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- PDB-5bv1: Crystal Structure of a Vps33-Vps16 Complex from Chaetomium thermo... -

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Basic information

Entry
Database: PDB / ID: 5bv1
TitleCrystal Structure of a Vps33-Vps16 Complex from Chaetomium thermophilum
Components
  • Putative vacuolar protein sorting-associated proteinVacuole
  • VPS33
KeywordsTRANSPORT PROTEIN / Membrane trafficking / SM protein / HOPS complex / thermophile
Function / homology
Function and homology information


vacuole organization / ligase activity / endomembrane system / vesicle-mediated transport / intracellular protein transport / intracellular membrane-bounded organelle / protein-containing complex / cytoplasm
Similarity search - Function
Sec1/Munc18 (SM) protein, domain 3b / Vps16, C-terminal / Vps16, N-terminal / Vacuolar protein sorting-associated protein 16 / Vps16, C-terminal domain superfamily / Vps16, C-terminal region / Vps16, N-terminal region / Vacuolar protein sorting-associated protein 33, domain 3b / Sec1/Munc18 (SM) protein, domain 2 / Syntaxin Binding Protein 1; Chain A, domain 2 ...Sec1/Munc18 (SM) protein, domain 3b / Vps16, C-terminal / Vps16, N-terminal / Vacuolar protein sorting-associated protein 16 / Vps16, C-terminal domain superfamily / Vps16, C-terminal region / Vps16, N-terminal region / Vacuolar protein sorting-associated protein 33, domain 3b / 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 / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / WD40/YVTN repeat-like-containing domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
D-MALATE / Probable vacuolar protein sorting-associated protein 16 homolog / Small conjugating protein ligase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.902 Å
AuthorsBaker, R.W. / Jeffrey, P.D. / Hughson, F.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071574 United States
Citation
Journal: Science / Year: 2015
Title: A direct role for the Sec1/Munc18-family protein Vps33 as a template for SNARE assembly.
Authors: Baker, R.W. / Jeffrey, P.D. / Zick, M. / Phillips, B.P. / Wickner, W.T. / Hughson, F.M.
#1: Journal: Plos One / Year: 2013
Title: Crystal Structures of the Sec1/Munc18 (SM) Protein Vps33, Alone and Bound to the Homotypic Fusion and Vacuolar Protein Sorting (HOPS) Subunit Vps16*
Authors: Baker, R.W. / Jeffrey, P.D. / Hughson, F.M.
History
DepositionJun 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VPS33
B: Putative vacuolar protein sorting-associated protein
C: VPS33
D: Putative vacuolar protein sorting-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,0736
Polymers223,8054
Non-polymers2682
Water0
1
A: VPS33
B: Putative vacuolar protein sorting-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0363
Polymers111,9022
Non-polymers1341
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-24 kcal/mol
Surface area40630 Å2
MethodPISA
2
C: VPS33
D: Putative vacuolar protein sorting-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0363
Polymers111,9022
Non-polymers1341
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-20 kcal/mol
Surface area40910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.280, 159.902, 97.394
Angle α, β, γ (deg.)90.000, 90.210, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUchain AAA5 - 6577 - 659
21GLUGLUchain CCC5 - 6577 - 659
12GLYGLYchain BBB532 - 82831 - 327
22GLYGLYchain DDD532 - 82831 - 327

NCS ensembles :
ID
1
2

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Components

#1: Protein VPS33


Mass: 73990.117 Da / Num. of mol.: 2 / Fragment: unp residues 139-806
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0057760 / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0SCM5
#2: Protein Putative vacuolar protein sorting-associated protein / Vacuole


Mass: 37912.211 Da / Num. of mol.: 2 / Fragment: unp residues 503-816 / Mutation: L672V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0026760 / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0S6M7
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
Sequence detailsAuthors have indicated that the sequence for the UNProt entries G0S6M7_CHATD and G0SCM5_CHATD are not correct

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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: 2.76 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: HEPES buffer, 8-10% w/v PEG 5000 monomethyl ether

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2014
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.902→159.902 Å / Num. obs: 53085 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 65.34 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 16.9 / Num. measured all: 300496
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.902-2.9125.80.8072.1318755098
13.469-159.9025.30.024292354997.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
CBASSdata collection
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KMO

4kmo


Resolution: 2.902→61.592 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2759 2699 5.09 %Random selection 5%
Rwork0.2115 50335 --
obs0.2148 53034 98.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.73 Å2 / Biso mean: 66.5912 Å2 / Biso min: 20.98 Å2
Refinement stepCycle: final / Resolution: 2.902→61.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14241 0 18 0 14259
Biso mean--78.03 --
Num. residues----1797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614485
X-RAY DIFFRACTIONf_angle_d1.05619538
X-RAY DIFFRACTIONf_chiral_restr0.042204
X-RAY DIFFRACTIONf_plane_restr0.0042549
X-RAY DIFFRACTIONf_dihedral_angle_d15.3085480
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5687X-RAY DIFFRACTION7.817TORSIONAL
12C5687X-RAY DIFFRACTION7.817TORSIONAL
21B2835X-RAY DIFFRACTION7.817TORSIONAL
22D2835X-RAY DIFFRACTION7.817TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9023-2.95510.37671260.29422677280399
2.9551-3.01190.34961440.27592604274899
3.0119-3.07340.32771200.27042684280499
3.0734-3.14020.3891390.26342637277699
3.1402-3.21330.32541230.26192648277199
3.2133-3.29360.30421490.25812635278499
3.2936-3.38270.31711420.25512643278599
3.3827-3.48220.33141460.2552637278399
3.4822-3.59460.28351510.24362636278799
3.5946-3.7230.35631490.23652640278999
3.723-3.87210.31191300.23412631276199
3.8721-4.04830.32891440.21492672281699
4.0483-4.26160.24271110.20482660277199
4.2616-4.52860.24451800.18682593277399
4.5286-4.87810.23491630.18122645280899
4.8781-5.36870.26991350.19422664279999
5.3687-6.1450.26151660.19442656282299
6.145-7.73960.23491360.18852681281799
7.7396-61.60620.20971450.16012692283798

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