PDB-7cyz: The structure of human ORP3 OSBP-related domain

ID or keywords:

Entry

Database: PDB / ID: 7cyz

Title

The structure of human ORP3 OSBP-related domain

Components

Oxysterol-binding protein-related protein 3

Keywords

LIPID BINDING PROTEIN / lipid transfer protein / OSBP related protein

Function / homology

Function and homology information

perinuclear endoplasmic reticulum / filopodium tip / bile acid biosynthetic process / lipid transport / cholesterol binding / Synthesis of bile acids and bile salts / nuclear membrane / endoplasmic reticulum membrane / membrane / plasma membrane / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Dong, X.

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: The crystal structure of ORP3 reveals the conservative PI4P binding pattern.
Authors: Dong, X. / Wang, Z. / Ye, S. / Zhang, R.

History

Deposition	Sep 5, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 28, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	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	7cyz.cif.gz	325.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7cyz.ent.gz	261.5 KB	Display	PDB format
PDBx/mmJSON format	7cyz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cy/7cyz ftp://data.pdbj.org/pub/pdb/validation_reports/cy/7cyz	HTTPS FTP

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Related structure data

Related structure data	4ic4S S: Starting model for refinement
Similar structure data	4q8p-d 4us4-d 1k4h-d 6vhx-2 1wke-d 7dej-2 3mn8-2 2v3r-d 4cae-3 2cz0-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#155 - Nov 2012 Vitamin D Receptor similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1)

Deposited unit

A: Oxysterol-binding protein-related protein 3

B: Oxysterol-binding protein-related protein 3

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

1

A: Oxysterol-binding protein-related protein 3

defined by author
Evidence: gel filtration
44.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Oxysterol-binding protein-related protein 3

defined by author
44.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	95.336, 95.336, 185.251
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	A-1183- HOH

#1: Protein	Oxysterol-binding protein-related protein 3 / OSBP-related protein 3 Mass: 44324.484 Da / Num. of mol.: 2 / Mutation: L579I, C615R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OSBPL3, KIAA0704, ORP3, OSBP3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H4L5
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 505 / Source method: isolated from a natural source / Formula: H₂O
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	Density Matthews: 2.75 Å³/Da / Density % sol: 55.19 %
Crystal grow	Temperature: 289.15 K / Method: evaporation Details: 0.08 M Cacodylate sodium pH 6.6, 4.2% PEG 8000, 0.16 M Magnesium acetate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL19U1 / Wavelength: 0.97852 Å

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 6, 2014

Radiation

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

Radiation wavelength

Wavelength: 0.97852 Å / Relative weight: 1

Reflection

Resolution: 2.09→50 Å / Num. obs: 57791 / % possible obs: 100 % / Redundancy: 9.8 % / B_iso Wilson estimate: 24.32 Å² / R_merge(I) obs: 0.074 / R_pim(I) all: 0.025 / R_rim(I) all: 0.078 / Χ²: 0.984 / Net I/σ(I): 7.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.1-2.14	9.2	0.717	2825	0.84	0.247	0.76	0.946	100
2.14-2.18	8.5	0.638	2872	0.849	0.23	0.679	0.932	100
2.18-2.22	10	0.549	2838	0.909	0.18	0.578	0.93	100
2.22-2.26	10.3	0.478	2837	0.936	0.154	0.503	0.949	100
2.26-2.31	10.2	0.406	2859	0.953	0.131	0.427	0.929	100
2.31-2.37	10.2	0.339	2857	0.963	0.11	0.356	0.924	100
2.37-2.42	10.2	0.292	2852	0.971	0.095	0.307	0.913	100
2.42-2.49	10.2	0.24	2859	0.984	0.078	0.252	0.924	100
2.49-2.56	10.1	0.21	2867	0.985	0.069	0.221	0.926	100
2.56-2.65	10	0.172	2865	0.989	0.057	0.181	0.901	100
2.65-2.74	9.4	0.135	2871	0.991	0.046	0.143	0.911	100
2.74-2.85	8.9	0.114	2883	0.992	0.04	0.12	0.939	100
2.85-2.98	10.5	0.096	2880	0.996	0.031	0.1	0.927	100
2.98-3.14	10.4	0.082	2865	0.996	0.026	0.086	0.968	100
3.14-3.33	10.3	0.071	2896	0.997	0.023	0.074	0.995	100
3.33-3.59	10.1	0.061	2921	0.998	0.02	0.065	1.072	100
3.59-3.95	9.4	0.057	2918	0.997	0.02	0.06	1.126	100
3.95-4.52	9.4	0.053	2943	0.998	0.018	0.056	1.206	100
4.52-5.7	10.2	0.053	2961	0.998	0.017	0.056	1.171	100
5.7-50	9.1	0.05	3122	0.997	0.017	0.053	1.082	99.5

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Processing

Software

Name	Version	Classification
PHENIX	1.8.2_1309	refinement
HKL-2000		data scaling
PDB_EXTRACT	3.25	data extraction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4IC4

4ic4

Resolution: 2.1→41.282 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.64 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2192	2920	5.07 %
R_work	0.173	54696	-
obs	0.1754	57616	99.75 %

Solvent computation

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

Displacement parameters

B_iso max: 177.94 Å² / B_iso mean: 40.46 Å² / B_iso min: 10.34 Å²

Refinement step

Cycle: final / Resolution: 2.1→41.282 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6052	0	0	505	6557
B_iso mean	-	-	-	41.56	-
Num. residues	-	-	-	-	732

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	6434
X-RAY DIFFRACTION	f_angle_d	1.199	8732
X-RAY DIFFRACTION	f_chiral_restr	0.085	892
X-RAY DIFFRACTION	f_plane_restr	0.006	1137
X-RAY DIFFRACTION	f_dihedral_angle_d	14.309	2397

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.1-2.1331	0.2945	136	0.218	2495	97
2.1331-2.1699	0.2487	150	0.2101	2551	99
2.1699-2.2094	0.2895	141	0.2064	2535	100
2.2094-2.2519	0.2539	111	0.2042	2620	100
2.2519-2.2978	0.2827	145	0.2002	2563	100
2.2978-2.3478	0.2197	134	0.1919	2585	100
2.3478-2.4024	0.2664	149	0.1857	2542	100
2.4024-2.4625	0.2228	126	0.1858	2620	100
2.4625-2.529	0.2503	122	0.1744	2592	100
2.529-2.6034	0.2492	123	0.1818	2619	100
2.6034-2.6875	0.2319	143	0.1767	2571	100
2.6875-2.7835	0.2422	160	0.1771	2587	100
2.7835-2.8949	0.2017	127	0.1789	2628	100
2.8949-3.0266	0.2359	145	0.1795	2573	100
3.0266-3.1861	0.2556	145	0.1803	2617	100
3.1861-3.3857	0.2102	146	0.1759	2592	100
3.3857-3.647	0.1932	121	0.1629	2668	100
3.647-4.0137	0.1952	148	0.1518	2609	100
4.0137-4.5938	0.1828	155	0.1332	2656	100
4.5938-5.7852	0.1878	152	0.156	2664	100

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	0.0398	0.0864	0.0767	0.194	0.1709	0.1518	0.1444	-0.0646	-0.0663	0.0368	0.24	-0.0331	0.0423	0.1367	0.1242	0.2002	0.0129	0.0276	0.3284	0.0318	0.3217	53.679	34.188	19.78
2	0.3059	0.061	0.0855	0.2102	0.2132	0.2164	0.121	0.0254	-0.082	-0.0502	0.0214	-0.0807	-0.0071	0.0524	0.1278	0.1516	0.0601	-0.018	0.126	-0.014	0.1514	36.146	27.377	19.472
3	0.092	0.0785	-0.0047	0.1179	0.1028	0.1717	0.2401	-0.0055	-0.1981	0.0726	-0.0169	-0.0839	0.1263	-0.0802	0.2193	0.1815	0.1548	-0.1874	0.0323	0.1152	0.1489	31.916	20.545	21.878
4	0.1391	-0.1228	-0.0516	0.2342	-0.1295	0.3924	0.1603	0.1059	-0.3141	-0.1308	0.032	0.0083	0.2787	0.0272	0.1386	0.2692	0.0752	-0.1297	0.1444	-0.0853	0.3579	31.196	11.345	8.861
5	0.4127	0.0352	0.2442	0.3174	0.273	0.3376	0.1037	-0.0948	-0.0352	0.0004	0.0159	-0.1157	-0.1153	0.0273	0.0378	0.1196	0.0244	0.0231	0.1666	0.0019	0.1437	40.836	34.038	30.624
6	0.3532	0.0022	-0.0173	0.089	-0.0949	0.1004	-0.0076	-0.184	0.0983	-0.0111	-0.0051	0.0526	-0.2009	-0.1098	-0.0273	0.2258	0.1146	-0.0117	0.1987	-0.056	0.1764	29.144	43.778	28.486
7	0.0244	-0.0203	0.0185	0.0153	-0.0139	0.0125	0.0056	-0.1557	0.0941	0.0758	0.0731	-0.2126	-0.0321	0.1463	0	0.3826	-0.0074	-0.0292	0.3494	-0.0345	0.3173	71.092	21.635	-1.124
8	0.1416	-0.115	0.0598	0.1437	-0.0128	0.0807	-0.0993	-0.0428	-0.1691	-0.02	-0.006	-0.1449	0.0981	0.0804	-0	0.2696	0.0403	0.0674	0.1678	0.0149	0.243	61.939	2.943	-4.765
9	0.3786	-0.0664	0.3828	0.3691	-0.0197	0.599	-0.1208	0.0839	-0.0879	-0.0054	-0.1377	-0.001	0.0251	0.1628	-0.3521	0.3372	0.0028	0.09	0.1398	-0.0504	0.1942	58.864	9.636	-11.518
10	0.0576	0.007	-0.0365	0.0093	-0.012	0.0276	0.0081	0.0728	-0.0038	-0.2075	0.0102	0.0787	-0.1323	0.0381	0	0.4304	-0.0278	0.0195	0.1508	-0.0104	0.1849	46.946	12.199	-11.782
11	0.0589	-0.043	-0.0062	0.0343	-0.0057	0.0218	-0.0957	-0.0881	-0.0776	-0.0906	0.0559	0.2815	0.0457	-0.0089	-0	0.3118	0.013	0.0268	0.1925	-0.0205	0.2377	39.818	6.283	-7.209
12	0.3607	0.1701	0.1526	0.3413	-0.0791	0.1557	-0.0889	-0.1062	-0.2599	0.1079	-0.1517	-0.4019	-0.0472	0.1114	-0.0151	0.296	0.0512	0.0392	0.3228	0.0493	0.4562	76.561	3.356	-3.797

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 511:522 )	A	511 - 522
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 544:634 )	A	544 - 634
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 635:698 )	A	635 - 698
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 699:771 )	A	699 - 771
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 772:862 )	A	772 - 862
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 863:887 )	A	863 - 887
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 511:546 )	B	511 - 546
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 547:642 )	B	547 - 642
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 643:698 )	B	643 - 698
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 699:733 )	B	699 - 733
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 734:771 )	B	734 - 771
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 772:887 )	B	772 - 887

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