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- PDB-1w80: Crystal structure of the alpha-adaptin appendage domain, from the... -

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Basic information

Entry
Database: PDB / ID: 1w80
TitleCrystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, bound to 2 peptides from Synaptojanin170
Components
  • (SYNAPTOJANIN ...) x 2
  • ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA 2 SUBUNIT
KeywordsENDOCYTOSIS/EXOCYTOSIS / ENDOCYTOSIS / ALPHA-ADAPTIN APPENDAGE / ADAPTOR COMPLEX / AP2 / SYNAPTOJANIN / EXOCYTOSIS / LIPID-BINDING / ENDOCYTOSIS-EXOCYTOSIS complex
Function / homology
Function and homology information


positive regulation of endosome organization / phosphatidylinositol phosphate 5-phosphatase activity / phosphatidylinositol-4-phosphate phosphatase activity / phosphatidylinositol phosphate 4-phosphatase activity / phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 ...positive regulation of endosome organization / phosphatidylinositol phosphate 5-phosphatase activity / phosphatidylinositol-4-phosphate phosphatase activity / phosphatidylinositol phosphate 4-phosphatase activity / phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / inositol phosphate metabolic process / Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / Recycling pathway of L1 / clathrin coat of coated pit / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / synaptic vesicle uncoating / inositol-1,4,5-trisphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol metabolic process / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / phosphatidylinositol dephosphorylation / membrane coat / membrane organization / clathrin-dependent endocytosis / MHC class II antigen presentation / phosphatidylinositol biosynthetic process / regulation of hematopoietic stem cell differentiation / vesicle membrane / neurotransmitter transport / synaptic vesicle priming / synaptic vesicle transport / Synthesis of IP3 and IP4 in the cytosol / Synthesis of PIPs at the plasma membrane / synaptic vesicle endocytosis / protein serine/threonine kinase binding / vesicle-mediated transport / Neutrophil degranulation / phosphatidylinositol binding / learning / secretory granule / synaptic membrane / intracellular protein transport / kinase binding / terminal bouton / SH3 domain binding / cytoplasmic side of plasma membrane / disordered domain specific binding / synaptic vesicle / Clathrin-mediated endocytosis / presynapse / cytoplasmic vesicle / postsynapse / protein domain specific binding / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / RNA binding / cytosol
Similarity search - Function
Synaptojanin-1, RNA recognition motif / Synaptojanin-1/2, RNA recognition motif / Domain of unknown function (DUF1866) / DUF1866 / SAC domain / SacI homology domain / Sac phosphatase domain profile. / : / Gamma-adaptin ear (GAE) domain / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain ...Synaptojanin-1, RNA recognition motif / Synaptojanin-1/2, RNA recognition motif / Domain of unknown function (DUF1866) / DUF1866 / SAC domain / SacI homology domain / Sac phosphatase domain profile. / : / Gamma-adaptin ear (GAE) domain / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / TATA-Binding Protein / : / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Inositol polyphosphate-related phosphatase / Endonuclease/Exonuclease/phosphatase family 2 / Inositol polyphosphate phosphatase, catalytic domain homologues / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily / TATA-Binding Protein / Endonuclease/exonuclease/phosphatase superfamily / TBP domain superfamily / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-like helical / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BENZAMIDINE / CARBONATE ION / DITHIANE DIOL / Synaptojanin-1 / AP-2 complex subunit alpha-2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFord, M.G.J. / Praefcke, G.J.K. / McMahon, H.T.
CitationJournal: Embo J. / Year: 2004
Title: Evolving Nature of the Ap2 Alpha-Appendage Hub During Clathrin-Coated Vesicle Endocytosis.
Authors: Praefcke, G.J.K. / Ford, M.G.J. / Schmid, E.M. / Olesen, L.E. / Gallop, J.L. / Peak-Chew, S.-Y. / Vallis, Y. / Babu, M.M. / Mills, I.G. / Mcmahon, H.T.
History
DepositionSep 14, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA 2 SUBUNIT
P: SYNAPTOJANIN 1
Q: SYNAPTOJANIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4049
Polymers30,8563
Non-polymers5486
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)146.599, 67.322, 39.721
Angle α, β, γ (deg.)90.00, 94.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA 2 SUBUNIT / ALPHA-ADAPTIN C / ADAPTOR PROTEIN COMPLEX AP-2 ALPHA-2 SUBUNIT / CLATHRIN ASSEMBLY / PROTEIN ...ALPHA-ADAPTIN C / ADAPTOR PROTEIN COMPLEX AP-2 ALPHA-2 SUBUNIT / CLATHRIN ASSEMBLY / PROTEIN COMPLEX 2 ALPHA-C LARGE CHAIN / 100 KDA COATED VESICLE PROTEIN / PLASMA MEMBRANE ADAPTOR HA2/AP2 ADAPTIN ALPHA C SUBUNIT / ALPHA-ADAPTIN APPENDAGE DOMAIN FROM AP2


Mass: 28047.973 Da / Num. of mol.: 1 / Fragment: APPENDAGE DOMAIN, RESIDUES 695-938
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGEX-4T2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P17427

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SYNAPTOJANIN ... , 2 types, 2 molecules PQ

#2: Protein/peptide SYNAPTOJANIN 1 / SYNAPTIC INOSITOL-1 / 4 / 5-TRISPHOSPHATE 5-PHOSPHATASE 1 / SYJ-P3


Mass: 1465.538 Da / Num. of mol.: 1 / Fragment: PEPTIDE CONTAINING WVXF MOTIF, RESIDUES 1479-1490 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O43426, phosphoinositide 5-phosphatase
#3: Protein/peptide SYNAPTOJANIN 1 / SYNAPTIC INOSITOL-1 / 4 / 5-TRISPHOSPHATE 5-PHOSPHATASE 1 / SYJ-P3


Mass: 1342.432 Da / Num. of mol.: 1
Fragment: PEPTIDE CONTAINING FXDXF MOTIF, RESIDUES 1460-1471
Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O43426, phosphoinositide 5-phosphatase

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Non-polymers , 5 types, 283 molecules

#4: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO3
#6: Chemical ChemComp-DTD / DITHIANE DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYSES THE FOLLOWING REACTION: 1-PHOSPHATIDYL-1D-MYO-INOSITOL 4,5-BISPHOSPHATE + H2O --> 1- ...CATALYSES THE FOLLOWING REACTION: 1-PHOSPHATIDYL-1D-MYO-INOSITOL 4,5-BISPHOSPHATE + H2O --> 1-PHOSPHATIDYL-1D-MYO-INOSITOL 4-PHOSPHATE + PHOSPHATE.
Sequence detailsAT RESIDUES 889 AND 890 FOR CHAIN A, THE SEQUENCE IN THE COORDINATES DISAGREES WITH THE UNIPROT ...AT RESIDUES 889 AND 890 FOR CHAIN A, THE SEQUENCE IN THE COORDINATES DISAGREES WITH THE UNIPROT ENTRY. THE SEQUENCE IN THE COORDINATES (GLY-ALA) AGREES WITH THE ELECTRON DENSITY AND SEQUENCING EXPERIMENTS. THE FIRST THREE RESIDUES FOR WHICH DENSITY IS OBSERVED FOR CHAIN A (PRO-GLY-ILE) ARE FROM THE EXPRESSION VECTOR (PGEX-4T2). THIS IS PRECEEDED BY GLY-SER FOR WHICH NO DENSITY IS OBSERVED. PRO-ILE-GLY IS FOLLOWED BY A LEU WHICH WAS INTRODUCED IN THE CLONING PRIMER. THE SEQUENCE FOLLOWING THIS RESIDUE MATCHES UNIPROT REFERENCE P17427.

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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: 3.6 Å3/Da / Density % sol: 65.9 %
Crystal growpH: 6.5
Details: 1.2M AMMONIUM SULFATE, 3% ISOPROPANOL, 0.05M SODIUM CITRATE, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 11, 2004 / Details: BENT MIRROR
RadiationMonochromator: DIAMOND (111), GE (220), DOUBLE CRYSTAL FOCUSSING MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→70 Å / Num. obs: 28939 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 27.28 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.09 / Net I/σ(I): 12.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.87 / % possible all: 73.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B9K

1b9k


Resolution: 1.9→72.55 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.451 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1467 5.1 %RANDOM
Rwork0.177 ---
obs0.179 27464 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.98 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å2-0.89 Å2
2--0.44 Å20 Å2
3----2.22 Å2
Refinement stepCycle: LAST / Resolution: 1.9→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2096 0 34 277 2407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0222204
X-RAY DIFFRACTIONr_bond_other_d0.0010.021950
X-RAY DIFFRACTIONr_angle_refined_deg2.2381.9632983
X-RAY DIFFRACTIONr_angle_other_deg1.01334571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7015269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.18425.688109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34115376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.341159
X-RAY DIFFRACTIONr_chiral_restr0.1320.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022464
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02438
X-RAY DIFFRACTIONr_nbd_refined0.2320.2393
X-RAY DIFFRACTIONr_nbd_other0.190.21956
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21059
X-RAY DIFFRACTIONr_nbtor_other0.0930.21392
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2460.2233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2950.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9271.51723
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.24622180
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6443960
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0764.5803
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.341 78
Rwork0.304 1434

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