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- PDB-4cca: Structure of human Munc18-2 -

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Basic information

Entry
Database: PDB / ID: 4cca
TitleStructure of human Munc18-2
ComponentsSYNTAXIN-BINDING PROTEIN 2
KeywordsPROTEIN TRANSPORT
Function / homology
Function and homology information


leukocyte mediated cytotoxicity / tertiary granule / cytolytic granule / syntaxin-3 binding / neutrophil degranulation / zymogen granule membrane / regulation of mast cell degranulation / platelet degranulation / specific granule / neurotransmitter secretion ...leukocyte mediated cytotoxicity / tertiary granule / cytolytic granule / syntaxin-3 binding / neutrophil degranulation / zymogen granule membrane / regulation of mast cell degranulation / platelet degranulation / specific granule / neurotransmitter secretion / vesicle docking involved in exocytosis / syntaxin-1 binding / syntaxin binding / azurophil granule / Other interleukin signaling / vesicle-mediated transport / phagocytic vesicle / secretory granule / intracellular protein transport / cellular response to type II interferon / presynapse / Platelet degranulation / apical plasma membrane / extracellular exosome / extracellular region / plasma membrane / cytosol
Similarity search - Function
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, domain 2 / Sec1-like, domain 3a / Sec1-like protein / Sec1-like superfamily ...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, domain 2 / Sec1-like, domain 3a / Sec1-like protein / Sec1-like superfamily / Sec1 family / 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
Syntaxin-binding protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHackmann, Y. / Graham, S.C. / Ehl, S. / Hoening, S. / Lehmberg, K. / Arico, M. / Owen, D.J. / Griffiths, G.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Syntaxin Binding Mechanism and Disease-Causing Mutations in Munc18-2
Authors: Hackmann, Y. / Graham, S.C. / Ehl, S. / Hoening, S. / Lehmberg, K. / Arico, M. / Owen, D.J. / Griffiths, G.G.
History
DepositionOct 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Atomic model / Other
Revision 1.2Nov 13, 2013Group: Database references
Revision 1.3Nov 20, 2013Group: Database references
Revision 1.4Dec 4, 2013Group: Database references
Revision 1.5May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.6May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.7Dec 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 / 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 / _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: SYNTAXIN-BINDING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0972
Polymers67,0611
Non-polymers351
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.550, 67.550, 284.651
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1594-

CL

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Components

#1: Protein SYNTAXIN-BINDING PROTEIN 2 / PROTEIN UNC-18 HOMOLOG 2 / UNC18-2 / PROTEIN UNC-18 HOMOLOG B / UNC-18B / MUNC18-2


Mass: 67061.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: CYTOTOXIC T LYMPHOCYTES / Plasmid: PFASBAC 1 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q15833
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsADDITIONAL GSPEF BEFORE STARTING METHIONINE RESIDUAL FROM PURIFICATION TAG.

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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: 2.42 Å3/Da / Density % sol: 59.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: SITTING DROPS CONTAINING 200 NL 8.85 MG/ML MUNC18-2 PLUS 200 NL RESERVOIR SOLUTION (0.1 M MES PH 6, 10% V/V 2-METHYL-2,4-PENTANEDIOL) EQUILIBRATED AGAINST 80 UL RESERVOIRS AT 20C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2011
Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.6→49 Å / Num. obs: 21395 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Biso Wilson estimate: 73.68 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.9
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C98, CHAIN A

3c98


Resolution: 2.6→47.765 Å / SU ML: 0.82 / σ(F): 1.92 / Phase error: 27.49 / Stereochemistry target values: ML
Details: PROTONS WERE MODELLED IN 'RIDING' POSITIONS. DISORDERED REGIONS WERE NOT MODELED
RfactorNum. reflection% reflection
Rfree0.2748 1095 5.1 %
Rwork0.2425 --
obs0.2441 21302 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.307 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso mean: 95.38 Å2
Baniso -1Baniso -2Baniso -3
1-5.1754 Å20 Å20 Å2
2--5.1754 Å20 Å2
3----10.3508 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4211 0 1 13 4225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034293
X-RAY DIFFRACTIONf_angle_d0.7985828
X-RAY DIFFRACTIONf_dihedral_angle_d12.4031599
X-RAY DIFFRACTIONf_chiral_restr0.042686
X-RAY DIFFRACTIONf_plane_restr0.003745
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6002-2.71850.36011390.33652427X-RAY DIFFRACTION100
2.7185-2.86180.36981410.32082452X-RAY DIFFRACTION100
2.8618-3.04110.34471160.29522495X-RAY DIFFRACTION100
3.0411-3.27590.31281440.29352470X-RAY DIFFRACTION100
3.2759-3.60540.33251520.27792488X-RAY DIFFRACTION100
3.6054-4.12690.26731420.24762527X-RAY DIFFRACTION100
4.1269-5.19840.25251250.1982599X-RAY DIFFRACTION100
5.1984-47.77320.22831360.22462749X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.519-0.4247-0.83011.041-0.53381.2693-0.62740.2038-1.3786-0.42950.2218-0.12050.5548-0.4786-0.20161.31240.51840.60670.51540.17971.296-18.03929.3389-18.5373
21.0330.099-0.49621.18590.19410.8873-0.2628-0.2635-0.1031-0.09980.148-0.12390.34710.5468-0.34180.41220.30230.08080.58360.0410.2583-1.171437.2178-17.1971
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 5:141
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 142:593

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