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- PDB-4afi: Complex between Vamp7 longin domain and fragment of delta-adaptin... -

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Basic information

Entry
Database: PDB / ID: 4afi
TitleComplex between Vamp7 longin domain and fragment of delta-adaptin from AP3
ComponentsAP-3 COMPLEX SUBUNIT DELTA-1, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
KeywordsENDOCYTOSIS / EXOCYTOSIS / CLATHRIN ADAPTOR / CHIMERA / FUSION PROTEIN
Function / homology
Function and homology information


regulation of protein targeting to vacuolar membrane / positive regulation of histamine secretion by mast cell / synaptic vesicle coating / synaptic vesicle budding from endosome / chylomicron assembly / clathrin-coated vesicle cargo loading, AP-3-mediated / neutrophil degranulation / synaptic vesicle membrane organization / zinc ion import into lysosome / AP-3 adaptor complex ...regulation of protein targeting to vacuolar membrane / positive regulation of histamine secretion by mast cell / synaptic vesicle coating / synaptic vesicle budding from endosome / chylomicron assembly / clathrin-coated vesicle cargo loading, AP-3-mediated / neutrophil degranulation / synaptic vesicle membrane organization / zinc ion import into lysosome / AP-3 adaptor complex / triglyceride transport / neurotransmitter receptor transport, postsynaptic endosome to lysosome / anterograde synaptic vesicle transport / natural killer cell degranulation / vesicle fusion with Golgi apparatus / endosome to melanosome transport / Golgi to vacuole transport / synaptic vesicle recycling / platelet dense granule organization / melanosome assembly / presynaptic endosome / eosinophil degranulation / positive regulation of NK T cell differentiation / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / SNARE complex / SNAP receptor activity / platelet alpha granule / calcium-ion regulated exocytosis / protein targeting to vacuole / vesicle fusion / melanosome organization / anterograde axonal transport / Golgi to plasma membrane protein transport / positive regulation of dendrite morphogenesis / vesicle transport along microtubule / protein localization to membrane / syntaxin binding / azurophil granule membrane / phagocytosis, engulfment / endosome to lysosome transport / SNARE complex assembly / exocytosis / pseudopodium / synaptic vesicle exocytosis / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular transport / transport vesicle / vesicle-mediated transport / phagocytic vesicle / axon cytoplasm / secretory granule membrane / secretory granule / hippocampal mossy fiber to CA3 synapse / SNARE binding / filopodium / intracellular protein transport / trans-Golgi network / phagocytic vesicle membrane / apical part of cell / terminal bouton / synaptic vesicle membrane / late endosome membrane / lamellipodium / early endosome / endosome membrane / neuron projection / postsynapse / Golgi membrane / lysosomal membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / glutamatergic synapse / cell surface / Golgi apparatus / positive regulation of transcription by RNA polymerase II / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / AP-3 complex subunit delta domain, metazoa / AP-3 complex subunit delta-1 / Bovine leukaemia virus receptor (BLVR) / Adaptor protein complex AP-3, delta subunit / Longin domain / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain ...: / AP-3 complex subunit delta domain, metazoa / AP-3 complex subunit delta-1 / Bovine leukaemia virus receptor (BLVR) / Adaptor protein complex AP-3, delta subunit / Longin domain / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Longin-like domain superfamily / Beta-Lactamase / Armadillo-like helical / Armadillo-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PRASEODYMIUM ION / AP-3 complex subunit delta-1 / Vesicle-associated membrane protein 7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKent, H.M. / Evans, P.R. / Luzio, J.P. / Peden, A.A. / Owen, D.J.
CitationJournal: Dev.Cell / Year: 2012
Title: Structural Basis of the Intracellular Sorting of the Snare Vamp7 by the Ap3 Adaptor Complex
Authors: Kent, H.M. / Evans, P.R. / Schaefer, I.B. / Gray, S.R. / Sanderson, C.M. / Luzio, J.P. / Peden, A.A. / Owen, D.J.
History
DepositionJan 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: AP-3 COMPLEX SUBUNIT DELTA-1, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
B: AP-3 COMPLEX SUBUNIT DELTA-1, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3944
Polymers39,1122
Non-polymers2822
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-48.7 kcal/mol
Surface area14850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.555, 63.555, 217.915
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.766, 0.632, 0.12), (-0.639, -0.768, -0.042), (0.066, -0.109, 0.992)
Vector: 62.345, -68.143, 13.245)

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Components

#1: Protein AP-3 COMPLEX SUBUNIT DELTA-1, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7 / AP-3 COMPLEX SUBUNIT DELTA / ADAPTER-RELATED PROTEIN COMPLEX 3 SUBUNIT DELTA-1 / DELTA-ADAPTIN / ...AP-3 COMPLEX SUBUNIT DELTA / ADAPTER-RELATED PROTEIN COMPLEX 3 SUBUNIT DELTA-1 / DELTA-ADAPTIN / VAMP-7 / SYNAPTOBREVIN-LIKE PROTEIN 1


Mass: 19556.240 Da / Num. of mol.: 2
Fragment: DELTA-ADAPTIN HINGE, RESIDUES 680-729, VAMP7 LONGIN DOMAIN, RESIDUES 1-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human), (gene. exp.) MUS MUSCULUS (house mouse)
Plasmid: PGEX4T2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS / References: UniProt: O14617, UniProt: P70280
#2: Chemical ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pr
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.28 %
Description: SIGNIFICANT ANISOTROPY IN DATA. SECOND DATA SET AT 1.5 ANGSTROM UNITS. COLLECTED TO ENHANCE ANOMALOUS DATA FROM PR3+ IONS.
Crystal growpH: 9
Details: 4 M NACL, 100 MM BICINE PH 9.0, 10 MM PRASEODYMIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9393
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.8→64 Å / Num. obs: 11810 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Rmerge(I) obs: 0.31 / Net I/σ(I): 7.3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 13.6 % / Rmerge(I) obs: 2.9 / Mean I/σ(I) obs: 1.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0002refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VX8

2vx8


Resolution: 2.8→61.01 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.937 / SU B: 18.216 / SU ML: 0.316 / Cross valid method: THROUGHOUT / ESU R: 0.863 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. NCS APPLIED AS LOCAL RESTRAINTS WITH ADDITIONAL TARGET OF PREVIOUS VAMP7 STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.25266 551 4.7 %RANDOM
Rwork0.23057 ---
obs0.23164 11194 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.83 Å2
Baniso -1Baniso -2Baniso -3
1-4.27 Å20 Å20 Å2
2--4.27 Å20 Å2
3----8.55 Å2
Refinement stepCycle: LAST / Resolution: 2.8→61.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 2 4 2445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192496
X-RAY DIFFRACTIONr_bond_other_d0.0040.021662
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.953387
X-RAY DIFFRACTIONr_angle_other_deg1.18934060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6125305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88824.087115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.50615420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4121512
X-RAY DIFFRACTIONr_chiral_restr0.0910.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212764
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02512
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 34 -
Rwork0.457 683 -
obs--99.72 %

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