PDB-9jyx: Crystal structure of Nir2 DDHD domain

ID or keywords:

Entry

Database: PDB / ID: 9jyx

Title

Crystal structure of Nir2 DDHD domain

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 / phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / phospholipid transport / phosphatidic acid binding / phosphatidylcholine binding / phosphatidylinositol biosynthetic process / Golgi cisterna membrane / cleavage furrow / phototransduction ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.798 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	9jyx.cif.gz	359 KB	Display	PDBx/mmCIF format
PDB format	pdb9jyx.ent.gz	296.1 KB	Display	PDB format
PDBx/mmJSON format	9jyx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9jyx_validation.pdf.gz	459 KB	Display	wwPDB validaton report
Full document	9jyx_full_validation.pdf.gz	474.3 KB	Display
Data in XML	9jyx_validation.xml.gz	36.6 KB	Display
Data in CIF	9jyx_validation.cif.gz	47.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jy/9jyx ftp://data.pdbj.org/pub/pdb/validation_reports/jy/9jyx	HTTPS FTP

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Related structure data

Related structure data	9jz1C 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

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

1

A: Membrane-associated phosphatidylinositol transfer protein 1

B: Membrane-associated phosphatidylinositol transfer protein 1

hetero molecules

defined by author&software
Evidence: gel filtration
77.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Membrane-associated phosphatidylinositol transfer protein 1

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

Unit cell

Length a, b, c (Å)	130.243, 130.243, 105.573
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Membrane-associated phosphatidylinositol transfer protein 1 / Drosophila retinal degeneration B homolog / Phosphatidylinositol transfer protein / membrane- ...Drosophila retinal degeneration B homolog / Phosphatidylinositol transfer protein / membrane-associated 1 / PITPnm 1 / Pyk2 N-terminal domain-interacting receptor 2 / NIR-2 Mass: 38509.840 Da / Num. of mol.: 3 / Fragment: DDHD domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PITPNM1, DRES9, NIR2, PITPNM / Production host: Escherichia coli (E. coli) / References: UniProt: O00562
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.24 Å³/Da / Density % sol: 45.15 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12% PEG 3350, 100mM HEPES pH 7.5, 0.15M ammonium sulfate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: PAL/PLS

/ Beamline: 11C / Wavelength: 0.9794 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2022

Radiation

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

Radiation wavelength

Wavelength: 0.9794 Å / Relative weight: 1

Reflection

Resolution: 2.79→50 Å / Num. obs: 25905 / % possible obs: 100 % / Redundancy: 10.9 % / CC_1/2: 0.99 / CC star: 0.998 / R_merge(I) obs: 0.089 / R_pim(I) all: 0.028 / R_rim(I) all: 0.093 / Χ²: 0.708 / Net I/σ(I): 5.7

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
2.8-2.85	9.9	0.996	1287	0.763	0.93	0.328	1.049	0.397	100
2.85-2.9	11.2	0.885	1274	0.812	0.947	0.275	0.928	0.443	100
2.9-2.96	11.2	0.779	1277	0.859	0.961	0.242	0.816	0.443	100
2.96-3.02	11.1	0.617	1245	0.918	0.978	0.192	0.647	0.443	100
3.02-3.08	11.2	0.544	1293	0.93	0.982	0.169	0.57	0.477	100
3.08-3.15	10.9	0.439	1276	0.95	0.987	0.138	0.46	0.481	100
3.15-3.23	11	0.346	1305	0.968	0.992	0.108	0.362	0.502	99.8
3.23-3.32	10.7	0.284	1274	0.977	0.994	0.09	0.298	0.523	100
3.32-3.42	10.3	0.214	1305	0.985	0.996	0.069	0.225	0.552	100
3.42-3.53	10.1	0.151	1259	0.991	0.998	0.049	0.159	0.586	99.9
3.53-3.65	11.5	0.138	1300	0.994	0.998	0.042	0.144	0.645	100
3.65-3.8	11.4	0.117	1275	0.996	0.999	0.036	0.122	0.698	100
3.8-3.97	11.2	0.097	1285	0.996	0.999	0.03	0.102	0.74	100
3.97-4.18	11.2	0.081	1302	0.997	0.999	0.025	0.085	0.818	99.9
4.18-4.44	10.8	0.073	1289	0.997	0.999	0.023	0.077	0.924	99.6
4.44-4.79	10.5	0.065	1306	0.998	0.999	0.021	0.068	0.985	100
4.79-5.27	11.4	0.065	1306	0.997	0.999	0.02	0.069	1.016	100
5.27-6.03	11.1	0.065	1310	0.998	0.999	0.02	0.068	1.015	100
6.03-7.59	10.3	0.058	1345	0.998	1	0.019	0.061	1.007	99.9
7.59-50	10.3	0.049	1392	0.998	1	0.016	0.051	1.398	99.9

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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: 2.798→49.744 Å / SU ML: 0.33 / Cross valid method: NONE / σ(F): 1.39 / Phase error: 26.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2506	1289	4.98 %
R_work	0.2005	-	-
obs	0.203	25883	99.95 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.798→49.744 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6867	0	5	1	6873

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	7150
X-RAY DIFFRACTION	f_angle_d	1.189	9755
X-RAY DIFFRACTION	f_dihedral_angle_d	13.237	2488
X-RAY DIFFRACTION	f_chiral_restr	0.045	1133
X-RAY DIFFRACTION	f_plane_restr	0.006	1249

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 (%)
2.798-2.91	0.3385	142	0.2673	2659	X-RAY DIFFRACTION	100
2.91-3.0425	0.322	145	0.2575	2722	X-RAY DIFFRACTION	100
3.0425-3.2028	0.2649	142	0.2441	2699	X-RAY DIFFRACTION	100
3.2028-3.4035	0.2676	139	0.2357	2718	X-RAY DIFFRACTION	100
3.4035-3.6662	0.2799	142	0.2128	2701	X-RAY DIFFRACTION	100
3.6662-4.035	0.254	142	0.2012	2725	X-RAY DIFFRACTION	100
4.035-4.6185	0.2457	142	0.1859	2738	X-RAY DIFFRACTION	100
4.6185-5.8174	0.2698	142	0.1905	2763	X-RAY DIFFRACTION	100
5.8174-49.744	0.2057	153	0.1802	2869	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	9.3747	-0.3343	0.0553	1.8621	2.4367	3.9803	-0.3263	0.0169	-0.5726	0.0503	0.1832	-0.7475	0.1846	0.6201	0.3218	0.6141	-0.0947	-0.0668	0.5668	0.0291	0.4998	79.451	12.614	-15.392
2	3.9174	1.4423	-1.4757	3.0223	-0.7566	4.6206	-0.4027	0.4707	-0.2675	-0.22	0.0129	-0.5829	-0.1475	0.1458	0.3318	0.5147	0.0015	-0.1242	0.4283	-0.1396	0.6469	73.808	9.985	-16.488
3	3.0979	1.5993	-1.748	1.7962	-0.2628	2.6576	-0.1807	0.0529	-0.0513	0.0418	0.008	-0.3126	-0.0399	0.3392	0.1234	0.6922	-0.0474	-0.1884	0.6052	0.0092	0.5803	77.121	14.281	-8.236
4	3.9696	-0.2356	-1.6211	2.7836	-0.7303	0.7492	0.2029	-0.7406	0.9643	0.6492	-0.2731	-0.5699	-0.6646	0.4226	-0.0127	0.8853	-0.1731	-0.201	0.4854	-0.1021	0.6455	72.031	24.109	-4.888
5	3.3946	-0.4854	-1.461	4.96	-0.0422	1.9681	0.049	0.2442	0.2841	-0.3442	-0.1673	0.2266	-0.5817	-0.0458	0.1181	0.7961	-0.0851	-0.2289	0.4262	-0.0087	0.5805	62.555	24.961	-18.369
6	7.5901	-2.0232	-1.5222	1.1535	2.5186	6.2324	-0.2295	-0.0221	0.7405	0.0064	0.4396	0.6919	0.32	-0.9161	-0.3143	0.8271	-0.1073	0.124	0.6232	-0.1231	0.7332	36.737	11.603	14.265
7	3.2647	0.4525	-0.8037	2.7353	-1.4408	1.9687	0.0367	-0.591	0.1962	0.9534	0.0583	0.5242	-0.6157	-0.241	-0.1381	0.9846	0.1028	0.1601	0.5686	-0.1904	0.5597	41.707	12.078	11.667
8	3.5919	-0.1803	-0.5013	5.6815	2.1929	4.7765	-0.5991	-1.1244	0.0358	1.2182	0.8521	0.1314	-0.2623	0.6676	-0.0851	1.3426	0.0943	0.1001	0.7526	-0.0489	0.533	47.019	8.992	22.89
9	5.1597	-0.0855	0.7781	4.3388	-1.6621	2.6042	0.1533	-0.3655	-0.4827	0.7013	-0.1377	0.0936	-0.0349	0.1697	-0.0445	0.8448	-0.0107	-0.0299	0.4668	-0.05	0.4022	50.922	-3.003	11.832
10	4.0413	-0.9744	1.5802	1.4339	0.8883	1.8602	0.0793	-0.3712	0.9116	1.929	0.072	0.4028	-1.4503	0.3047	-0.4452	1.5199	0.1059	0.6813	0.6363	0.0843	1.1382	27.089	27.628	-9.965
11	6.4193	-0.0886	1.2759	4.9737	1.3931	5.3936	0.7653	-0.5185	-1.0245	1.0295	0.343	0.9692	-0.0038	-0.0159	-0.8035	0.8096	-0.0816	0.2913	0.5585	0.1229	1.2104	25.158	-0.924	-7.19
12	1.6545	-1.3884	0.0002	2.9928	-1.0917	2.3727	0.0302	-0.3771	0.5329	1.0339	0.6451	2.4247	-0.9354	-0.7138	-0.2028	0.9204	0.3039	0.5562	0.7584	0.1655	1.7582	16.15	20.824	-16.97
13	2.5735	-0.2193	1.6827	8.5858	-1.1154	6.355	0.4641	0.4202	0.2932	-0.2605	0.0379	1.0019	-0.6519	0.3315	-0.3666	0.7461	0.0759	0.1284	0.6372	0.1161	0.8197	29.317	20.044	-27.475

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 423:448 )	A	423 - 448
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 449:504 )	A	449 - 504
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 505:564 )	A	505 - 564
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 565:717 )	A	565 - 717
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 718:879 )	A	718 - 879
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 424:448 )	B	424 - 448
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 449:576 )	B	449 - 576
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 577:698 )	B	577 - 698
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 699:880 )	B	699 - 880
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 425:486 )	C	425 - 486
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 487:527 )	C	487 - 527
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 528:740 )	C	528 - 740
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 741:880 )	C	741 - 880

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