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- PDB-3i00: Crystal Structure of the huntingtin interacting protein 1 coiled ... -

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Basic information

Entry
Database: PDB / ID: 3i00
TitleCrystal Structure of the huntingtin interacting protein 1 coiled coil domain
ComponentsHuntingtin-interacting protein 1
KeywordsTRANSCRIPTION
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-phosphate binding / phosphatidylinositol-3,4-bisphosphate 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-phosphate binding / phosphatidylinositol-3,4-bisphosphate 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 / 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 / activation of cysteine-type endopeptidase activity involved in apoptotic process / actin filament binding / Signaling by ALK fusions and activated point mutants / presynapse / Clathrin-mediated endocytosis / presynaptic membrane / postsynapse / postsynaptic membrane / regulation of apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / cytoskeleton / protein stabilization / protein heterodimerization activity / intracellular membrane-bounded organelle / glutamatergic synapse / apoptotic process / Golgi apparatus / protein homodimerization activity / membrane / nucleus / cytoplasm / cytosol
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsWilbur, J.D. / Hwang, P.K. / Brodsky, F.M. / Fletterick, R.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Accommodation of structural rearrangements in the huntingtin-interacting protein 1 coiled-coil domain.
Authors: Wilbur, J.D. / Hwang, P.K. / Brodsky, F.M. / Fletterick, R.J.
History
DepositionJun 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software

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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


Theoretical massNumber of molelcules
Total (without water)28,3872
Polymers28,3872
Non-polymers00
Water1,17165
1
A: Huntingtin-interacting protein 1

B: Huntingtin-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)28,3872
Polymers28,3872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area4180 Å2
ΔGint-41 kcal/mol
Surface area11200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.801, 57.092, 81.161
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14193.721 Da / Num. of mol.: 2 / Fragment: Residues 361-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIP1, huntingtin interactin protein 1 (HIP1) / Plasmid: modified pRSF-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00291
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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

Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 6.5
Details: 50mM MES pH 6.5, 17.5% PEG 6000, sitting drop vapor diffusion, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→40.59 Å / Num. obs: 7765 / % possible obs: 99.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 32.784
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.3-2.383.40.176196.8
2.38-2.4840.136199.1
2.48-2.594.10.104199.4
2.59-2.734.10.094199.2
2.73-2.94.10.066199.7
2.9-3.1240.047199.7
3.12-3.4440.036199.7
3.44-3.9340.03199.7
3.93-4.953.90.025199.7
4.95-503.60.018198.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→40.59 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 21.984 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28038 394 5.1 %RANDOM
Rwork0.23462 ---
obs0.23709 7331 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.344 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1281 0 0 65 1346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211289
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9721721
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4335154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80324.81581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.25915266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0341516
X-RAY DIFFRACTIONr_chiral_restr0.1080.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02982
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.2560
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2830.2870
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.2113
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2550.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.231.5804
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.97721224
X-RAY DIFFRACTIONr_scbond_it1.8213524
X-RAY DIFFRACTIONr_scangle_it2.7724.5497
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 17 -
Rwork0.266 511 -
obs--95.65 %
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)
17.49083.1901-11.83694.9645-13.943754.105-0.64280.4057-0.2366-0.4742-0.3005-0.21552.99280.05160.9433-0.0366-0.3361-0.1657-0.2351-0.3152-0.02314.574-4.536-61.963
20.66690.1389-0.15981.74-9.581958.335-0.10210.05970.02030.27980.1292-0.0207-0.109-0.9555-0.0271-0.1508-0.2386-0.2273-0.2165-0.2174-0.02387.077-11.651-5.351
33.93550.7353-3.63494.90650.863126.25450.23740.85480.1339-0.3467-0.0087-0.30650.6737-1.5773-0.2287-0.3045-0.2707-0.2567-0.0761-0.1983-0.0384-1.663-5.172-27.792
40.83412.1415.46987.32218.637153.4396-0.06610.0195-0.0408-0.04470.0250.019-0.5496-0.51550.0411-0.264-0.2081-0.2236-0.1257-0.2676-0.03514.42914.13929.784
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A370 - 398
2X-RAY DIFFRACTION2A399 - 445
3X-RAY DIFFRACTION3B367 - 389
4X-RAY DIFFRACTION4B390 - 446

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