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- PDB-4kmo: Crystal Structure of the Vps33-Vps16 HOPS subcomplex from Chaetom... -

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Basic information

Entry
Database: PDB / ID: 4kmo
TitleCrystal Structure of the Vps33-Vps16 HOPS subcomplex from Chaetomium thermophilum
Components
  • Putative vacuolar protein sorting-associated proteinVacuole
  • Small conjugating protein ligase-like protein
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
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: 2.6 Å
AuthorsBaker, R.W. / Jeffrey, P.D. / Hughson, F.M.
CitationJournal: 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
DepositionMay 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small conjugating protein ligase-like protein
B: Putative vacuolar protein sorting-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,7493
Polymers112,6532
Non-polymers961
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-35 kcal/mol
Surface area37340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.274, 100.274, 176.225
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Small conjugating protein ligase-like protein


Mass: 74365.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: thermophilum / Gene: CTHT_0057760 / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0SCM5*PLUS
#2: Protein Putative vacuolar protein sorting-associated protein / Vacuole


Mass: 38287.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: thermophilum DSM 1495 / Gene: CTHT_0026760 / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0S6M7*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PUBLISHED SEQUENCE OF VPS33 ERRONEOUSLY CONTAINS AN E2 DOMAIN AT THE N-TERMINUS. THE SEQUENCE ...THE PUBLISHED SEQUENCE OF VPS33 ERRONEOUSLY CONTAINS AN E2 DOMAIN AT THE N-TERMINUS. THE SEQUENCE IN THIS ENTRY CORRESPONDS TO THE CORRECT SEQUENCE OF CHAETOMIUM THERMOPHILUM VPS33 THAT CONTAINS JUST THE SM PROTEIN THE PUBLISHED SEQUENCE OF VPS16 IS ALSO IN ERROR. THE SEQUENCE HEREIN CORRESPONDS TO THE CORRECT SEQUENCE FOR RESIDUES 505-834 AND CONTAINS AN INSERTION AT 672-690 RELATIVE TO THE PUBLISHED SEQUENCE

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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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 12-16% (w/v) PEG 4000, 150 mM ammonium sulfate, 100 mM MES buffer , pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2012
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 31686 / Num. obs: 31686 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.6-2.649.40.873194
2.64-2.699.20.726197.9
2.69-2.749.20.66196.7
2.74-2.89.10.567196.2
2.8-2.869.20.5196.6
2.86-2.939.20.449198.3
2.93-39.20.369197.3
3-3.089.10.298197.8
3.08-3.179.20.247198.3
3.17-3.289.10.212198.4
3.28-3.399.20.175198.8
3.39-3.539.20.138198.7
3.53-3.699.20.112199.1
3.69-3.889.30.106198.9
3.88-4.139.30.094199.8
4.13-4.459.40.0851100
4.45-4.899.60.076199.9
4.89-5.69.90.076199.9
5.6-7.0510.60.084199.8
7.05-509.10.079196.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JC8

4jc8


Resolution: 2.6→48.656 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / σ(F): 1.34 / Phase error: 26.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2537 1600 5.06 %
Rwork0.2252 --
obs0.2267 31605 98.08 %
all-31605 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.9167 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6658 0 5 147 6810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026768
X-RAY DIFFRACTIONf_angle_d0.6349127
X-RAY DIFFRACTIONf_dihedral_angle_d13.4222558
X-RAY DIFFRACTIONf_chiral_restr0.0461037
X-RAY DIFFRACTIONf_plane_restr0.0031182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.68390.33081400.26232582X-RAY DIFFRACTION95
2.6839-2.77990.29051300.25182663X-RAY DIFFRACTION96
2.7799-2.89120.2921400.24992664X-RAY DIFFRACTION97
2.8912-3.02270.27181330.24972700X-RAY DIFFRACTION98
3.0227-3.18210.31311480.24632666X-RAY DIFFRACTION98
3.1821-3.38140.32231570.24742722X-RAY DIFFRACTION98
3.3814-3.64240.23521460.22672727X-RAY DIFFRACTION99
3.6424-4.00880.25561270.21532782X-RAY DIFFRACTION99
4.0088-4.58850.22931570.19812798X-RAY DIFFRACTION100
4.5885-5.77950.22421810.21592784X-RAY DIFFRACTION100
5.7795-48.6640.24141410.22422917X-RAY DIFFRACTION98
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)
10.1474-0.0488-0.0850.02160.03750.0494-0.1663-0.15010.02190.3401-0.0598-0.0692-0.25850.1282-0.09320.7072-0.1668-0.27690.43670.02820.350545.188-22.82836.0736
20.0660.0991-0.0190.12-0.02110.0273-0.0535-0.00670.18140.0592-0.0993-0.2825-0.41640.1504-0.09680.2813-0.4987-0.17260.40450.1060.509350.4506-19.943926.2588
30.0729-0.01130.07790.0003-0.02890.1362-0.00280.0526-0.00680.0881-0.1043-0.13140.07080.038-0.13760.24830.02710.0090.18110.05860.28836.1673-38.422616.7154
40.0433-0.0026-0.0090.00590.02470.05630.1154-0.17350.09530.305-0.07650.0325-0.31210.00710.00030.4259-0.07680.03270.3398-0.03570.338815.1951-23.963837.1892
50.0443-0.0320.01550.07940.00960.01170.07070.0932-0.0035-0.0328-0.03210.1839-0.1614-0.42650.02990.30590.1007-0.01390.34890.02530.375810.0928-17.72718.1444
60.2028-0.20390.02230.2122-0.01240.16330.22590.15410.0425-0.1369-0.21470.21570.1021-0.09750.02370.29860.0238-0.04930.3448-0.06230.340816.9636-30.72415.9127
70.00870.0055-0.01630.00620.00040.02750.05550.0207-0.0643-0.00130.02380.02930.174-0.02130.03910.3399-0.08040.01390.2812-0.00760.274814.1326-45.039317.4562
80.14450.05350.07060.1380.06270.1154-0.0115-0.0233-0.0252-0.0149-0.0652-0.17280.1136-0.0889-0.10430.3276-0.05160.01610.23370.01730.281824.992-37.392418.2086
90.00180.0014-0.0029-0.0002-0.00160.00160.0075-0.03520.0030.0194-0.01830.02580.01990.026401.1010.24970.12240.78360.01611.035657.9462-41.95513.5329
100.0545-0.0170.02110.0489-0.04330.02620.1008-0.1965-0.2603-0.10710.0021-0.06550.04080.04270.05010.40050.0210.09250.30660.08520.593548.9023-23.47150.9726
110.01950.0129-0.00820.0143-0.01760.0233-0.22880.00550.0348-0.0173-0.0743-0.1063-0.0889-0.0470.0020.41870.07850.02750.4210.05670.530833.6159-5.13021.5262
120.00470.0002-0.00760.0051-0.00740.0163-0.06850.19750.0423-0.04280.0978-0.01020.0013-0.0398-00.50970.01490.0820.37460.06120.449929.8764-4.2323-6.7804
130.0425-0.0033-0.0110.080.05170.03940.10470.05020.0736-0.00150.07940.1147-0.195-0.11940.09140.66690.20010.07820.34390.1350.320.60744.66730.5716
140.02290.0169-0.00310.0987-0.05640.03780.12170.13020.0526-0.01980.07890.0395-0.078-0.10660.34530.65350.51380.07280.50140.10460.260411.78875.50387.2887
150.02210.0176-0.020.0142-0.01260.02530.19390.15270.03480.0097-0.01710.0811-0.05250.10160.02610.51360.33960.06950.63890.04320.4326-1.18032.465213.2593
160.0449-0.07930.02440.1484-0.04810.01750.05910.0396-0.08280.13320.01020.26930.0807-0.09110.04610.55830.28320.11780.70810.07930.3741-10.3942-6.514717.5932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 83 )
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 150 )
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 251 )
4X-RAY DIFFRACTION4chain 'A' and (resid 252 through 378 )
5X-RAY DIFFRACTION5chain 'A' and (resid 379 through 449 )
6X-RAY DIFFRACTION6chain 'A' and (resid 450 through 513 )
7X-RAY DIFFRACTION7chain 'A' and (resid 514 through 559 )
8X-RAY DIFFRACTION8chain 'A' and (resid 560 through 657 )
9X-RAY DIFFRACTION9chain 'B' and (resid 520 through 535 )
10X-RAY DIFFRACTION10chain 'B' and (resid 536 through 618 )
11X-RAY DIFFRACTION11chain 'B' and (resid 619 through 635 )
12X-RAY DIFFRACTION12chain 'B' and (resid 636 through 657 )
13X-RAY DIFFRACTION13chain 'B' and (resid 658 through 681 )
14X-RAY DIFFRACTION14chain 'B' and (resid 682 through 716 )
15X-RAY DIFFRACTION15chain 'B' and (resid 717 through 742 )
16X-RAY DIFFRACTION16chain 'B' and (resid 743 through 791 )

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