PDB-9jz1: Crystal structure of Nir2 C-terminal domain in complex with phosphate

ID or keywords:

Entry

Database: PDB / ID: 9jz1

Title

Crystal structure of Nir2 C-terminal domain in complex with phosphate

Components

Membrane-associated phosphatidylinositol transfer protein 1

Keywords

LIPID BINDING PROTEIN / PLC signaling / PI cycle / Membrane contact site / lipid transfer / lipid binding

Function / homology

Function and homology information

Synthesis of PI / phosphatidylinositol transfer activity / phosphatidic acid binding / phosphatidylcholine binding / Golgi cisterna membrane / cleavage furrow / lipid droplet / phosphatidylinositol binding / receptor tyrosine kinase binding / phospholipid binding ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.402 Å

Authors

Kim, D. / Lee, C.

Funding support

Korea, Republic Of, 2items

Citation

Journal: To Be Published
Title: Ni r2 crystal structures reveal a phosphatidic acid sensing mechanism at ER-PM contact sites
Authors: Kim, D. / Lee, S. / Jun, Y. / Lee, C.

History

Deposition	Oct 13, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 15, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9jz1.cif.gz	299.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9jz1.ent.gz	243 KB	Display	PDB format
PDBx/mmJSON format	9jz1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9jz1_validation.pdf.gz	979.3 KB	Display	wwPDB validaton report
Full document	9jz1_full_validation.pdf.gz	993.1 KB	Display
Data in XML	9jz1_validation.xml.gz	32.7 KB	Display
Data in CIF	9jz1_validation.cif.gz	43.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jz/9jz1 ftp://data.pdbj.org/pub/pdb/validation_reports/jz/9jz1	HTTPS FTP

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Related structure data

Related structure data	9jyxC 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

Deposited unit

A: Membrane-associated phosphatidylinositol transfer protein 1

B: Membrane-associated phosphatidylinositol transfer protein 1

C: Membrane-associated phosphatidylinositol transfer protein 1

hetero molecules

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

1

A: Membrane-associated phosphatidylinositol transfer protein 1

hetero molecules

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

2

B: Membrane-associated phosphatidylinositol transfer protein 1

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

3

C: Membrane-associated phosphatidylinositol transfer protein 1

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

Unit cell

Length a, b, c (Å)	69.978, 108.844, 120.582
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Membrane-associated phosphatidylinositol transfer protein 1 / Drosophila retinal degeneration B homolog 1 / RdgB1 / Mpt-1 / Phosphatidylinositol transfer protein ...Drosophila retinal degeneration B homolog 1 / RdgB1 / Mpt-1 / Phosphatidylinositol transfer protein / membrane-associated 1 / PITPnm 1 / Pyk2 N-terminal domain-interacting receptor 2 / NIR-2 Mass: 30703.957 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pitpnm1, Dres9, Mpt1, Nir2, Pitpnm / Production host: Escherichia coli (E. coli) / References: UniProt: O35954
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.51 Å³/Da / Density % sol: 51.03 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 9% polyethylene glycol (PEG) 4000, 100mM HEPES pH 7.5, 1% ethanol, 4mM calcium chloride

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: PAL/PLS

/ Beamline: 5C (4A) / Wavelength: 0.9794 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 22, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.9794 Å / Relative weight: 1

Reflection

Resolution: 2.4→50 Å / Num. obs: 36175 / % possible obs: 98.6 % / Redundancy: 5.4 % / CC_1/2: 0.981 / CC star: 0.995 / R_merge(I) obs: 0.108 / R_pim(I) all: 0.047 / R_rim(I) all: 0.118 / Χ²: 1.717 / Net I/σ(I): 8 / Num. measured all: 193557

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
2.4-2.44	3.6	0.456	1738	0.152	0.513	0.259	0.528	0.853	97.8
2.44-2.49	3.7	0.44	1765	0.198	0.574	0.245	0.507	0.899	96.7
2.49-2.53	3.8	0.439	1764	0.203	0.58	0.246	0.506	0.928	97.6
2.53-2.59	4	0.419	1760	0.289	0.67	0.225	0.479	0.961	97.5
2.59-2.64	4.1	0.412	1740	0.369	0.734	0.217	0.469	1.048	97
2.64-2.7	4.1	0.392	1755	0.576	0.855	0.207	0.447	1.121	97.5
2.7-2.77	4.4	0.365	1768	0.611	0.871	0.183	0.41	1.143	98.1
2.77-2.85	4.6	0.332	1797	0.726	0.917	0.163	0.372	1.168	98.4
2.85-2.93	4.8	0.305	1799	0.821	0.95	0.146	0.34	1.211	98.6
2.93-3.02	5	0.264	1807	0.893	0.971	0.123	0.292	1.367	99.2
3.02-3.13	5.3	0.227	1776	0.933	0.983	0.103	0.25	1.422	98.9
3.13-3.26	5.8	0.181	1815	0.967	0.992	0.079	0.198	1.556	99.3
3.26-3.41	6.2	0.154	1844	0.98	0.995	0.065	0.167	1.708	99.6
3.41-3.58	6.5	0.127	1807	0.989	0.997	0.052	0.137	1.892	99.8
3.58-3.81	6.7	0.108	1831	0.991	0.998	0.044	0.116	2.052	99.7
3.81-4.1	6.6	0.092	1849	0.994	0.999	0.037	0.099	2.232	99.5
4.1-4.52	6.8	0.076	1838	0.995	0.999	0.03	0.082	2.405	99.5
4.52-5.17	7	0.069	1859	0.996	0.999	0.027	0.074	2.464	99.5
5.17-6.51	6.8	0.069	1891	0.996	0.999	0.028	0.074	2.165	99.7
6.51-50	6.6	0.058	1972	0.997	0.999	0.024	0.063	2.461	98.3

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.402→33.603 Å / SU ML: 0.4 / Cross valid method: NONE / σ(F): 1.46 / Phase error: 26.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2602	1808	5 %
R_work	0.2108	-	-
obs	0.2133	36142	98.68 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.402→33.603 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5737	0	6	116	5859

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5777
X-RAY DIFFRACTION	f_angle_d	1.03	7873
X-RAY DIFFRACTION	f_dihedral_angle_d	12.689	2012
X-RAY DIFFRACTION	f_chiral_restr	0.041	905
X-RAY DIFFRACTION	f_plane_restr	0.005	1015

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 (%)
2.402-2.4669	0.3658	134	0.3565	2541	X-RAY DIFFRACTION	97
2.4669-2.5395	0.344	135	0.332	2570	X-RAY DIFFRACTION	97
2.5395-2.6214	0.3289	135	0.3022	2555	X-RAY DIFFRACTION	98
2.6214-2.7151	0.3633	135	0.2917	2576	X-RAY DIFFRACTION	97
2.7151-2.8237	0.3094	137	0.2649	2606	X-RAY DIFFRACTION	98
2.8237-2.9522	0.3005	138	0.2485	2611	X-RAY DIFFRACTION	99
2.9522-3.1077	0.3168	139	0.247	2647	X-RAY DIFFRACTION	99
3.1077-3.3022	0.2977	137	0.2335	2619	X-RAY DIFFRACTION	99
3.3022-3.557	0.2689	141	0.2054	2674	X-RAY DIFFRACTION	100
3.557-3.9144	0.2453	141	0.1864	2677	X-RAY DIFFRACTION	100
3.9144-4.4797	0.2051	142	0.1614	2690	X-RAY DIFFRACTION	100
4.4797-5.6396	0.1891	144	0.1504	2722	X-RAY DIFFRACTION	100
5.6396-33.603	0.2331	150	0.1812	2846	X-RAY DIFFRACTION	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	0.8068	0.03	0.1835	0.446	0.0329	1.4764	0.457	0.3323	0.1701	0.0167	-0.3453	-0.2877	-0.4723	1.2576	0.0338	0.2929	0.0181	0.1582	0.4283	0.0129	0.3131	-23.6707	11.4424	1.3691
2	0.1791	-0.1573	-0.7174	-0.0553	0.1527	1.6978	0.1617	-0.3244	-0.0906	-0.0242	0.0139	-0.0363	-0.3302	0.4021	0.0641	0.1989	-0.0404	0.001	0.3639	-0.0339	0.2504	-26.1314	11.1616	9.328
3	0.2542	0.1928	-0.1045	0.6278	0.4512	1.1131	-0.1029	-0.1454	0.0318	-0.1213	0.0296	0.0425	-0.069	0.0336	-0.0007	0.3647	0.0654	0.0076	0.1261	-0.0041	0.2917	-32.117	8.5579	-13.4564
4	-0.0418	-0.0982	0.1285	0.3038	-0.2114	0.7394	0.1821	-0.1486	-0.1747	-0.3964	-0.4294	0.3049	-0.5751	-0.1397	-0.0231	0.3926	0.0569	0.0381	0.2113	0.0184	0.2811	-32.1017	14.7496	-9.7597
5	0.3641	-0.1087	-0.0488	0.8044	-0.3984	0.2331	-0.7349	-0.1795	0.1719	-0.5759	0.3461	-0.0547	-0.745	-0.0318	-0.1	0.4004	-0.0887	-0.012	0.295	-0.0054	0.3562	-29.6191	14.8535	-9.7007
6	0.4536	0.3283	-0.4446	0.3876	-0.2561	0.5269	0.081	0.0259	-0.1668	-0.1763	0.0616	-0.0635	-0.3495	0.7877	0.026	0.3406	-0.0333	0.1159	0.3345	0.028	0.3578	-19.1898	11.6246	-16.8298
7	0.9672	-0.0073	0.0399	2.413	-0.4515	0.6213	-0.6439	-0.0794	-0.4852	-0.4829	0.9421	0.3187	0.395	-0.4124	0.0318	0.4435	-0.0364	0.0636	0.5019	0.0549	0.2998	-25.4838	12.1298	-28.9392
8	0.3975	0.0621	0.3796	0.0619	0.0769	0.3552	-0.4503	0.6607	-0.7715	-0.968	0.5663	0.2961	0.152	0.1409	-0.0065	0.5557	0.0209	0.0156	0.4761	-0.0741	0.5013	-26.1179	15.2469	-33.578
9	0.2392	-0.4272	-0.1045	1.3651	0.3542	0.1171	-0.0895	0.1256	0.5054	-1.3505	0.2658	0.0985	-0.0931	-0.0098	0.0547	0.5299	-0.0548	-0.094	0.325	0.015	0.3224	-35.1958	3.5359	-28.4418
10	0.5774	0.4258	0.6776	0.4281	-0.2661	0.8868	-0.032	0.0986	0.019	-0.0107	0.0945	0.0813	0.0656	0.2101	0.0001	0.2865	-0.0133	0.0018	0.2747	0.0112	0.2927	-12.279	40.8009	-27.1871
11	0.5641	-0.0351	0.3511	0.5698	-0.015	0.169	0.1155	0.0886	0.1667	-0.0666	-0.0958	0.1751	-0.2	0.2689	0.0005	0.3876	-0.0156	0.0434	0.3955	0.048	0.3535	-23.5604	41.9403	-38.3708
12	0.5094	-0.1203	0.578	0.0491	-0.2942	0.4177	0.0794	-0.1993	-0.2974	-0.5852	0.1839	0.9039	0.3486	-0.3307	0.0167	0.4166	-0.0999	-0.0879	0.404	0.0471	0.6801	-39.994	36.9586	-36.7543
13	0.3066	-0.4487	0.37	0.6118	-0.3368	0.3422	0.0509	-0.0599	0.3491	-0.1568	0.4648	-0.4803	0.1712	-0.1885	0.0138	0.3872	-0.159	0.005	0.6319	-0.0573	0.4288	-26.6889	59.645	0.7714
14	0.2307	0.2023	0.3078	0.7278	0.6051	0.5911	0.0616	-0.2766	-0.1491	0.4898	-0.4402	-0.1611	0.6551	-0.4668	-0.0169	0.4245	-0.1857	0.0199	0.8392	0.0207	0.4418	-31.8747	59.3069	10.261
15	0.4657	-0.0635	-0.0113	0.6764	0.2897	0.2311	-0.1102	0.0856	0.0773	-0.0315	0.0081	-0.137	0.7807	-1.2968	-0.001	0.6427	-0.2441	0.0298	0.9557	-0.0277	0.5682	-33.8726	55.2758	-2.913
16	0.1456	-0.212	-0.0315	1.2329	0.1425	0.0613	0.1071	0.0185	0.2525	-0.3512	0.0108	-0.0271	-0.2105	-0.4167	0.02	0.3474	-0.0989	0.016	0.6533	-0.0239	0.3319	-26.1868	63.7065	-3.3779
17	0.0475	-0.0295	-0.0109	0.1129	0.1071	0.0182	0.2739	0.2072	0.587	-0.2183	0.2074	0.0554	0.0161	0.2742	-0.0006	0.6173	-0.0252	0.0322	0.6432	0.1429	0.622	-14.8679	79.5656	-6.8839
18	0.0844	0.0355	0.0435	0.0377	0.0668	0.0329	-0.0857	0.0525	0.3213	-0.2039	-0.0976	-0.194	0.0054	-0.5253	0.0007	0.3601	-0.1014	0.0348	0.482	0.0703	0.4272	-16.1459	68.8814	-4.5426
19	0.5991	-0.0162	0.6273	0.4761	-0.4381	0.776	0.4337	-0.3046	0.477	0.134	-0.2616	0.2902	-0.0719	-0.5243	0.0461	0.4813	0.0296	0.0301	0.5013	-0.005	0.4206	-23.3957	73.4043	5.2793
20	0.3248	0.0422	-0.4469	0.3287	0.3269	0.7385	-0.0669	0.0213	0.3389	0.6469	-0.0631	0.2545	-0.2374	-0.4007	0.0002	0.529	-0.0286	0.0566	0.5001	0.0413	0.4067	-17.242	65.2567	2.3374
21	0.3399	-0.2772	0.1103	0.2352	-0.2351	0.2858	-0.3546	0.1118	-0.1988	-0.1146	0.4288	-0.4822	0.4248	-0.1239	0.0002	0.4876	-0.0705	0.0484	0.4406	0.0235	0.3985	-10.3714	61.1697	-5.4297
22	0.0687	-0.1707	0.2036	0.8677	-0.7311	0.7821	0.216	-0.0557	0.3281	0.0267	-0.4243	-0.5614	0.716	-0.1508	-0.0259	0.4127	-0.1068	0.0477	0.4528	0.0624	0.6156	-2.0799	68.3263	-5.7782
23	0.1847	-0.223	-0.1361	0.3389	0.4816	1.7966	0.2929	0.291	1.2394	0.3184	0.1037	-0.2871	-0.6401	1.0149	0.1117	0.5563	-0.073	0.206	0.3532	0.0982	1.0076	-1.054	79.1573	-7.1079

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 915 through 937 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 938 through 1006 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1007 through 1056 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1057 through 1081 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1082 through 1098 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 1099 through 1134 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 1135 through 1148 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 1149 through 1161 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 1162 through 1174 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 914 through 1081 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1082 through 1134 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 1135 through 1174 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 914 through 932 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 933 through 957 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 958 through 992 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 993 through 1029 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 1030 through 1056 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 1057 through 1068 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 1069 through 1081 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 1082 through 1101 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 1102 through 1124 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 1125 through 1143 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 1144 through 1168 )

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