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- PDB-3c5n: Structure of human TULP1 in complex with IP3 -

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Basic information

Entry
Database: PDB / ID: 3c5n
TitleStructure of human TULP1 in complex with IP3
ComponentsTubby-related protein 1
KeywordsSIGNALING PROTEIN / Tubby / inositol / signalling / Alternative splicing / Disease mutation / Polymorphism / Retinitis pigmentosa / Sensory transduction / Vision / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


protein localization to photoreceptor outer segment / detection of light stimulus involved in visual perception / eye photoreceptor cell development / phagocytosis, recognition / protein localization to cilium / photoreceptor cell maintenance / retina homeostasis / dendrite development / photoreceptor outer segment / positive regulation of phagocytosis ...protein localization to photoreceptor outer segment / detection of light stimulus involved in visual perception / eye photoreceptor cell development / phagocytosis, recognition / protein localization to cilium / photoreceptor cell maintenance / retina homeostasis / dendrite development / photoreceptor outer segment / positive regulation of phagocytosis / axon terminus / phosphatidylinositol-4,5-bisphosphate binding / visual perception / photoreceptor inner segment / cell projection / cilium / actin filament binding / retina development in camera-type eye / synapse / extracellular region / plasma membrane / cytosol
Similarity search - Function
Tubby Protein; Chain A / Tubby Protein; Chain A / Tubby, C-terminal / Tubby, C-terminal, conserved site / Tub family / Tub family signature 1. / Tub family signature 2. / Tubby-like, C-terminal / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Tubby-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsBusam, R.D. / Lehtio, L. / Arrowsmith, C.H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. ...Busam, R.D. / Lehtio, L. / Arrowsmith, C.H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Herman, M.D. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van den Berg, S. / Weigelt, J. / Welin, M. / Berglund, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Structure of human TULP1 in complex with IP3
Authors: Busam, R.D. / Lehtio, L. / Arrowsmith, C.H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Herman, M.D. / ...Authors: Busam, R.D. / Lehtio, L. / Arrowsmith, C.H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Herman, M.D. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van den Berg, S. / Weigelt, J. / Welin, M. / Berglund, H. / Structural Genomics Consortium (SGC)
History
DepositionJan 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubby-related protein 1
B: Tubby-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3105
Polymers56,0502
Non-polymers1,2603
Water4,432246
1
A: Tubby-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4452
Polymers28,0251
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tubby-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8653
Polymers28,0251
Non-polymers8402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.310, 83.630, 57.680
Angle α, β, γ (deg.)90.000, 94.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tubby-related protein 1 / Tubby-like protein 1


Mass: 28024.957 Da / Num. of mol.: 2 / Fragment: UNP residues 291-536
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TULP1, TUBL1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00294
#2: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol trisphosphate


Mass: 420.096 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H15O15P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, 10 mM myo-inositol 1,4,5 trisphosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.97874 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 11, 2006 / Details: Si111
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97874 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 49455 / Num. obs: 48246 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rsym value: 0.048 / Net I/σ(I): 15.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.48 / Num. unique all: 7383 / Rsym value: 0.0538 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.004data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementResolution: 1.8→23.702 Å / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 1952 4.05 %
Rwork0.189 --
obs0.191 48245 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 6.4 Å2 / Biso mean: 33.13 Å2 / Biso min: 289.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.098 Å20 Å2-0.215 Å2
2--0.124 Å20 Å2
3----0.222 Å2
Refinement stepCycle: LAST / Resolution: 1.8→23.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7335 0 72 246 7653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097484
X-RAY DIFFRACTIONf_angle_d1.02913471
X-RAY DIFFRACTIONf_chiral_restr0.089587
X-RAY DIFFRACTIONf_plane_restr0.0061129
X-RAY DIFFRACTIONf_dihedral_angle_d16.1711939
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8450.2821250.23333923517100
1.845-1.8950.251390.2213333347299
1.895-1.9510.2471210.2093377349899
1.951-2.0130.2521290.1853325345499
2.013-2.0860.2581280.1913387351599
2.086-2.1690.2171710.1793290346199
2.169-2.2670.2321410.1713338347999
2.267-2.3870.2191690.1753298346798
2.387-2.5360.2571400.1813319345998
2.536-2.7320.2261300.1783307343797
2.732-3.0060.2081300.1883305343597
3.006-3.440.2111260.1783285341197
3.44-4.330.1921690.1693191336094
4.33-23.7040.1931340.1923146328091
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.840.33360.89992.1964-0.67684.13460.0419-0.1866-0.00570.43140.05530.04930.3434-0.1468-0.08160.10960.03320.01490.11840.00930.089287.9905-5.004131.2609
20.08450.0427-0.20610.942-0.62480.1162-0.0331-0.0238-0.0357-0.11810.00690.21250.0752-0.0805-0.05730.2426-0.0888-0.00330.15560.07370.193578.8174-19.279522.1853
32.2841-0.35080.26482.0256-0.38632.62980.1286-0.25430.1869-0.3113-0.02760.03410.0902-0.1748-0.09410.10350.020.00160.16610.00660.1585.8088-1.860315.7493
41.0306-0.78680.71651.6871-0.23972.51890.12660.1757-0.2045-1.35120.23010.47260.84860.0786-0.41130.5995-0.0985-0.11380.2167-0.02540.189880.9949-13.374310.7463
50.6857-0.5033-0.67050.5229-0.98171.4990.14540.10380.07010.07530.142-0.1131-0.22560.0414-0.20850.1713-0.0070.02560.16130.01750.195892.027811.485117.232
60.05580.1278-0.00861.40530.20932.01910.041-0.01410.04910.10970.0716-0.0389-0.0744-0.0868-0.09590.09730.0320.00890.13280.00790.136688.99384.5523.6205
71.93051.3158-0.86642.59720.18251.47850.04730.20810.0793-0.01960.0290.48250.0838-0.3776-0.03480.1047-0.0217-0.04190.18090.01570.176452.528921.04153.7847
82.06031.4669-0.76860.77071.22181.3488-0.1361-0.0481-0.63440.214-0.04160.30610.2941-0.14680.15680.1497-0.04290.02240.13690.02920.272154.31329.75527.8973
9-0.3052-0.2519-0.10711.00030.19931.3532-0.03750.08-0.1523-0.07480.0428-0.3920.05560.1476-0.00120.12-0.01910.00460.13660.00560.254868.50668.50271.5081
101.7760.2516-0.61392.39580.39011.1239-0.28250.3132-0.2969-0.46960.172-0.29010.06880.02920.1040.2387-0.08070.06010.1665-0.03490.19467.238114.767-6.1132
111.57611.0176-0.57591.392-1.11971.4557-0.21690.1478-0.1464-0.27020.0558-0.5597-0.00170.25720.0070.1189-0.02830.07530.1846-0.00430.238872.204420.3157-1.2136
121.51860.2577-0.31992.43340.3655-0.2406-0.0089-0.01080.01220.0737-0.0149-0.04690.03280.02210.01050.1116-0.0245-0.01160.13530.01130.106262.849725.04075.1775
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A238 - 327
2X-RAY DIFFRACTION2A328 - 351
3X-RAY DIFFRACTION3A352 - 383
4X-RAY DIFFRACTION4A384 - 401
5X-RAY DIFFRACTION5A402 - 432
6X-RAY DIFFRACTION6A433 - 483
7X-RAY DIFFRACTION7B238 - 278
8X-RAY DIFFRACTION8B279 - 318
9X-RAY DIFFRACTION9B319 - 363
10X-RAY DIFFRACTION10B364 - 388
11X-RAY DIFFRACTION11B389 - 430
12X-RAY DIFFRACTION12B431 - 483

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