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- PDB-1nhl: SNAP-23N Structure -

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Basic information

Entry
Database: PDB / ID: 1nhl
TitleSNAP-23N Structure
ComponentsSynaptosomal-associated protein 23
KeywordsPROTEIN TRANSPORT / SNARE / COILED-COIL
Function / homology
Function and homology information


vesicle targeting / trans-Golgi Network Vesicle Budding / post-Golgi vesicle-mediated transport / synaptic vesicle fusion to presynaptic active zone membrane / specific granule / SNARE complex / SNAP receptor activity / histamine secretion by mast cell / RHOF GTPase cycle / syntaxin binding ...vesicle targeting / trans-Golgi Network Vesicle Budding / post-Golgi vesicle-mediated transport / synaptic vesicle fusion to presynaptic active zone membrane / specific granule / SNARE complex / SNAP receptor activity / histamine secretion by mast cell / RHOF GTPase cycle / syntaxin binding / azurophil granule / RHOB GTPase cycle / RHOJ GTPase cycle / synaptic vesicle priming / RHOQ GTPase cycle / exocytosis / CDC42 GTPase cycle / tertiary granule membrane / RHOA GTPase cycle / RAC3 GTPase cycle / specific granule membrane / RAC1 GTPase cycle / adherens junction / Translocation of SLC2A4 (GLUT4) to the plasma membrane / phagocytic vesicle membrane / protein transport / presynapse / ER-Phagosome pathway / membrane fusion / neuron projection / cilium / focal adhesion / Neutrophil degranulation / mitochondrion / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / SNAP-25 domain / SNAP-25 family / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Synaptosomal-associated protein 23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsFreedman, S.J. / Song, H.K. / Xu, Y. / Eck, M.J.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Homotetrameric Structure of the SNAP-23 N-terminal Coiled-coil Domain
Authors: Freedman, S.J. / Song, H.K. / Xu, Y. / Sun, Z.Y. / Eck, M.J.
History
DepositionDec 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synaptosomal-associated protein 23


Theoretical massNumber of molelcules
Total (without water)6,3191
Polymers6,3191
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Synaptosomal-associated protein 23

A: Synaptosomal-associated protein 23

A: Synaptosomal-associated protein 23

A: Synaptosomal-associated protein 23


Theoretical massNumber of molelcules
Total (without water)25,2754
Polymers25,2754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_645-y+3/2,x-1/2,z1
crystal symmetry operation4_565y+1/2,-x+3/2,z1
Buried area9670 Å2
ΔGint-78 kcal/mol
Surface area12230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)34.905, 34.905, 81.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsThe biological assembly is a tetramer.

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Components

#1: Protein Synaptosomal-associated protein 23 / SNAP-23 / Vesicle-membrane fusion protein SNAP-23


Mass: 6318.813 Da / Num. of mol.: 1 / Fragment: SNAP-23 N-terminal coiled-coil domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAP23 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O00161
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, CALCIUM CHLORIDE, PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 23 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11-4 mg/mlprotein1drop
250 mMTris-HCl1droppH7.5
3100 mM1dropNaCl
40.1 MHEPES1reservoirpH7.5
50.2 M1reservoirCaCl2
628 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 2, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→50 Å / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 1801 / % possible obs: 91.7 % / Rmerge(I) obs: 0.044

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.316 -RANDOM
Rwork0.273 --
all0.281 --
obs0.277 2381 -
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms433 0 0 43 476
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.005
X-RAY DIFFRACTIONr_angle_refined_deg1
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1

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