	0.2129	0.5562	0.0386	-0.0069	0.2298	0.0186	0.3015	-29.1009	30.7707	21.5167
7	7.1588	3.3387	-0.059	7.1102	3.9908	9.419	0.1521	0.0074	0.0874	0.1537	-0.0273	0.264	0.2821	-0.07	-0.1257	0.2681	-0.019	0.0146	0.1935	0.0132	0.2336	-20.2104	-10.5429	26.6085
8	4.7601	1.904	-0.3719	5.6932	1.0388	2.6058	-0.0482	-0.1268	0.5484	-0.0904	0.14	0.0475	-0.0728	0.3902	-0.1164	0.2123	-0.0354	-0.0112	0.2715	-0.0028	0.2493	-11.0117	-0.1484	33.1567
9	3.0034	1.0359	-2.3823	6.7223	-1.572	7.9934	-0.2198	-0.3528	-0.1431	0.2878	0.392	-0.2712	0.1594	0.3762	-0.1016	0.1539	0.0072	-0.0461	0.3693	-0.034	0.2822	-10.8621	-2.3771	36.3777
10	4.8852	0.5773	0.0043	6.3623	-0.9396	2.7378	-0.2904	-0.0536	0.0149	-0.5828	0.1298	-0.775	0.2649	0.3577	0.0331	0.286	0.1064	0.0249	0.5079	-0.045	0.3419	0.2578	-6.9308	32.0474
11	1.7017	-0.51	0.5031	1.6593	0.8577	2.7	0.0833	-0.7681	0.4063	0.1573	0.4876	-1.0824	-0.1862	1.1277	0.0683	0.2777	-0.0075	-0.0859	0.8652	-0.214	0.7462	5.3654	1.5485	38.6267
12	8.0068	2.1295	-2.5761	3.7324	-2.0166	3.8527	-0.1676	0.1056	-0.0292	-0.2085	0.3888	-1.1448	0.3021	1.034	-0.0044	0.3397	-0.0307	0.1624	0.5791	-0.1835	0.6218	4.8265	-2.1911	27.6245

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 241 through 316 )	A	241 - 316
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 317 through 414 )	A	317 - 414
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 415 through 455 )	A	415 - 455
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 241 through 316 )	B	241 - 316
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 317 through 379 )	B	317 - 379
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 380 through 454 )	B	380 - 454
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 241 through 262 )	C	241 - 262
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 263 through 304 )	C	263 - 304
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 305 through 328 )	C	305 - 328
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 329 through 367 )	C	329 - 367
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 368 through 431 )	C	368 - 431
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 432 through 454 )	C	432 - 454

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