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- PDB-2vj0: Crystal structure of the alpha-adaptin appendage domain, from the... -

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Basic information

Entry
Database: PDB / ID: 2vj0
TitleCrystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, in complex with an FXDNF peptide from amphiphysin1 and a WVXF peptide from synaptojanin P170
Components
  • AMPHIPHYSIN
  • AP-2 COMPLEX SUBUNIT ALPHA-2
  • SYNAPTOJANIN-1
KeywordsPROTEIN TRANSPORT / CYTOPLASMIC VESICLE / ALTERNATIVE SPLICING / TRANSPORT / COATED PIT / SH3 DOMAIN / ENDOCYTOSIS / ALPHA-ADAPTIN / GOLGI APPARATUS / PHOSPHORYLATION / AP2 / SYNAPSE / MEMBRANE / CYTOPLASM / COILED COIL / AMPHIPHYSIN / CYTOSKELETON / SYNAPTOJANIN / LIPID-BINDING / CELL JUNCTION
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 / presynaptic endocytic zone / inositol-1,4,5-trisphosphate 5-phosphatase activity / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol ...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 / presynaptic endocytic zone / inositol-1,4,5-trisphosphate 5-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 / postsynaptic endocytic zone / synaptic vesicle uncoating / Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / inositol phosphate metabolic process / VLDLR internalisation and degradation / Recycling pathway of L1 / clathrin coat of coated pit / AP-2 adaptor complex / phosphoinositide 5-phosphatase / postsynaptic neurotransmitter receptor internalization / photoreceptor ribbon synapse / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / Cargo recognition for clathrin-mediated endocytosis / extrinsic component of synaptic vesicle membrane / phosphatidylinositol metabolic process / Clathrin-mediated endocytosis / phosphatidylinositol dephosphorylation / clathrin adaptor activity / leading edge membrane / Clathrin-mediated endocytosis / membrane coat / clathrin-dependent endocytosis / MHC class II antigen presentation / phosphatidylinositol biosynthetic process / membrane organization / vesicle membrane / regulation of hematopoietic stem cell differentiation / neurotransmitter transport / synaptic vesicle priming / synaptic vesicle transport / Synthesis of IP3 and IP4 in the cytosol / Synthesis of PIPs at the plasma membrane / positive regulation of endocytosis / synaptic vesicle endocytosis / phosphatase binding / vesicle-mediated transport / axon terminus / Neutrophil degranulation / secretory granule / learning / intracellular protein transport / synaptic membrane / terminal bouton / phospholipid binding / cytoplasmic side of plasma membrane / kinase binding / disordered domain specific binding / synaptic vesicle / presynapse / Clathrin-mediated endocytosis / cytoplasmic vesicle / cytoskeleton / postsynapse / protein domain specific binding / lipid binding / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / RNA binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Synaptojanin-1, RNA recognition motif / Synaptojanin-1/2, RNA recognition motif / Domain of unknown function (DUF1866) / DUF1866 / Amphiphysin, isoform 1 / Amphiphysin I, SH3 domain / SAC domain / SacI homology domain / Sac phosphatase domain profile. / Amphiphysin ...Synaptojanin-1, RNA recognition motif / Synaptojanin-1/2, RNA recognition motif / Domain of unknown function (DUF1866) / DUF1866 / Amphiphysin, isoform 1 / Amphiphysin I, SH3 domain / SAC domain / SacI homology domain / Sac phosphatase domain profile. / Amphiphysin / : / 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 / BAR domain / BAR domain profile. / BAR / TATA-Binding Protein / BAR domain / : / 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 / AH/BAR domain 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 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 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 / DITHIANE DIOL / Amphiphysin / Synaptojanin-1 / AP-2 complex subunit alpha-2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
RATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFord, M.G.J. / Praefcke, G.J.K. / McMahon, H.T.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Solitary and Repetitive Binding Motifs for the Ap2 Complex {Alpha}-Appendage in Amphiphysin and Other Accessory Proteins.
Authors: Olesen, L.E. / Ford, M.G.J. / Schmid, E.M. / Vallis, Y. / Madan Babu, M. / Li, P.H. / Mills, I.G. / Mcmahon, H.T. / Praefcke, G.J.K.
History
DepositionDec 6, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2007Provider: 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

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Assembly

Deposited unit
A: AP-2 COMPLEX SUBUNIT ALPHA-2
P: SYNAPTOJANIN-1
Q: AMPHIPHYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9769
Polymers30,3803
Non-polymers5966
Water6,179343
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-14.4 kcal/mol
Surface area15760 Å2
MethodPQS
Unit cell
Length a, b, c (Å)144.508, 66.980, 39.730
Angle α, β, γ (deg.)90.00, 94.92, 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 AP-2 COMPLEX SUBUNIT ALPHA-2 / ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA-2 SUBUNIT / ALPHA-ADAPTIN C / ADAPTOR PROTEIN COMPLEX AP-2 ...ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA-2 SUBUNIT / 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 C / PLASMA MEMBRANE ADAPTOR HA2/AP2 ADAPTIN ALPHA C SUBUNIT


Mass: 28047.973 Da / Num. of mol.: 1 / Fragment: APPENDAGE DOMAIN, RESIDUES 693-938
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Organ: BRAIN / Plasmid: PGEX-4T2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: P17427

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Protein/peptide , 2 types, 2 molecules PQ

#2: Protein/peptide SYNAPTOJANIN-1 / SYNAPTIC INOSITOL-1 / 4 / 5-TRISPHOSPHATE 5-PHOSPHATASE 1 / SYNAPTOJANIN-1 P170


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
#3: Protein/peptide AMPHIPHYSIN / AMPHIPHYSIN1


Mass: 866.913 Da / Num. of mol.: 1 / Fragment: PEPTIDE CONTAINING FXDNF MOTIF, RESIDUES 324-330 / Source method: obtained synthetically / Source: (synth.) RATTUS NORVEGICUS (Norway rat) / References: UniProt: O08838

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Non-polymers , 5 types, 349 molecules

#4: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#5: Chemical ChemComp-DTD / DITHIANE DIOL


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 3.2 Å3/Da / Density % sol: 61.1 %
Description: THE ORIGINAL STRUCTURE BOUND ONLY TO THE SYNAPTOJANIN-1 P170 PEPTIDE, NOT REPORTED IN THE PAPER, WAS SOLVED BY MOLECULAR REPLACEMENT. A DIFFERENCE FOURIER WAS CALCULATED FOR THE SOAK OF ...Description: THE ORIGINAL STRUCTURE BOUND ONLY TO THE SYNAPTOJANIN-1 P170 PEPTIDE, NOT REPORTED IN THE PAPER, WAS SOLVED BY MOLECULAR REPLACEMENT. A DIFFERENCE FOURIER WAS CALCULATED FOR THE SOAK OF THE AMPHIPHYSIN PEPTIDE.
Crystal growpH: 6.5
Details: 1.2M AMMONIUM SULPHATE, 3% ISOPROPANOL AND 0.05M SODIUM CITRATE PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 27, 2004 / Details: BENT MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.6→17.76 Å / Num. obs: 47896 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Biso Wilson estimate: 17.59 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2 / % possible all: 89.2

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B9K

1b9k


Resolution: 1.6→17.76 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.42 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2427 5.18 %RANDOM
Rwork0.181 ---
obs0.182 47892 96.2 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 16.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.205 Å20 Å20.164 Å2
2---0.34 Å20 Å2
3---0.164 Å2
Refinement stepCycle: LAST / Resolution: 1.6→17.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 33 343 2444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222164
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.9672941
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0995268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26925.524105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.20615365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.453159
X-RAY DIFFRACTIONr_chiral_restr0.0780.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022393
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.2382
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21074
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.27
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0011.51402
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42622146
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1973896
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3624.5790
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: 6.66→17.76 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.158 33
Rwork0.189 585

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