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- PDB-1hx8: CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF DROSOPHILA AP180 -

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Basic information

Entry
Database: PDB / ID: 1hx8
TitleCRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF DROSOPHILA AP180
ComponentsSYNAPSE-ENRICHED CLATHRIN ADAPTOR PROTEIN LAP
KeywordsENDOCYTOSIS/EXOCYTOSIS / all alpha / alpha helices repeats / coiled-coil / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


Golgi Associated Vesicle Biogenesis / Cargo recognition for clathrin-mediated endocytosis / clathrin-dependent synaptic vesicle endocytosis / synaptic vesicle budding from presynaptic endocytic zone membrane / positive regulation of clathrin-dependent endocytosis / phototaxis / Clathrin-mediated endocytosis / neuron-neuron synaptic transmission / 1-phosphatidylinositol binding / extrinsic component of presynaptic endocytic zone membrane ...Golgi Associated Vesicle Biogenesis / Cargo recognition for clathrin-mediated endocytosis / clathrin-dependent synaptic vesicle endocytosis / synaptic vesicle budding from presynaptic endocytic zone membrane / positive regulation of clathrin-dependent endocytosis / phototaxis / Clathrin-mediated endocytosis / neuron-neuron synaptic transmission / 1-phosphatidylinositol binding / extrinsic component of presynaptic endocytic zone membrane / clathrin heavy chain binding / clathrin coat assembly / vesicle budding from membrane / clathrin-dependent endocytosis / clathrin-coated vesicle / synaptic vesicle transport / clathrin binding / synaptic vesicle endocytosis / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / receptor-mediated endocytosis / SNARE binding / endocytosis / synaptic vesicle / presynaptic membrane / chemical synaptic transmission / Golgi apparatus / plasma membrane
Similarity search - Function
ANTH domain / ANTH domain superfamily / AP180 N-terminal homology (ANTH) domain / ANTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...ANTH domain / ANTH domain superfamily / AP180 N-terminal homology (ANTH) domain / ANTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphatidylinositol-binding clathrin assembly protein LAP
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsMao, Y. / Chen, J. / Maynard, J.A. / Zhang, B. / Quiocho, F.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: A novel all helix fold of the AP180 amino-terminal domain for phosphoinositide binding and clathrin assembly in synaptic vesicle endocytosis.
Authors: Mao, Y. / Chen, J. / Maynard, J.A. / Zhang, B. / Quiocho, F.A.
History
DepositionJan 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: SYNAPSE-ENRICHED CLATHRIN ADAPTOR PROTEIN LAP
B: SYNAPSE-ENRICHED CLATHRIN ADAPTOR PROTEIN LAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4884
Polymers67,2962
Non-polymers1922
Water3,459192
1
A: SYNAPSE-ENRICHED CLATHRIN ADAPTOR PROTEIN LAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7442
Polymers33,6481
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SYNAPSE-ENRICHED CLATHRIN ADAPTOR PROTEIN LAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7442
Polymers33,6481
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.632, 106.933, 79.207
Angle α, β, γ (deg.)90.00, 119.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SYNAPSE-ENRICHED CLATHRIN ADAPTOR PROTEIN LAP


Mass: 33647.914 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN (RESIDUES 1-299)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: LAP / Plasmid: PGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9VI75
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG MME 5000, amonium sulphate 0.2M, MES 0.1M, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 5.5
Details: drop contains protein and reservoir solution in a 1:1 ratio
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21 mMdithiothreitol1drop
350 mMcitrate1drop
430 %mPEG50001reservoir
5200 mMammonium sulfate1reservoir
6100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793, 0.9788, 0.9712
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 24, 2000 / Details: KOHZU double crystal monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97881
30.97121
ReflectionResolution: 2.2→50 Å / Num. all: 38772 / Num. obs: 274148 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.07 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 33
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 5.4 / Num. unique all: 3893 / Rsym value: 33.7 / % possible all: 100
Reflection
*PLUS
Num. obs: 38772 / Num. measured all: 274148
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→26 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1807 -RANDOM
Rwork0.211 ---
all0.221 38986 --
obs0.221 36413 93.4 %-
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.2→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4230 0 10 192 4432
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_improper_angle_d0.92
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

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