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- PDB-4bx9: Human Vps33A in complex with a fragment of human Vps16 -

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Basic information

Entry
Database: PDB / ID: 4bx9
TitleHuman Vps33A in complex with a fragment of human Vps16
Components(VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN ...) x 2
KeywordsPROTEIN TRANSPORT / HOPS / MEMBRANE TRAFFICKING / SEC1/MUNC18 PROTEINS / TETHERING
Function / homology
Function and homology information


CORVET complex / HOPS complex / regulation of SNARE complex assembly / endosomal vesicle fusion / melanosome localization / regulation of developmental pigmentation / vacuole fusion, non-autophagic / SARS-CoV-2 modulates autophagy / regulation of lysosomal lumen pH / lysosome localization ...CORVET complex / HOPS complex / regulation of SNARE complex assembly / endosomal vesicle fusion / melanosome localization / regulation of developmental pigmentation / vacuole fusion, non-autophagic / SARS-CoV-2 modulates autophagy / regulation of lysosomal lumen pH / lysosome localization / clathrin-coated vesicle / platelet formation / endosomal transport / endosome to lysosome transport / autophagosome maturation / vesicle-mediated transport / autophagosome / intracellular protein transport / recycling endosome / late endosome / late endosome membrane / actin binding / early endosome / lysosome / endosome membrane / endosome / lysosomal membrane / perinuclear region of cytoplasm
Similarity search - Function
Vps16, C-terminal region / 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 ...Vps16, C-terminal region / 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 protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / DNA polymerase; domain 1 / Alpha Horseshoe / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / (2S)-2-hydroxybutanedioic acid / MALONIC ACID / Vacuolar protein sorting-associated protein 33A / Vacuolar protein sorting-associated protein 16 homolog
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGraham, S.C. / Wartosch, L. / Gray, S.R. / Scourfield, E.J. / Deane, J.E. / Luzio, J.P. / Owen, D.J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2013
Title: Structural basis of Vps33A recruitment to the human HOPS complex by Vps16.
Authors: Graham, S.C. / Wartosch, L. / Gray, S.R. / Scourfield, E.J. / Deane, J.E. / Luzio, J.P. / Owen, D.J.
History
DepositionJul 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3Apr 22, 2015Group: Non-polymer description
Revision 1.4Mar 13, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.5Dec 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: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 33A
B: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 33A
C: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 16 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,8958
Polymers149,5183
Non-polymers3765
Water3,513195
1
A: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 33A
C: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 16 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7245
Polymers80,4402
Non-polymers2843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 33A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1703
Polymers69,0781
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.410, 128.410, 263.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN ... , 2 types, 3 molecules ABC

#1: Protein VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 33A / HVPS33A / VPS33A


Mass: 69078.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q96AX1
#2: Protein VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 16 HOMOLOG / HVPS16 / VPS16


Mass: 11362.010 Da / Num. of mol.: 1 / Fragment: RESIDUES 642-736
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPT3G / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9H269

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Non-polymers , 4 types, 200 molecules

#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#5: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsADDITIONAL C-TERMINAL RESIDUES ARE DERIVED FROM THE EXPRESSION VECTOR. ADDITIONAL N-TERMINAL ...ADDITIONAL C-TERMINAL RESIDUES ARE DERIVED FROM THE EXPRESSION VECTOR. ADDITIONAL N-TERMINAL RESIDUES ARE RESIDUAL FROM CLEAVAGE OF GST 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: 3.64 Å3/Da / Density % sol: 66.19 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: CRYSTALS WERE GROWN IN SITTING DROPS AT 20C. VPS33A:VPS16 COMPLEX (200 NL; A280 = 7.13, APPROX. 8.7 MG/ML) WAS MIXED 1:1 WITH RESERVOIR SOLUTION AND EQUILIBRATED AGAINST 80 UL RESERVOIRS ...Details: CRYSTALS WERE GROWN IN SITTING DROPS AT 20C. VPS33A:VPS16 COMPLEX (200 NL; A280 = 7.13, APPROX. 8.7 MG/ML) WAS MIXED 1:1 WITH RESERVOIR SOLUTION AND EQUILIBRATED AGAINST 80 UL RESERVOIRS CONTAINING 4% TACSIMATE PH 6.0, 12% PEG 3350 (HAMPTON RESEARCH). CRYSTALS WERE CRYOPROTECTED BY BRIEF IMMERSION IN RESERVOIR SOLUTION SUPPLEMENTED WITH 30% ETHYLENE GLYCOL AND CRYO-COOLED BY PLUNGING INTO LIQUID NITROGEN.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 10, 2012 / Details: TOROIDAL
RadiationMonochromator: SINGLE BOUNCE SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 2.6→87.8 Å / Num. obs: 68560 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 15.2 % / Biso Wilson estimate: 76.138 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.8
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 14 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BX8

4bx8


Resolution: 2.6→85.84 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 15.437 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21024 3465 5.1 %RANDOM
Rwork0.17594 ---
obs0.17762 65003 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.508 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2---0.75 Å20 Å2
3---1.49 Å2
Refinement stepCycle: LAST / Resolution: 2.6→85.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9973 0 25 195 10193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01910178
X-RAY DIFFRACTIONr_bond_other_d0.0050.029905
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.97613743
X-RAY DIFFRACTIONr_angle_other_deg1.092322744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23951243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52923.958480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.432151841
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.911577
X-RAY DIFFRACTIONr_chiral_restr0.0940.21549
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211434
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022339
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
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: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 248 -
Rwork0.377 4749 -
obs--100 %
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)
11.61530.83190.11524.3494-1.30831.4261-0.08210.1606-0.00010.019-0.0417-0.15290.03650.29430.12370.03290.03160.02530.45510.21850.117855.29984.765302.87
21.2554-0.23110.33291.1622-0.38831.55950.04340.2058-0.1265-0.07230.05380.07050.3515-0.0091-0.09720.14750.01310.02350.23340.14460.160732.27762.726305.801
35.45732.38991.52312.76131.35713.98730.1449-1.00320.24760.4421-0.29730.2694-0.21080.23450.15240.3373-0.0782-0.0260.69940.07140.067637.391117.505290.289
42.29220.29930.36311.4672-0.42721.3855-0.14150.2203-0.0933-0.3643-0.01520.0710.01520.35150.15670.2103-0.0929-0.04850.50530.15280.07438.169103.333262.875
53.2542-0.7265-2.53351.5673-0.31896.87020.0625-0.05390.61130.11960.1245-0.0092-0.5097-0.1516-0.18690.32970.0664-0.00320.78630.30530.64166.69692.018304.788
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 146
2X-RAY DIFFRACTION2A147 - 600
3X-RAY DIFFRACTION3B1 - 146
4X-RAY DIFFRACTION4B147 - 600
5X-RAY DIFFRACTION5C640 - 736

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