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- PDB-4xhv: Crystal structure of Drosophila Spinophilin-PDZ and a C-terminal ... -

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Basic information

Entry
Database: PDB / ID: 4xhv
TitleCrystal structure of Drosophila Spinophilin-PDZ and a C-terminal peptide of Neurexin
Components
  • LP20995p
  • Neurexin 1
KeywordsSIGNALING PROTEIN / Spinophilin / Neurexin / Praesynaptic density / SYNAPSE
Function / homology
Function and homology information


vitamin A transport / negative regulation of presynaptic active zone assembly / regulation of neuromuscular synaptic transmission / type I terminal bouton / regulation of terminal button organization / neuroligin family protein binding / neurexin family protein binding / neuromuscular synaptic transmission / apical cortex / positive regulation of synaptic vesicle endocytosis ...vitamin A transport / negative regulation of presynaptic active zone assembly / regulation of neuromuscular synaptic transmission / type I terminal bouton / regulation of terminal button organization / neuroligin family protein binding / neurexin family protein binding / neuromuscular synaptic transmission / apical cortex / positive regulation of synaptic vesicle endocytosis / locomotion / synaptic assembly at neuromuscular junction / regulation of locomotion / associative learning / apolipoprotein binding / synaptic vesicle endocytosis / synapse assembly / actin filament organization / calcium-mediated signaling / synapse organization / neuromuscular junction / actin filament binding / neuron projection development / actin cytoskeleton / presynaptic membrane / nervous system development / chemical synaptic transmission / postsynaptic membrane / postsynaptic density / cytoskeleton / dendrite / metal ion binding / cytoplasm
Similarity search - Function
Neurabin-1/2, PDZ domain / Neurabin-like family / PDZ domain / : / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / SAM domain (Sterile alpha motif) / PDZ domain ...Neurabin-1/2, PDZ domain / Neurabin-like family / PDZ domain / : / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / SAM domain (Sterile alpha motif) / PDZ domain / Pdz3 Domain / EGF-like domain / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Epidermal growth factor-like domain. / Sterile alpha motif/pointed domain superfamily / EGF-like domain profile. / PDZ domain / EGF-like domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
LP20995p / Spinophilin, isoform J / Neurexin 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsDriller, J.H. / Muhammad, K.G.H. / Reddy, S. / Rey, U. / Boehme, M.A. / Hollmann, C. / Ramesh, N. / Depner, H. / Luetzkendorf, J. / Matkovic, T. ...Driller, J.H. / Muhammad, K.G.H. / Reddy, S. / Rey, U. / Boehme, M.A. / Hollmann, C. / Ramesh, N. / Depner, H. / Luetzkendorf, J. / Matkovic, T. / Bergeron, D. / Quentin, C. / Schmoranzer, J. / Goettfert, F. / Holt, M. / Wahl, M.C. / Hell, S.W. / Walter, A. / Sigrist, S.J. / Loll, B.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB958/A3 Germany
German Research FoundationSFB958/A6 Germany
CitationJournal: Nat Commun / Year: 2015
Title: Presynaptic spinophilin tunes neurexin signalling to control active zone architecture and function.
Authors: Muhammad, K. / Reddy-Alla, S. / Driller, J.H. / Schreiner, D. / Rey, U. / Bohme, M.A. / Hollmann, C. / Ramesh, N. / Depner, H. / Lutzkendorf, J. / Matkovic, T. / Gotz, T. / Bergeron, D.D. / ...Authors: Muhammad, K. / Reddy-Alla, S. / Driller, J.H. / Schreiner, D. / Rey, U. / Bohme, M.A. / Hollmann, C. / Ramesh, N. / Depner, H. / Lutzkendorf, J. / Matkovic, T. / Gotz, T. / Bergeron, D.D. / Schmoranzer, J. / Goettfert, F. / Holt, M. / Wahl, M.C. / Hell, S.W. / Scheiffele, P. / Walter, A.M. / Loll, B. / Sigrist, S.J.
History
DepositionJan 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 2.0Jan 10, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num / _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.ptnr2_symmetry / _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 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_symmetry / _struct_site_gen.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LP20995p
B: Neurexin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1245
Polymers10,9622
Non-polymers1633
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-26 kcal/mol
Surface area6420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.302, 45.302, 94.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein LP20995p


Mass: 9691.182 Da / Num. of mol.: 1 / Fragment: UNP residues 1258-1347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Spn-RA / Plasmid: pET-MBP1a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): T1R / References: UniProt: D1Z359, UniProt: M9NFI9*PLUS
#2: Protein/peptide Neurexin 1


Mass: 1270.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: Q3KN41

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Non-polymers , 4 types, 179 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl at pH 8.5 adjusted at RT, 0.01 M nickel chloride, 20% (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 23, 2014
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.23→45.3 Å / Num. obs: 29395 / % possible obs: 99.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 21.6
Reflection shellResolution: 1.23→1.3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.4 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EGG

3egg


Resolution: 1.23→32.033 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1622 1470 5 %
Rwork0.1377 --
obs0.139 29383 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.6 Å2
Refinement stepCycle: LAST / Resolution: 1.23→32.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms769 0 6 176 951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016868
X-RAY DIFFRACTIONf_angle_d1.6281185
X-RAY DIFFRACTIONf_dihedral_angle_d12.03344
X-RAY DIFFRACTIONf_chiral_restr0.098137
X-RAY DIFFRACTIONf_plane_restr0.009156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.229-1.26860.21011270.20712422X-RAY DIFFRACTION98
1.2686-1.3140.22661320.17552492X-RAY DIFFRACTION100
1.314-1.36660.15261310.14092492X-RAY DIFFRACTION100
1.3666-1.42880.16461320.12612518X-RAY DIFFRACTION100
1.4288-1.50410.16221320.11372502X-RAY DIFFRACTION100
1.5041-1.59840.16551320.10712512X-RAY DIFFRACTION100
1.5984-1.72180.12611330.11132533X-RAY DIFFRACTION100
1.7218-1.8950.15521340.11912546X-RAY DIFFRACTION100
1.895-2.16920.16171350.12762563X-RAY DIFFRACTION100
2.1692-2.73270.15661370.13562600X-RAY DIFFRACTION100
2.7327-32.04420.16351450.15382733X-RAY DIFFRACTION99

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