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- PDB-2cay: Vps36 N-terminal PH domain -

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Basic information

Entry
Database: PDB / ID: 2cay
TitleVps36 N-terminal PH domain
ComponentsVACUOLAR PROTEIN SORTING PROTEIN 36
KeywordsTRANSPORT / VPS36 / PH DOMAIN / ESCRT-II / LIPID-BINDING / MULTIVESICULAR BODIES / MEMBRANE / METAL-BINDING / PROTEIN TRANSPORT / ZINC / ZINC-FINGER
Function / homology
Function and homology information


ESCRT II complex / carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / ATP export / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / cytoplasm to vacuole targeting by the Cvt pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to vacuole / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / phosphatidylinositol-3-phosphate binding ...ESCRT II complex / carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / ATP export / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / cytoplasm to vacuole targeting by the Cvt pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to vacuole / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / phosphatidylinositol-3-phosphate binding / localization / ubiquitin binding / macroautophagy / late endosome membrane / metal ion binding
Similarity search - Function
Vacuolar protein-sorting-associated protein 36, NZF-N zinc-finger domain / Vacuolar protein sorting 36 NZF-N zinc-finger domain / Vacuolar protein sorting protein 36, GLUE domain / Vacuolar protein sorting protein 36 / Snf8/Vps36 family / EAP30/Vps36 family / Vacuolar protein sorting protein 36 Vps36 / GLUE domain profile. / Zinc finger domain / Zinc finger, RanBP2-type superfamily ...Vacuolar protein-sorting-associated protein 36, NZF-N zinc-finger domain / Vacuolar protein sorting 36 NZF-N zinc-finger domain / Vacuolar protein sorting protein 36, GLUE domain / Vacuolar protein sorting protein 36 / Snf8/Vps36 family / EAP30/Vps36 family / Vacuolar protein sorting protein 36 Vps36 / GLUE domain profile. / Zinc finger domain / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Vacuolar protein-sorting-associated protein 36
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsTeo, H. / Williams, R.L. / Perisic, O. / Gill, D.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Escrt-I Core and Escrt-II Glue Domain Structures Reveal Role for Glue in Linking to Escrt-I and Membranes.
Authors: Teo, H. / Gill, D.J. / Sun, J. / Perisic, O. / Veprintsev, D.B. / Wallis, Y. / Emr, S.D. / Williams, R.L.
History
DepositionDec 23, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VACUOLAR PROTEIN SORTING PROTEIN 36
B: VACUOLAR PROTEIN SORTING PROTEIN 36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9784
Polymers33,7862
Non-polymers1922
Water3,171176
1
A: VACUOLAR PROTEIN SORTING PROTEIN 36
B: VACUOLAR PROTEIN SORTING PROTEIN 36
hetero molecules

A: VACUOLAR PROTEIN SORTING PROTEIN 36
B: VACUOLAR PROTEIN SORTING PROTEIN 36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9568
Polymers67,5724
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)94.451, 88.375, 45.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.95843, -0.28493, 0.01506), (-0.28513, -0.95839, 0.01357), (0.01056, -0.0173, -0.99979)
Vector: 12.04569, 86.18025, 33.1378)

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Components

#1: Protein VACUOLAR PROTEIN SORTING PROTEIN 36 / VPS36 PH DOMAIN


Mass: 16893.018 Da / Num. of mol.: 2 / Fragment: PH DOMAIN, RESIDUES 1-99 AND 252-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: POPTH / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q06696
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Compound detailsREQUIRED FOR MULTIVESICULAR BODIES (MVBS) FORMATION AND SORTING OF ENDOSOMAL CARGO PROTEINS INTO MVBS
Sequence detailsRESIDUE 100-251 DELETED

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 48.4 %
Crystal growpH: 9.5 / Details: 1M AMSO4, 0.2M NACL, 6% GLYCEROL 0.1M TRIS PH 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 19, 2005 / Details: TORROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→44.19 Å / Num. obs: 31078 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.54 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.34
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.61 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.55 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
SHARPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→44.19 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.679 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1556 5 %RANDOM
Rwork0.191 ---
obs0.193 29476 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2145 0 10 176 2331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222197
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9622962
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4855259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.28923.333111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15715390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7521518
X-RAY DIFFRACTIONr_chiral_restr0.120.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021654
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.2844
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21459
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2146
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1671.51344
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9422104
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8813963
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5934.5858
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.319 106
Rwork0.246 2133

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