PDB-1uw5: Structure of PITP-alpha complexed to phosphatidylinositol

ID or keywords:

Entry

Database: PDB / ID: 1uw5

Title

Structure of PITP-alpha complexed to phosphatidylinositol

Components

PHOSPHATIDYLINOSITOL TRANSFER PROTEIN ALPHA ISOFORM

Keywords

TRANSPORT / TRANSFER PROTEIN / LIPID-BINDING

Function / homology

Function and homology information

phosphatidylcholine intramembrane carrier activity / phosphatidylcholine transfer activity / phosphatidylglycerol binding / phosphatidylinositol transfer activity / Role of second messengers in netrin-1 signaling / phospholipid transport / phosphatidylcholine binding / visual perception / axonogenesis / phosphatidylinositol binding ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Tilley, S.J. / Skippen, A. / Murray-Rust, J. / Cockcroft, S. / McDonald, N.Q.

Citation

Journal: Structure / Year: 2004
Title: Structure-Function Analysis of Human [Corrected] Phosphatidylinositol Transfer Protein Alpha Bound to Phosphatidylinositol.
Authors: Tilley, S.J. / Skippen, A. / Murray-Rust, J. / Swigart, P.M. / Stewart, A. / Morgan, C.P. / Cockcroft, S. / Mcdonald, N.Q.

History

Deposition	Jan 30, 2004	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 4, 2004	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.5	Dec 24, 2025	Group: Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_contact_author / pdbx_entity_nonpoly Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_contact_author.country / _pdbx_entity_nonpoly.name

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	1uw5.cif.gz	223.5 KB	Display	PDBx/mmCIF format
PDB format	pdb1uw5.ent.gz	179.3 KB	Display	PDB format
PDBx/mmJSON format	1uw5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uw/1uw5 ftp://data.pdbj.org/pub/pdb/validation_reports/uw/1uw5	HTTPS FTP

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Related structure data

Related structure data	1fvz PDB Unreleased entryS S: Starting model for refinement
Similar structure data	3d9w-3 5yli-1 5ocr-1 5y33-d 4jvl-1 3t6a-4 6qvt-2 4lrr-d 2aam-1 3av9-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) 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

Related structure data

1fvz
PDB Unreleased entryS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#128 - Aug 2010 Interferons similarity (1) #94 - Oct 2007 Superoxide Dismutase similarity (1) #163 - Jul 2013 HIV Capsid similarity (1)

Deposited unit

A: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN ALPHA ISOFORM

B: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN ALPHA ISOFORM

C: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN ALPHA ISOFORM

D: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN ALPHA ISOFORM

hetero molecules

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

1

A: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN ALPHA ISOFORM

hetero molecules

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

2

B: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN ALPHA ISOFORM

hetero molecules

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

3

C: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN ALPHA ISOFORM

hetero molecules

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

4

D: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN ALPHA ISOFORM

hetero molecules

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

Unit cell

Length a, b, c (Å)	83.262, 93.173, 161.732
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	A
2	1	B
3	1	C
4	1	D
1	2	A
2	2	B
3	2	C
4	2	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	MSE	MSE	ASN	ASN	2	A	A	1 - 45	1 - 45
2	1	1	MSE	MSE	ASN	ASN	2	B	B	1 - 45	1 - 45
3	1	1	MSE	MSE	ASN	ASN	2	C	C	1 - 45	1 - 45
4	1	1	MSE	MSE	ASN	ASN	2	D	D	1 - 45	1 - 45
1	2	1	GLU	GLU	THR	THR	6	A	A	46 - 58	46 - 58
2	2	1	GLU	GLU	THR	THR	6	B	B	46 - 58	46 - 58
3	2	1	GLU	GLU	THR	THR	6	C	C	46 - 58	46 - 58
4	2	1	GLU	GLU	THR	THR	6	D	D	46 - 58	46 - 58
1	3	1	TYR	TYR	ILE	ILE	2	A	A	57 - 98	57 - 98
2	3	1	TYR	TYR	ILE	ILE	2	B	B	57 - 98	57 - 98
3	3	1	TYR	TYR	ILE	ILE	2	C	C	57 - 98	57 - 98
4	3	1	TYR	TYR	ILE	ILE	2	D	D	57 - 98	57 - 98
1	4	1	THR	THR	LYS	LYS	6	A	A	99 - 104	99 - 104
2	4	1	THR	THR	LYS	LYS	6	B	B	99 - 104	99 - 104
3	4	1	THR	THR	LYS	LYS	6	C	C	99 - 104	99 - 104
4	4	1	THR	THR	LYS	LYS	6	D	D	99 - 104	99 - 104
1	5	1	GLU	GLU	PRO	PRO	2	A	A	105 - 262	105 - 262
2	5	1	GLU	GLU	PRO	PRO	2	B	B	105 - 262	105 - 262
3	5	1	GLU	GLU	PRO	PRO	2	C	C	105 - 262	105 - 262
4	5	1	GLU	GLU	PRO	PRO	2	D	D	105 - 262	105 - 262
1	6	1	VAL	VAL	ALA	ALA	6	A	A	263 - 268	263 - 268
2	6	1	VAL	VAL	ALA	ALA	6	B	B	263 - 268	263 - 268
3	6	1	VAL	VAL	ALA	ALA	6	C	C	263 - 268	263 - 268
4	6	1	VAL	VAL	ALA	ALA	6	D	D	263 - 268	263 - 268
1	1	2	PIE	PIE	PIE	PIE	1	A	E	1270
2	1	2	PIE	PIE	PIE	PIE	1	B	F	1270
3	1	2	PIE	PIE	PIE	PIE	1	C	G	1270
4	1	2	PIE	PIE	PIE	PIE	1	D	H	1270

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.04951, 0.92861, 0.36775), (0.94937, 0.15812, -0.27146), (-0.31023, 0.33569, -0.88942)	-48.51646, 51.89321, 105.85816
2	given	(0.20705, 0.74191, 0.63773), (-0.76701, -0.28155, 0.57657), (0.60732, -0.60852, 0.51076)	-104.35179, 95.33217, 8.54063
3	given	(-0.51518, -0.47881, 0.71087), (0.42467, 0.57783, 0.69697), (-0.74448, 0.66095, -0.09436)	45.68114, -85.81669, 82.18861

#1: Protein	PHOSPHATIDYLINOSITOL TRANSFER PROTEIN ALPHA ISOFORM / PTDINS TRANSFER PROTEIN ALPHA / PTDINSTP / PI-TP-ALPHA Mass: 32229.510 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: SELENOMETHIONINE DERIVATISED PROTEIN / Source: (gene. exp.) HOMO SAPIENS (human) / Description: ENGINEERED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q00169
#2: Chemical	ChemComp-PIE / 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol Mass: 836.061 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄₃H₈₀O₁₃P
Compound details	CATALYZES THE TRANSFER OF PTDINS AND PHOSPHATIDYLCHOLINE BETWEEN MEMBRANES.
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal

Density Matthews: 2.43 Å³/Da / Density % sol: 49 %

Crystal grow

pH: 7.5
Details: CRYSTALS WERE GROWN FROM 1.5 MICROLITRES EACH OF PROTEIN STOCK (4MG/ML, 2MM DTT) AND RESERVOIR SOLUTION (20%PEG 10K, 0.1M HEPES PH 7.5

Crystal grow

*PLUS

pH: 7.5 / Method: vapor diffusion

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Details (eV)
1	14 mg/ml	protein	1	drop
2	2 mM	dithiothreitol	1	drop
3	20 %	PEG10000	1	reservoir
4	0.1 M	HEPES	1	reservoir	pH7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.784
Detector	Type: MARRESEARCH / Detector: CCD / Date: Sep 15, 1999
Radiation	Monochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.784 Å / Relative weight: 1
Reflection	Resolution: 2.9→49.3 Å / Num. obs: 24051 / % possible obs: 85 % / Redundancy: 4.1 % / R_merge(I) obs: 0.082 / Net I/σ(I): 7.2
Reflection shell	Resolution: 2.9→3.06 Å / Redundancy: 4 % / R_merge(I) obs: 0.307 / Mean I/σ(I) obs: 2.1 / % possible all: 85
Reflection	PLUS Highest resolution: 2.9 Å / Lowest resolution: 49.3 Å / % possible obs: 84.6 % / Num. measured all: 97905 / R_merge(I) obs*: 0.082
Reflection shell	PLUS % possible obs: 84.5 % / R_merge(I) obs: 0.307 / Mean I/σ(I) obs*: 2.1

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FVZ WITH LIGAND AND MOBILE REGIONS EXCLUDED

1fvz
PDB Unreleased entry

Resolution: 2.9→15 Å / Cor.coef. F_o:F_c: 0.893 / Cor.coef. F_o:F_c free: 0.815 / SU B: 23.35 / SU ML: 0.445 / Cross valid method: THROUGHOUT / ESU R Free: 0.595 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.307	1211	5.1 %	RANDOM
R_work	0.237	-	-	-
obs	-	22663	84.2 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 15.19 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.62 Å²	0 Å²	0 Å²
2-	-	1.47 Å²	0 Å²
3-	-	-	2.15 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8563	0	164	0	8727

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.021	8951
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.062	1.954	12152
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.538	5	1071
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.13	0.2	1319
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	6752
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.277	0.2	4120
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.168	0.2	385
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.239	0.2	60
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.125	0.2	5
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.342	1.5	5363
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.722	2	8609
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.713	3	3588
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.172	4.5	3543
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	980	tight positional	0.08	0.05
1	2	B	980	tight positional	0.08	0.05
1	3	C	980	tight positional	0.08	0.05
1	4	D	980	tight positional	0.08	0.05
2	1	A	41	tight positional	0.08	0.05
2	2	B	41	tight positional	0.06	0.05
2	3	C	41	tight positional	0.07	0.05
2	4	D	41	tight positional	0.07	0.05
1	1	A	983	medium positional	0.3	0.5
1	2	B	983	medium positional	0.32	0.5
1	3	C	983	medium positional	0.36	0.5
1	4	D	983	medium positional	0.36	0.5
1	1	A	186	loose positional	1.1	5
1	2	B	186	loose positional	0.68	5
1	3	C	186	loose positional	0.57	5
1	4	D	186	loose positional	0.56	5
1	1	A	980	tight thermal	0.16	0.5
1	2	B	980	tight thermal	0.13	0.5
1	3	C	980	tight thermal	0.14	0.5
1	4	D	980	tight thermal	0.16	0.5
2	1	A	41	tight thermal	0.19	0.5
2	2	B	41	tight thermal	0.19	0.5
2	3	C	41	tight thermal	0.17	0.5
2	4	D	41	tight thermal	0.26	0.5
1	1	A	983	medium thermal	1.17	2
1	2	B	983	medium thermal	0.96	2
1	3	C	983	medium thermal	0.94	2
1	4	D	983	medium thermal	1.09	2
1	1	A	186	loose thermal	1.48	10
1	2	B	186	loose thermal	1.57	10
1	3	C	186	loose thermal	1.89	10
1	4	D	186	loose thermal	2.18	10

LS refinement shell

Resolution: 2.9→2.97 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.398	85
R_work	0.315	1599

Refinement TLS params.

Method: refined / Origin x: 33.4997 Å / Origin y: 65.4574 Å / Origin z: 61.8125 Å

	11	12	13	21	22	23	31	32	33
T	0.052 Å²	0.0359 Å²	0.0052 Å²	-	0.0483 Å²	-0.0196 Å²	-	-	0.0864 Å²
L	0.2685 °²	-0.1539 °²	0.1181 °²	-	0.2578 °²	-0.0675 °²	-	-	0.1396 °²
S	-0.0117 Å °	-0.003 Å °	0 Å °	0.0204 Å °	0.0355 Å °	-0.0734 Å °	0.0351 Å °	-0.0277 Å °	-0.0238 Å °

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 269
2	X-RAY DIFFRACTION	1	B	1 - 269
3	X-RAY DIFFRACTION	1	C	1 - 269
4	X-RAY DIFFRACTION	1	D	1 - 268

Refinement

*PLUS

Highest resolution: 2.9 Å

Solvent computation

*PLUS

Displacement parameters

*PLUS

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