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- PDB-2qa7: Crystal structure of Huntingtin-interacting protein 1 (HIP1) coil... -

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Basic information

Entry
Database: PDB / ID: 2qa7
TitleCrystal structure of Huntingtin-interacting protein 1 (HIP1) coiled-coil domain with a basic surface suitable for HIP-protein interactor (HIPPI)
ComponentsHuntingtin-interacting protein 1
KeywordsActin Binding / HIPPI-binding / Huntington's disease / apoptosis / coiled-coil
Function / homology
Function and homology information


neurotransmitter receptor transport / clathrin light chain binding / AP-2 adaptor complex binding / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / clathrin coat assembly / clathrin-coated vesicle membrane / clathrin adaptor activity / ALK mutants bind TKIs / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3-phosphate binding ...neurotransmitter receptor transport / clathrin light chain binding / AP-2 adaptor complex binding / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / clathrin coat assembly / clathrin-coated vesicle membrane / clathrin adaptor activity / ALK mutants bind TKIs / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3-phosphate binding / regulation of postsynaptic neurotransmitter receptor internalization / phosphatidylinositol-3,5-bisphosphate binding / clathrin-coated vesicle / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / clathrin binding / cortical actin cytoskeleton / regulation of endocytosis / glutamate receptor binding / presynaptic modulation of chemical synaptic transmission / phosphatidylinositol binding / apoptotic signaling pathway / actin filament organization / Schaffer collateral - CA1 synapse / : / structural constituent of cytoskeleton / positive regulation of receptor-mediated endocytosis / endocytosis / actin filament binding / Signaling by ALK fusions and activated point mutants / Clathrin-mediated endocytosis / presynapse / presynaptic membrane / regulation of apoptotic process / postsynaptic membrane / postsynapse / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / protein stabilization / protein heterodimerization activity / intracellular membrane-bounded organelle / glutamatergic synapse / apoptotic process / Golgi apparatus / protein homodimerization activity / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Huntingtin-interacting protein 1, clathrin-binding domain / Clathrin-binding domain of Huntingtin-interacting protein 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1700 / Sla2 family / AP180 N-terminal homology (ANTH) domain / ANTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / I/LWEQ domain ...Huntingtin-interacting protein 1, clathrin-binding domain / Clathrin-binding domain of Huntingtin-interacting protein 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1700 / Sla2 family / AP180 N-terminal homology (ANTH) domain / ANTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / ENTH/VHS / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Huntingtin-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsNiu, Q. / Ybe, J.A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structure at 2.8 A of Huntingtin-interacting protein 1 (HIP1) coiled-coil domain reveals a charged surface suitable for HIP1 protein interactor (HIPPI)
Authors: Ybe, J.A. / Niu, Q.
History
DepositionJun 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Huntingtin-interacting protein 1
B: Huntingtin-interacting protein 1
C: Huntingtin-interacting protein 1
D: Huntingtin-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)53,9084
Polymers53,9084
Non-polymers00
Water362
1
A: Huntingtin-interacting protein 1
B: Huntingtin-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)26,9542
Polymers26,9542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-46 kcal/mol
Surface area13370 Å2
MethodPISA
2
C: Huntingtin-interacting protein 1
D: Huntingtin-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)26,9542
Polymers26,9542
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-45 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.900, 72.900, 106.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Huntingtin-interacting protein 1 / HIP-I


Mass: 13476.979 Da / Num. of mol.: 4 / Fragment: UNP residues 363-474
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIP1 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) pLysS / References: UniProt: O00291
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG 3350, 0.1 M succinate, 0.2 M potassium sodium tartrate, 0.01 M nickle chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.96407, 0.97907, 0.97892
DetectorType: NOIR-1 / Detector: CCD / Date: Feb 7, 2007
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.964071
20.979071
30.978921
ReflectionResolution: 2.7→46.39 Å / Num. all: 15320 / Num. obs: 15320 / % possible obs: 99.8 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 7.07 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.085 / Χ2: 0.99 / Net I/σ(I): 10.3 / Scaling rejects: 820
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.72 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.9 / Num. measured all: 10273 / Num. unique all: 1523 / Rsym value: 0.45 / Χ2: 1.15 / % possible all: 99.9

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Phasing

Phasing dmFOM : 0.52 / FOM acentric: 0.52 / FOM centric: 0.57 / Reflection: 13706 / Reflection acentric: 13194 / Reflection centric: 512
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8-27.8050.890.90.8658953653
5-80.750.750.721846174799
4-50.760.760.752285219590
3.5-40.640.640.572342226379
3-3.50.380.380.4141063982124
2.8-30.170.170.22538247167

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Processing

Software
NameVersionClassificationNB
d*TREK9.7LDzdata scaling
RESOLVE2.03phasing
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
d*TREKdata reduction
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: none

Resolution: 2.8→30 Å / FOM work R set: 0.716 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: none
RfactorNum. reflection% reflectionSelection details
Rfree0.324 2030 7.5 %random
Rwork0.265 ---
obs0.32 15216 98.6 %-
all-28577 --
Solvent computationBsol: 45.382 Å2
Displacement parametersBiso mean: 61.916 Å2
Baniso -1Baniso -2Baniso -3
1-12.664 Å20 Å20 Å2
2--12.664 Å20 Å2
3----25.328 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.65 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 0 2 2814
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.19
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 40

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.8-2.820.413627
2.82-2.850.443635
2.85-2.870.382638
2.87-2.90.411671
2.9-2.930.443656
2.93-2.960.42667
2.96-2.990.359626
2.99-3.020.372280.393658686
3.02-3.050.508680.375579647
3.05-3.080.4530.327612665
3.08-3.120.438500.343561611
3.12-3.150.481690.356647716
3.15-3.190.383600.334577637
3.19-3.230.357620.309619681
3.23-3.270.391610.336579640
3.27-3.320.366860.282618704
3.32-3.370.362390.295562601
3.37-3.420.39600.314665725
3.42-3.470.417640.283621685
3.47-3.530.391760.25563639
3.53-3.590.291610.289604665
3.59-3.650.39670.274623690
3.65-3.720.337630.264607670
3.72-3.80.288710.246635706
3.8-3.880.388540.256590644
3.88-3.970.349680.264570638
3.97-4.070.221620.205641703
4.07-4.180.238600.205601661
4.18-4.30.28890.208605694
4.3-4.440.33480.197579627
4.44-4.60.292660.2622688
4.6-4.780.389470.194627674
4.78-50.285520.196592644
5-5.260.242390.213660699
5.26-5.590.398750.346584659
5.59-6.020.402640.352611675
6.02-6.620.423640.32590654
6.62-7.560.359580.263612670
7.56-9.480.176680.158605673
9.48-300.28780.227578656
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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