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

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Basic information

Entry
Database: PDB / ID: 1uw5
TitleStructure of PITP-alpha complexed to phosphatidylinositol
ComponentsPHOSPHATIDYLINOSITOL TRANSFER PROTEIN ALPHA ISOFORM
KeywordsTRANSPORT / TRANSFER PROTEIN / LIPID-BINDING
Function / homology
Function and homology information


phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / phosphatidylglycerol binding / Role of second messengers in netrin-1 signaling / phosphatidylcholine binding / phospholipid transport / interleukin-12-mediated signaling pathway / visual perception / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / phosphatidylinositol binding ...phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / phosphatidylglycerol binding / Role of second messengers in netrin-1 signaling / phosphatidylcholine binding / phospholipid transport / interleukin-12-mediated signaling pathway / visual perception / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / phosphatidylinositol binding / axonogenesis / lipid metabolic process / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Phosphatidylinositol transfer protein / Phosphatidylinositol transfer protein / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL / Phosphatidylinositol transfer protein alpha isoform
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTilley, S.J. / Skippen, A. / Murray-Rust, J. / Cockcroft, S. / McDonald, N.Q.
CitationJournal: 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
DepositionJan 30, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)132,2628
Polymers128,9184
Non-polymers3,3444
Water0
1
A: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN ALPHA ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0662
Polymers32,2301
Non-polymers8361
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN ALPHA ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0662
Polymers32,2301
Non-polymers8361
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN ALPHA ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0662
Polymers32,2301
Non-polymers8361
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN ALPHA ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0662
Polymers32,2301
Non-polymers8361
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
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 number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111MSEMSEASNASN2AA1 - 451 - 45
211MSEMSEASNASN2BB1 - 451 - 45
311MSEMSEASNASN2CC1 - 451 - 45
411MSEMSEASNASN2DD1 - 451 - 45
121GLUGLUTHRTHR6AA46 - 5846 - 58
221GLUGLUTHRTHR6BB46 - 5846 - 58
321GLUGLUTHRTHR6CC46 - 5846 - 58
421GLUGLUTHRTHR6DD46 - 5846 - 58
131TYRTYRILEILE2AA57 - 9857 - 98
231TYRTYRILEILE2BB57 - 9857 - 98
331TYRTYRILEILE2CC57 - 9857 - 98
431TYRTYRILEILE2DD57 - 9857 - 98
141THRTHRLYSLYS6AA99 - 10499 - 104
241THRTHRLYSLYS6BB99 - 10499 - 104
341THRTHRLYSLYS6CC99 - 10499 - 104
441THRTHRLYSLYS6DD99 - 10499 - 104
151GLUGLUPROPRO2AA105 - 262105 - 262
251GLUGLUPROPRO2BB105 - 262105 - 262
351GLUGLUPROPRO2CC105 - 262105 - 262
451GLUGLUPROPRO2DD105 - 262105 - 262
161VALVALALAALA6AA263 - 268263 - 268
261VALVALALAALA6BB263 - 268263 - 268
361VALVALALAALA6CC263 - 268263 - 268
461VALVALALAALA6DD263 - 268263 - 268
112PIEPIEPIEPIE1AE1270
212PIEPIEPIEPIE1BF1270
312PIEPIEPIEPIE1CG1270
412PIEPIEPIEPIE1DH1270

NCS ensembles :
ID
1
2

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

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Components

#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 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL


Mass: 836.061 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C43H80O13P
Compound detailsCATALYZES THE TRANSFER OF PTDINS AND PHOSPHATIDYLCHOLINE BETWEEN MEMBRANES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-IDDetails
114 mg/mlprotein1drop
22 mMdithiothreitol1drop
320 %PEG100001reservoir
40.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.784
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 1999
RadiationMonochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.784 Å / Relative weight: 1
ReflectionResolution: 2.9→49.3 Å / Num. obs: 24051 / % possible obs: 85 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 7.2
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 4 % / Rmerge(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 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 84.5 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod 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. Fo:Fc: 0.893 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflectionSelection details
Rfree0.307 1211 5.1 %RANDOM
Rwork0.237 ---
obs-22663 84.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 15.19 Å2
Baniso -1Baniso -2Baniso -3
1--3.62 Å20 Å20 Å2
2--1.47 Å20 Å2
3---2.15 Å2
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8563 0 164 0 8727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0218951
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0621.95412152
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53851071
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.130.21319
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026752
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2770.24120
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2385
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3421.55363
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.72228609
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.71333588
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1724.53543
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A980tight positional0.080.05
12B980tight positional0.080.05
13C980tight positional0.080.05
14D980tight positional0.080.05
21A41tight positional0.080.05
22B41tight positional0.060.05
23C41tight positional0.070.05
24D41tight positional0.070.05
11A983medium positional0.30.5
12B983medium positional0.320.5
13C983medium positional0.360.5
14D983medium positional0.360.5
11A186loose positional1.15
12B186loose positional0.685
13C186loose positional0.575
14D186loose positional0.565
11A980tight thermal0.160.5
12B980tight thermal0.130.5
13C980tight thermal0.140.5
14D980tight thermal0.160.5
21A41tight thermal0.190.5
22B41tight thermal0.190.5
23C41tight thermal0.170.5
24D41tight thermal0.260.5
11A983medium thermal1.172
12B983medium thermal0.962
13C983medium thermal0.942
14D983medium thermal1.092
11A186loose thermal1.4810
12B186loose thermal1.5710
13C186loose thermal1.8910
14D186loose thermal2.1810
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.398 85
Rwork0.315 1599
Refinement TLS params.Method: refined / Origin x: 33.4997 Å / Origin y: 65.4574 Å / Origin z: 61.8125 Å
111213212223313233
T0.052 Å20.0359 Å20.0052 Å2-0.0483 Å2-0.0196 Å2--0.0864 Å2
L0.2685 °2-0.1539 °20.1181 °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
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 269
2X-RAY DIFFRACTION1B1 - 269
3X-RAY DIFFRACTION1C1 - 269
4X-RAY DIFFRACTION1D1 - 268
Refinement
*PLUS
Highest resolution: 2.9 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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