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- PDB-6cbc: Crystal structure of an N-terminal fragment of Vps13. -

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Basic information

Entry
Database: PDB / ID: 6cbc
TitleCrystal structure of an N-terminal fragment of Vps13.
ComponentsVacuolar protein sorting-associated protein
KeywordsLIPID BINDING PROTEIN / Lipid transfer protein / Membrane trafficking / Endoplasmic reticulum / Mitochondria / Endosomes
Function / homology
Function and homology information


phospholipid transfer activity / intermembrane lipid transfer / phospholipid binding / membrane
Similarity search - Function
Vacuolar protein sorting-associated protein 13, VPS13 adaptor binding domain / Vacuolar protein sorting-associated protein 13, fungi / Vacuolar protein sorting-associated protein 13 / VPS13, repeated region / Vacuolar protein sorting-associated protein 13, DH-like domain / Vacuolar protein sorting-associated protein 13, second N-terminal domain / : / Vacuolar-sorting associated protein 13, adaptor binding domain / Vacuolar sorting-associated protein 13, extended-chorein / Vacuolar-sorting-associated 13 protein, DH-like domain ...Vacuolar protein sorting-associated protein 13, VPS13 adaptor binding domain / Vacuolar protein sorting-associated protein 13, fungi / Vacuolar protein sorting-associated protein 13 / VPS13, repeated region / Vacuolar protein sorting-associated protein 13, DH-like domain / Vacuolar protein sorting-associated protein 13, second N-terminal domain / : / Vacuolar-sorting associated protein 13, adaptor binding domain / Vacuolar sorting-associated protein 13, extended-chorein / Vacuolar-sorting-associated 13 protein, DH-like domain / VPS13, central RBG modules / Intermembrane lipid transfer protein VPS13, C-terminal / Vacuolar protein sorting-associated protein 13-like, N-terminal domain / VPS13-like, N-terminal / Cytosolic fatty-acid binding proteins signature.
Similarity search - Domain/homology
Intermembrane lipid transfer protein VPS13
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsKumar, N. / Horenkamp, F.A. / Reinisch, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM08616 United States
CitationJournal: J. Cell Biol. / Year: 2018
Title: VPS13A and VPS13C are lipid transport proteins differentially localized at ER contact sites.
Authors: Kumar, N. / Leonzino, M. / Hancock-Cerutti, W. / Horenkamp, F.A. / Li, P. / Lees, J.A. / Wheeler, H. / Reinisch, K.M. / De Camilli, P.
History
DepositionFeb 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Database references
Category: citation / citation_author / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: Vacuolar protein sorting-associated protein


Theoretical massNumber of molelcules
Total (without water)78,4692
Polymers78,4692
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-9 kcal/mol
Surface area30040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.933, 85.984, 71.027
Angle α, β, γ (deg.)90.00, 93.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Vacuolar protein sorting-associated protein


Mass: 39234.477 Da / Num. of mol.: 2 / Mutation: P228H, P236E
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_0020450 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: G0S3B8
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop
Details: 100 mM Bis-Tris pH 6.5-6.7 and 34-38% 7 15/4 Pentaerythritol ethoxylate (Hampton). Drops were equilibrated against well solution containing 1 M NaCl
PH range: 6.5-6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→48.6 Å / Num. obs: 28582 / % possible obs: 99.9 % / Redundancy: 20.4 % / Net I/σ(I): 21.9
Reflection shellResolution: 3→3.18 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3→48.543 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.9
RfactorNum. reflection% reflection
Rfree0.2642 1355 4.88 %
Rwork0.2301 --
obs0.2317 27771 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→48.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4003 0 0 0 4003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114084
X-RAY DIFFRACTIONf_angle_d1.4525545
X-RAY DIFFRACTIONf_dihedral_angle_d20.7421430
X-RAY DIFFRACTIONf_chiral_restr0.096651
X-RAY DIFFRACTIONf_plane_restr0.007702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10720.39691420.32542666X-RAY DIFFRACTION99
3.1072-3.23160.40351270.27852600X-RAY DIFFRACTION100
3.2316-3.37870.27081490.25162698X-RAY DIFFRACTION100
3.3787-3.55670.26971410.21562572X-RAY DIFFRACTION99
3.5567-3.77950.24251310.22322641X-RAY DIFFRACTION100
3.7795-4.07120.27011480.22772629X-RAY DIFFRACTION100
4.0712-4.48060.30051120.21052712X-RAY DIFFRACTION100
4.4806-5.12840.24671270.20462622X-RAY DIFFRACTION100
5.1284-6.45880.26861440.24622640X-RAY DIFFRACTION100
6.4588-48.54940.22281340.22832636X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 41.6662 Å / Origin y: 61.5358 Å / Origin z: 54.9668 Å
111213212223313233
T0.6218 Å20.0763 Å20.0231 Å2-0.5793 Å2-0.0274 Å2--0.4308 Å2
L1.2789 °20.1412 °20.2098 °2-1.9302 °21.1191 °2--4.8326 °2
S0.052 Å °0.1806 Å °-0.0557 Å °0.0584 Å °-0.2508 Å °0.084 Å °0.2212 Å °-1.0996 Å °0.1803 Å °
Refinement TLS groupSelection details: all

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