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- PDB-4bx8: Human Vps33A -

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Basic information

Entry
Database: PDB / ID: 4bx8
TitleHuman Vps33A
ComponentsVACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 33A
KeywordsPROTEIN TRANSPORT / HOPS / MEMBRANE TRAFFICKING / SEC1/MUNC18 PROTEINS / TETHERING
Function / homology
Function and homology information


endosomal vesicle fusion / regulation of SNARE complex assembly / CORVET complex / HOPS complex / melanosome localization / regulation of developmental pigmentation / SARS-CoV-2 modulates autophagy / regulation of lysosomal lumen pH / lysosome localization / clathrin-coated vesicle ...endosomal vesicle fusion / regulation of SNARE complex assembly / CORVET complex / HOPS complex / melanosome localization / regulation of developmental pigmentation / SARS-CoV-2 modulates autophagy / regulation of lysosomal lumen pH / lysosome localization / clathrin-coated vesicle / platelet formation / endosome to lysosome transport / autophagosome maturation / autophagosome / vesicle-mediated transport / intracellular protein transport / late endosome / late endosome membrane / lysosome / early endosome / endosome membrane / lysosomal membrane / perinuclear region of cytoplasm
Similarity search - Function
Sec1/Munc18 (SM) protein, domain 3b / 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/Munc18 (SM) protein, domain 3b / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 33A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.4 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.USA / 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 1.2Aug 28, 2013Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,5044
Polymers138,4332
Non-polymers712
Water1,31573
1
A: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 33A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2522
Polymers69,2161
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 33A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2522
Polymers69,2161
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.470, 125.010, 83.280
Angle α, β, γ (deg.)90.00, 115.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 69216.352 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.43 Å3/Da / Density % sol: 49.47 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: CRYSTALS WERE GROWN IN SITTING DROPS AT 20 C. VPS33A-HIS10 (200 NL; 3.2 MG/ML) WAS EQUILIBRATED AGAINST 80 UL RESERVOIRS CONTAINING 14.3-12.8% (W/V) PEG 3350 AND 143-128 MM AMMONIUM ACETATE ...Details: CRYSTALS WERE GROWN IN SITTING DROPS AT 20 C. VPS33A-HIS10 (200 NL; 3.2 MG/ML) WAS EQUILIBRATED AGAINST 80 UL RESERVOIRS CONTAINING 14.3-12.8% (W/V) PEG 3350 AND 143-128 MM AMMONIUM ACETATE (HAMPTON RESEARCH). CRYSTALS WERE CRYOPROTECTED BY ADDING RESERVOIR SOLUTION SUPPLEMENTED WITH 30% (V/V) ETHYLENE GLYCOL TO THE MOTHER LIQUOR IMMEDIATELY BEFORE HARVESTING AND CRYO-COOLING BY PLUNGING INTO LIQUID NITROGEN. ANNEALING BY BLOCKING THE CRYOSTREAM FOR 5 S GREATLY ENHANCED THE DIFFRACTION OF VPS33A CRYSTALS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2011
Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.4→64.5 Å / Num. obs: 49915 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 53.776 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.7 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.4→64.61 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 18.921 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.438 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24377 2103 4.2 %RANDOM
Rwork0.19721 ---
obs0.19914 47789 96.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.244 Å2
Baniso -1Baniso -2Baniso -3
1--4.9 Å20 Å20.19 Å2
2--4.65 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.4→64.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9062 0 2 73 9137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199238
X-RAY DIFFRACTIONr_bond_other_d0.0040.028947
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.97512489
X-RAY DIFFRACTIONr_angle_other_deg0.979320556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31551131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86224.023435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.568151650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1171566
X-RAY DIFFRACTIONr_chiral_restr0.0810.21405
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110384
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022120
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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 156 -
Rwork0.271 3558 -
obs--97.12 %
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)
13.9593-0.53772.58771.9005-0.59399.38710.2248-0.8734-0.00840.38260.10520.16920.7924-0.8-0.330.4105-0.18020.04350.27650.04620.12134.83729.437570.2112
21.6137-0.22210.31360.9987-0.1690.83330.0668-0.0695-0.1937-0.0156-0.02160.15180.039-0.0244-0.04520.2881-0.0206-0.0260.03690.02920.058944.70640.215744.3178
35.92791.26044.73030.74540.84276.317-0.197-0.23860.3510.0397-0.1547-0.1036-0.3560.15960.35170.3119-0.0501-0.01580.07850.04590.179945.83867.817518.8229
41.08590.1259-0.3850.99860.10491.14910.08210.01320.1185-0.0854-0.05730.07640.00380.0118-0.02480.24860.0116-0.01650.0045-0.00320.024720.109856.495410.0759
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 156
2X-RAY DIFFRACTION2A157 - 600
3X-RAY DIFFRACTION3B1 - 156
4X-RAY DIFFRACTION4B157 - 600

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