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- PDB-1mqs: Crystal structure of Sly1p in complex with an N-terminal peptide ... -

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Basic information

Entry
Database: PDB / ID: 1mqs
TitleCrystal structure of Sly1p in complex with an N-terminal peptide of Sed5p
Components
  • Integral Membrane Protein SED5
  • Sly1 Protein
KeywordsENDOCYTOSIS/EXOCYTOSIS / SM-protein / SNARE / syntaxin / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


regulation of inclusion body assembly / Cargo concentration in the ER / RHOC GTPase cycle / Golgi cis cisterna membrane / vesicle fusion with Golgi apparatus / RHOA GTPase cycle / Intra-Golgi traffic / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / regulation of Ras protein signal transduction / COPI-mediated anterograde transport ...regulation of inclusion body assembly / Cargo concentration in the ER / RHOC GTPase cycle / Golgi cis cisterna membrane / vesicle fusion with Golgi apparatus / RHOA GTPase cycle / Intra-Golgi traffic / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / regulation of Ras protein signal transduction / COPI-mediated anterograde transport / COPII-mediated vesicle transport / vesicle docking / SNAP receptor activity / SNARE complex / vesicle fusion / intra-Golgi vesicle-mediated transport / cis-Golgi network / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / positive regulation of SNARE complex assembly / syntaxin binding / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / SNARE binding / intracellular protein transport / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / cytosol / cytoplasm
Similarity search - Function
Syntaxin-5, N-terminal, Sly1p-binding domain / Syntaxin-5 N-terminal, Sly1p-binding domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #60 / Sec1/Munc18 (SM) protein, domain 2 / Syntaxin Binding Protein 1; Chain A, domain 2 / Sec1/Munc18 (SM) protein, domain 3a / Sec1/Munc18 (SM) protein, domain 1 / Sec1-like, domain 1 / Sec1-like protein / Sec1-like, domain 2 ...Syntaxin-5, N-terminal, Sly1p-binding domain / Syntaxin-5 N-terminal, Sly1p-binding domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #60 / Sec1/Munc18 (SM) protein, domain 2 / Syntaxin Binding Protein 1; Chain A, domain 2 / Sec1/Munc18 (SM) protein, domain 3a / Sec1/Munc18 (SM) protein, domain 1 / Sec1-like, domain 1 / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family / SNARE domain / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Protein SLY1 / Integral membrane protein SED5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsBracher, A. / Weissenhorn, W.
Citation
Journal: Embo J. / Year: 2002
Title: Structural basis for the Golgi membrane recruitment of Sly1p by Sed5p
Authors: Bracher, A. / Weissenhorn, W.
#1: Journal: Nature / Year: 2000
Title: Three-dimensional structure of the neuronal-Sec1-syntaxin 1a complex
Authors: Misura, K.M.S. / Scheller, R.H. / Weis, W.I.
#2: Journal: Structure / Year: 2000
Title: The X-ray crystal structure of neuronal Sec1 from squid sheds new light on the role of this protein in exocytosis
Authors: Bracher, A. / Perrakis, A. / Dresbach, T. / Betz, H. / Weissenhorn, W.
#3: Journal: J.Mol.Biol. / Year: 2001
Title: Crystal structures of neuronal squid Sec1 implicate inter-domain hinge movement in the release of t-SNAREs
Authors: Bracher, A. / Weissenhorn, W.
History
DepositionSep 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 30, 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

Downloads & links

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Assembly

Deposited unit
A: Sly1 Protein
B: Integral Membrane Protein SED5


Theoretical massNumber of molelcules
Total (without water)81,6052
Polymers81,6052
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-12 kcal/mol
Surface area27500 Å2
MethodPISA
2
A: Sly1 Protein
B: Integral Membrane Protein SED5

A: Sly1 Protein
B: Integral Membrane Protein SED5


Theoretical massNumber of molelcules
Total (without water)163,2114
Polymers163,2114
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7640 Å2
ΔGint-53 kcal/mol
Surface area51420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.056, 161.056, 88.209
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Sly1 Protein / Sly1p


Mass: 75655.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PMAL-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 codon+ / References: UniProt: P22213
#2: Protein/peptide Integral Membrane Protein SED5 / Sed5p


Mass: 5949.565 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pETM30 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 codon+ / References: UniProt: Q01590
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.5 Å3/Da / Density % sol: 64.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 3.5M sodium formate, 20mM Tris HCl pH 7.2, 50mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
111 mg/mlprotein1drop
23.4-3.6 Msodium formate1reservoir
320 mMTris-HCl1droppH7.2
450 mM1NaCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9875,0.9793,0.9789,0.9184
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJun 15, 2002
MARRESEARCH2CCDJun 17, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98751
20.97931
30.97891
40.91841
ReflectionResolution: 2.9→30 Å / Num. all: 26182 / Num. obs: 26182 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 92.3 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 13.3
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.552 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 100 % / Num. measured all: 200527
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEmodel building
CNS1refinement
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3→30 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2904 1201 5.1 %RANDOM
Rwork0.2573 ---
all-23743 --
obs-23743 99.9 %-
Solvent computationBsol: 52.0133 Å2 / ksol: 0.31282 e/Å3
Displacement parametersBiso mean: 97.7 Å2
Baniso -1Baniso -2Baniso -3
1--34.65 Å20 Å20 Å2
2---34.65 Å20 Å2
3---69.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.49 Å
Luzzati d res low-30 Å
Luzzati sigma a0.66 Å0.67 Å
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4705 0 0 20 4725
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d1.03
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03

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