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- PDB-4b93: Complex of Vamp7 cytoplasmic domain with 2nd ankyrin repeat domai... -

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Basic information

Entry
Database: PDB / ID: 4b93
TitleComplex of Vamp7 cytoplasmic domain with 2nd ankyrin repeat domain of Varp
Components
  • ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
  • VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
KeywordsEXOCYTOSIS / ENDOCYTOSIS / SNARE
Function / homology
Function and homology information


regulation of protein targeting to vacuolar membrane / negative regulation of SNARE complex assembly / triglyceride transport / tubular endosome / vesicle fusion with Golgi apparatus / endosome to melanosome transport / neutrophil degranulation / eosinophil degranulation / vesicle fusion / vesicle transport along microtubule ...regulation of protein targeting to vacuolar membrane / negative regulation of SNARE complex assembly / triglyceride transport / tubular endosome / vesicle fusion with Golgi apparatus / endosome to melanosome transport / neutrophil degranulation / eosinophil degranulation / vesicle fusion / vesicle transport along microtubule / SNARE complex / SNAP receptor activity / calcium-ion regulated exocytosis / Golgi to plasma membrane protein transport / early endosome to late endosome transport / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / positive regulation of dendrite morphogenesis / SNARE complex assembly / syntaxin binding / phagocytosis, engulfment / endosome to lysosome transport / exocytosis / pseudopodium / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / transport vesicle / phagocytic vesicle / hippocampal mossy fiber to CA3 synapse / GTPase activator activity / guanyl-nucleotide exchange factor activity / neuron projection morphogenesis / SNARE binding / filopodium / cytoplasmic vesicle membrane / synaptic vesicle membrane / small GTPase binding / positive regulation of neuron projection development / phagocytic vesicle membrane / melanosome / protein transport / synaptic vesicle / late endosome / lamellipodium / apical part of cell / late endosome membrane / lysosome / early endosome / neuron projection / lysosomal membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / cell surface / membrane / plasma membrane / cytosol
Similarity search - Function
VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / Longin domain / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain ...VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / 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. / Longin-like domain superfamily / Ankyrin repeat-containing domain / Beta-Lactamase / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Vesicle-associated membrane protein 7 / Ankyrin repeat domain-containing protein 27
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å
AuthorsSchaefer, I.B. / Owen, D.J. / Luzio, J.P. / Evans, P.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: The Binding of Varp to Vamp7 Traps Vamp7 in a Closed, Fusogenically Inactive Conformation.
Authors: Schafer, I.B. / Hesketh, G.G. / Bright, N.A. / Gray, S.R. / Pryor, P.R. / Evans, P.R. / Luzio, J.P. / Owen, D.J.
History
DepositionAug 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Jan 25, 2017Group: Data collection
Revision 1.3Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
B: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27


Theoretical massNumber of molelcules
Total (without water)51,0132
Polymers51,0132
Non-polymers00
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.570, 122.660, 158.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein VESICLE-ASSOCIATED MEMBRANE PROTEIN 7 / VAMP-7 / SYNAPTOBREVIN-LIKE PROTEIN 1


Mass: 21520.695 Da / Num. of mol.: 1 / Fragment: CYTOPLASMIC DOMAIN, RESIDUES 1-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: VAMP7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS / References: UniProt: P70280
#2: Protein ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27 / VARP / VPS9 DOMAIN-CONTAINING PROTEIN


Mass: 29492.562 Da / Num. of mol.: 1 / Fragment: 2ND ANKYRIN REPEAT DOMAIN, RESIDUES 659-921
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: VARP658-921 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS / References: UniProt: Q96NW4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.91 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 5 TO 7.5 % (V/V) ISOPROPANOL AND 0.1 M IMIDAZOLE PH 6.5-7.8 IN HANGING AND SITTING DROPS AT 4 DEGREES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2009 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→56 Å / Num. obs: 43692 / % possible obs: 99.7 % / Observed criterion σ(I): 100 / Redundancy: 4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 0.9 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0018refinement
MOSFLMdata reduction
Aimlessdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2→39.85 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.895 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 2332 5.1 %RANDOM
Rwork0.21312 ---
obs0.21505 43692 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.152 Å2
Baniso -1Baniso -2Baniso -3
1-2.83 Å20 Å20 Å2
2--1.07 Å20 Å2
3----3.9 Å2
Refinement stepCycle: LAST / Resolution: 2→39.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 0 209 2916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192758
X-RAY DIFFRACTIONr_bond_other_d0.0010.022695
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.9513728
X-RAY DIFFRACTIONr_angle_other_deg0.87636169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8845346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26224.58131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70115488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7851517
X-RAY DIFFRACTIONr_chiral_restr0.1070.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023151
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02646
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_it4.2834.8772758
X-RAY DIFFRACTIONr_mcbond_other1.2364.982695
X-RAY DIFFRACTIONr_mcangle_it6.1897.2233727
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: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 172 -
Rwork0.391 3184 -
obs--99 %

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