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- PDB-2no2: Crystal structure of the DLLRKN-containing coiled-coil domain of ... -

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Basic information

Entry
Database: PDB / ID: 2no2
TitleCrystal structure of the DLLRKN-containing coiled-coil domain of Huntingtin-interacting protein 1
ComponentsHuntingtin-interacting protein 1
KeywordsCELL ADHESION / clathrin light chain binding / HIP1 coiled-coil domain / endocytosis / clathrin self-assembly
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 / Signaling by ALK fusions and activated point mutants / structural constituent of cytoskeleton / positive regulation of receptor-mediated endocytosis / endocytosis / activation of cysteine-type endopeptidase activity involved in apoptotic process / actin filament binding / 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 / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #920 / Huntingtin-interacting protein 1, clathrin-binding domain / Clathrin-binding domain of Huntingtin-interacting protein 1 / Sla2 family / AP180 N-terminal homology (ANTH) domain / ANTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / I/LWEQ domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #920 / Huntingtin-interacting protein 1, clathrin-binding domain / Clathrin-binding domain of Huntingtin-interacting protein 1 / 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 / Helix non-globular / Special
Similarity search - Domain/homology
Huntingtin-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsYbe, J.A. / Mishra, S. / Helms, S. / Nix, J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structure at 2.8 A of the DLLRKN-containing coiled-coil domain of huntingtin-interacting protein 1 (HIP1) reveals a surface suitable for clathrin light chain binding
Authors: Ybe, J.A. / Mishra, S. / Helms, S. / Nix, J.
History
DepositionOct 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Huntingtin-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)12,0351
Polymers12,0351
Non-polymers00
Water25214
1
A: Huntingtin-interacting protein 1

A: Huntingtin-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)24,0702
Polymers24,0702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area2580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.200, 54.200, 152.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsThe second part of the dimer assembly is generated by two fold axis: -x, -y, z

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Components

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


Mass: 12035.186 Da / Num. of mol.: 1 / Fragment: residues 480-586
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIP1 / Plasmid: pGST-HIP1_482586 / 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.: 14 / 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: 4.64 Å3/Da / Density % sol: 73.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% (v/v) PEG 3350, 0.2 M Li2SO4, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97878, 0.97863, 0.96409
DetectorType: NOIR-1 / Detector: CCD / Date: Oct 22, 2005
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978781
20.978631
30.964091
Reflection

D res high: 2.6 Å / % possible obs: 100

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res low (Å)Num. obs
13.4112.9983410.0880.9443.517284
13.4212.3983390.0910.9643.517284
13.3539.2977250.133143.487268
Diffraction reflection shell

% possible obs: 100 %

Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancyRejects
5.643.5110.0460.8211.7950
4.445.610.0550.913.1561
3.884.4410.0780.8813.4480
3.533.8810.1030.8713.5564
3.283.5310.1650.9713.6677
3.083.2810.176113.7479
2.933.0810.1690.9313.9868
2.82.9310.2130.9413.9159
2.692.810.3491.0813.9998
2.62.6910.41.0613.11102
5.643.5120.0460.7511.8148
4.445.620.0580.913.1659
3.884.4420.080.8513.4669
3.533.8820.1080.8713.5556
3.283.5320.1710.9413.6862
3.083.2820.1861.0113.7670
2.933.0820.1830.9714.0161
2.82.9320.2280.9513.9164
2.692.820.3591.113.99118
2.62.6920.4351.2712.97131
5.643.4830.0560.8111.6869
4.455.630.0740.913.0177
3.884.4530.1080.9213.1366
3.533.8830.1541.0313.2277
3.283.5330.2721.0613.5594
3.083.2830.2991.0413.7284
2.933.0830.3031.0613.8769
2.82.9330.3740.9913.8102
2.692.830.5691.113.9547
2.62.6930.5971.0813.8848
ReflectionResolution: 2.6→43.51 Å / Num. all: 10622 / Num. obs: 7284 / % possible obs: 100 % / Observed criterion σ(I): 5 / Redundancy: 13.4 % / Rmerge(I) obs: 0.088 / Χ2: 0.94 / Net I/σ(I): 12.9 / Scaling rejects: 738
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 13.11 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.8 / Num. measured all: 9435 / Num. unique all: 712 / Χ2: 1.06 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 3.12 Å / D res low: 20 Å / FOM : 0.44 / Reflection: 4188
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97887.26-17.04
13 wavelength20.978612.64-9.37
13 wavelength30.96415.07-3.14
Phasing MAD set siteAtom type symbol: Se / B iso: 60 / Fract x: 0.331 / Fract y: 0.141 / Fract z: 0.017 / Occupancy: 0.489
Phasing MAD shell
Resolution (Å)FOM Reflection
10.21-200.64264
6.79-10.210.65375
5.41-6.790.61454
4.63-5.410.53500
4.11-4.630.38587
3.73-4.110.36626
3.44-3.730.36671
3.21-3.440.26711
Phasing dmFOM : 0.59 / FOM acentric: 0.57 / FOM centric: 0.64 / Reflection: 5704 / Reflection acentric: 4263 / Reflection centric: 1441
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8-19.9530.870.940.81277128149
5-80.840.860.8806526280
4-50.80.810.78959700259
3.5-40.730.730.7949734215
3-3.50.440.440.4716751329346
2.8-30.240.220.331038846192

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Processing

Software
NameVersionClassificationNB
d*TREK9.4LDzdata scaling
SOLVE2.09phasing
RESOLVE2.09phasing
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.8→30 Å / FOM work R set: 0.696 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.313 1062 9.9 %random
Rwork0.286 ---
all0.403 10622 --
obs0.429 10622 99.4 %-
Solvent computationBsol: 101.84 Å2
Displacement parametersBiso mean: 77.739 Å2
Baniso -1Baniso -2Baniso -3
1--30.976 Å20 Å20 Å2
2---30.976 Å20 Å2
3---61.952 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.53 Å
Luzzati d res low-5 Å
Luzzati sigma a0.76 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms812 0 0 14 826
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d0.942
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.8-2.850.431550.415474529
2.85-2.890.482520.387431483
2.89-2.950.387380.384476514
2.95-30.419590.402444503
3-3.070.351450.386452497
3.07-3.130.525490.384439488
3.13-3.20.394720.426448520
3.2-3.280.428470.359446493
3.28-3.370.451470.357464511
3.37-3.470.319460.357458504
3.47-3.580.386520.326456508
3.58-3.710.318470.29440487
3.71-3.860.286470.271484531
3.86-4.040.359430.263460503
4.04-4.250.244510.255459510
4.25-4.510.196640.24450514
4.51-4.860.269390.238459498
4.86-5.350.382410.249452493
5.35-6.120.326690.333441510
6.12-7.680.193610.194460521
7.68-300.319380.222467505
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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