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- PDB-1r0d: HIP1R THATCH DOMAIN CORE -

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Basic information

Entry
Database: PDB / ID: 1r0d
TitleHIP1R THATCH DOMAIN CORE
ComponentsHuntingtin Interacting Protein 12
KeywordsSTRUCTURAL PROTEIN / Endocytosis / Actin-binding / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


positive regulation of clathrin coat assembly / digestive system development / regulation of clathrin-dependent endocytosis / regulation of gastric acid secretion / postsynapse organization / clathrin light chain binding / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / postsynaptic endocytic zone / negative regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of actin filament polymerization ...positive regulation of clathrin coat assembly / digestive system development / regulation of clathrin-dependent endocytosis / regulation of gastric acid secretion / postsynapse organization / clathrin light chain binding / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / postsynaptic endocytic zone / negative regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of actin filament polymerization / clathrin-coated vesicle membrane / clathrin coat assembly / clathrin adaptor activity / phosphatidylinositol-3,4-bisphosphate binding / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / phosphatidylinositol-3,5-bisphosphate binding / clathrin-coated vesicle / positive regulation of epidermal growth factor receptor signaling pathway / clathrin binding / cortical actin cytoskeleton / Golgi Associated Vesicle Biogenesis / regulation of endocytosis / phosphatidylinositol-3,4,5-trisphosphate binding / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / intrinsic apoptotic signaling pathway / dendrite cytoplasm / receptor-mediated endocytosis / synaptic membrane / actin filament organization / regulation of actin cytoskeleton organization / SH3 domain binding / ruffle membrane / endocytosis / actin filament binding / Clathrin-mediated endocytosis / regulation of apoptotic process / dendritic spine / postsynaptic density / protein stabilization / apical plasma membrane / protein heterodimerization activity / neuronal cell body / intracellular membrane-bounded organelle / negative regulation of apoptotic process / perinuclear region of cytoplasm / glutamatergic synapse / protein homodimerization activity / mitochondrion / identical protein binding / plasma membrane / cytosol
Similarity search - Function
I/LWEQ domain / I/LWEQ domain / 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 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Huntingtin-interacting protein 1-related protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsBrett, T.J. / Fremont, D.H. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structural definition of the F-actin-binding THATCH domain from HIP1R
Authors: Brett, T.J. / Legendre-Guillemin, V. / McPherson, P.S. / Fremont, D.H.
History
DepositionSep 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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_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 12
B: Huntingtin Interacting Protein 12
D: Huntingtin Interacting Protein 12
E: Huntingtin Interacting Protein 12
F: Huntingtin Interacting Protein 12
G: Huntingtin Interacting Protein 12
H: Huntingtin Interacting Protein 12
I: Huntingtin Interacting Protein 12


Theoretical massNumber of molelcules
Total (without water)180,8778
Polymers180,8778
Non-polymers00
Water20,6991149
1
A: Huntingtin Interacting Protein 12


Theoretical massNumber of molelcules
Total (without water)22,6101
Polymers22,6101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Huntingtin Interacting Protein 12


Theoretical massNumber of molelcules
Total (without water)22,6101
Polymers22,6101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: Huntingtin Interacting Protein 12


Theoretical massNumber of molelcules
Total (without water)22,6101
Polymers22,6101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: Huntingtin Interacting Protein 12


Theoretical massNumber of molelcules
Total (without water)22,6101
Polymers22,6101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
F: Huntingtin Interacting Protein 12


Theoretical massNumber of molelcules
Total (without water)22,6101
Polymers22,6101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
G: Huntingtin Interacting Protein 12


Theoretical massNumber of molelcules
Total (without water)22,6101
Polymers22,6101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
H: Huntingtin Interacting Protein 12


Theoretical massNumber of molelcules
Total (without water)22,6101
Polymers22,6101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
I: Huntingtin Interacting Protein 12


Theoretical massNumber of molelcules
Total (without water)22,6101
Polymers22,6101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)148.200, 165.900, 109.800
Angle α, β, γ (deg.)90.00, 132.40, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein
Huntingtin Interacting Protein 12 / Hip1-related / Hip 12


Mass: 22609.607 Da / Num. of mol.: 8 / Fragment: C-TERMINAL THATCH DOMAIN, RESIDUES 771-971
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIP1R, HIP12, KIAA0655 / Plasmid: PGEX-4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: O75146
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1149 / 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: 2.76 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 1.75 M ammonium sulfate, 2.5% ethylene glycol, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 19-ID11.0332, 0.97967, 0.97954, 0.96430
ROTATING ANODERIGAKU RU30021.5418
Detector
TypeIDDetectorDateDetails
CUSTOM-MADE1CCDDec 6, 2002
RIGAKU RAXIS IV2IMAGE PLATEOct 27, 2002Yale Mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SiMADMx-ray1
2Yale MirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
20.979671
30.979541
40.96431
51.54181
ReflectionResolution: 1.9→50 Å / Num. all: 147170 / Num. obs: 147170 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 23.5
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.433 / % possible all: 95.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→19.88 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 13317 4.9 %RANDOM
Rwork0.224 ---
all0.2241 147170 --
obs0.2241 147170 89.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.952 Å2 / ksol: 0.362315 e/Å3
Displacement parametersBiso mean: 36.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.55 Å20 Å2-1.35 Å2
2--9.25 Å20 Å2
3----4.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11598 0 0 1149 12747
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d16.4
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it2.282
X-RAY DIFFRACTIONc_mcangle_it3.13
X-RAY DIFFRACTIONc_scbond_it5.394.5
X-RAY DIFFRACTIONc_scangle_it7.236
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 1880 4.8 %
Rwork0.346 37251 -
obs--77.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.PARAM

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