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- PDB-7u8t: Vps13 adaptor binding domain in complex with Mcp1 PxP motif peptide -

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Basic information

Entry
Database: PDB / ID: 7u8t
TitleVps13 adaptor binding domain in complex with Mcp1 PxP motif peptide
ComponentsMcp1 PxP motif,Putative vacuolar protein sorting-associated protein
KeywordsLIPID TRANSPORT / Adaptor binding domain
Function / homology
Function and homology information


phospholipid transfer activity / protein retention in Golgi apparatus / intermembrane lipid transfer / protein targeting to vacuole / late endosome to vacuole transport / lipid homeostasis / mitochondrion organization / phospholipid binding / membrane
Similarity search - Function
Mitochondrial adapter protein MCP1, transmembrane domain / Mitochondrial adapter protein MCP1 / MDM10-complementing protein 1, transmembrane domain / Vacuolar protein sorting-associated protein 13, VPS13 adaptor binding domain / Vacuolar protein sorting-associated protein 13, fungi / Vacuolar protein sorting-associated protein 13 / Vacuolar protein sorting-associated protein 13-like, N-terminal domain / : / : / VPS13-like family middle region ...Mitochondrial adapter protein MCP1, transmembrane domain / Mitochondrial adapter protein MCP1 / MDM10-complementing protein 1, transmembrane domain / Vacuolar protein sorting-associated protein 13, VPS13 adaptor binding domain / Vacuolar protein sorting-associated protein 13, fungi / Vacuolar protein sorting-associated protein 13 / Vacuolar protein sorting-associated protein 13-like, N-terminal domain / : / : / VPS13-like family middle region / Vacuolar-sorting associated protein 13, adaptor binding domain / Intermembrane lipid transfer protein VPS13, C-terminal / VPS13-like family N-terminal region / Cytosolic fatty-acid binding proteins signature.
Similarity search - Domain/homology
Mitochondrial adapter protein MCP1 transmembrane domain-containing protein / Intermembrane lipid transfer protein VPS13
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsAdlakha, J. / Reinisch, K.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131715 United States
Michael J. Fox FoundationASAP-000580 United States
CitationJournal: J.Cell Biol. / Year: 2022
Title: Structural and biochemical insights into lipid transport by VPS13 proteins.
Authors: Adlakha, J. / Hong, Z. / Li, P. / Reinisch, K.M.
History
DepositionMar 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 20, 2022Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mcp1 PxP motif,Putative vacuolar protein sorting-associated protein
B: Mcp1 PxP motif,Putative vacuolar protein sorting-associated protein


Theoretical massNumber of molelcules
Total (without water)163,6192
Polymers163,6192
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-11 kcal/mol
Surface area53860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.735, 91.225, 132.769
Angle α, β, γ (deg.)90.000, 102.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mcp1 PxP motif,Putative vacuolar protein sorting-associated protein


Mass: 81809.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0011170, CTHT_0020450 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S0T5, UniProt: G0S3B8

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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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 75 mM imidazole pH 8.2, 70 mM lithium sulfate, 500 mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3→48.36 Å / Num. obs: 39383 / % possible obs: 98.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 88.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.028 / Rrim(I) all: 0.052 / Net I/σ(I): 17.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 3799 / CC1/2: 0.97 / Rpim(I) all: 0.197 / Rrim(I) all: 0.378 / % possible all: 97.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.20rc3_4411refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2 model

Resolution: 3→48.36 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2848 1894 4.89 %
Rwork0.2496 36813 -
obs0.2514 38707 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 222.49 Å2 / Biso mean: 105.4699 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8697 0 0 0 8697
Num. residues----1145
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.070.42511550.36352578273398
3.08-3.160.39961270.31862631275899
3.16-3.250.3621200.28912633275398
3.25-3.360.3031130.28742674278799
3.36-3.480.36921460.29682586273299
3.48-3.620.36191320.30432623275598
3.62-3.780.3391420.28722562270497
3.78-3.980.3151350.25392666280199
3.98-4.230.29061330.2452618275199
4.23-4.550.21921510.21082644279599
4.55-5.010.21931310.19152630276198
5.01-5.740.21851400.22232623276398
5.74-7.220.34061230.25642675279899
7.23-48.360.26271460.25082670281697
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)
12.97980.16732.85490.84942.28664.36710.14760.3933-0.0786-0.02790.3966-0.37520.13180.3483-0.52920.7451-0.02890.04540.6597-0.0370.788962.6583.18841.6108
25.30722.129-1.50227.2484-1.87885.6077-0.12380.344-0.1489-0.18960.31080.1216-0.11270.0008-0.18530.4530.02650.04460.5065-0.03210.434145.4316-11.1865-9.4894
37.95680.8872-3.30132.92791.115.6998-0.05420.31570.0807-0.22540.29620.112-0.1669-0.5108-0.26490.6320.18390.06160.62160.15970.67921.7829-16.85655.8423
47.882-1.4797-4.15443.70794.98398.79350.28850.0020.2683-0.1436-0.23030.1334-0.5199-0.08890.09090.71120.21050.19530.57510.27250.86339.1623-7.584128.3595
50.61951.34221.34474.26933.33744.18070.3123-1.559-0.5740.8772-0.3311-0.17860.2586-0.06740.14310.78410.06250.05641.68140.46080.906216.5702-4.140955.0407
61.0312-0.4578-1.0560.20260.46831.0821-0.1864-1.0678-0.1979-0.07880.5359-0.73560.79081.9343-0.06180.66110.61040.07232.7171-0.77920.870926.21228.470466.7803
74.1427-0.7042.33762.96570.21215.0728-1.0390.0652-0.42250.3806-0.0518-0.25110.3158-0.22961.0141.8818-0.42360.55220.7571-0.11491.2093-12.03689.185485.3447
83.4870.10720.51443.4242-0.97097.0007-0.1753-0.099-0.3310.2615-0.82410.5411-0.1752-2.00350.89981.0144-0.15980.18540.9738-0.5351.0705-23.528621.55169.2872
95.06470.5783-2.37711.5780.7776.85910.18950.44860.2874-0.1423-0.55990.5911-0.5589-1.03910.37190.70970.2152-0.02150.6561-0.21520.912-12.275126.2843.7773
108.4575-1.4798-2.8294.69431.99345.0114-0.26590.6616-0.0684-0.0797-0.20580.1602-0.2635-0.09490.55880.62190.0938-0.01280.66930.17280.81298.963717.050728.4009
116.0913-1.7614-1.4026.1868-0.34865.3955-0.3418-0.66570.53270.23520.5219-0.0435-0.08980.2317-0.24940.49290.1845-0.01410.92320.08990.622737.012615.913131.9058
124.0421-1.8494-2.75134.62331.58554.4366-0.2146-0.6556-0.39950.21040.1928-0.11630.13210.1529-0.05480.61990.1449-0.01160.86570.06090.776256.8346-2.970233.114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 5:144)A5 - 144
2X-RAY DIFFRACTION2(chain A and resseq 145:261)A145 - 261
3X-RAY DIFFRACTION3(chain A and resseq 262:372)A262 - 372
4X-RAY DIFFRACTION4(chain A and resseq 373:488)A373 - 488
5X-RAY DIFFRACTION5(chain A and resseq 489:590)A489 - 590
6X-RAY DIFFRACTION6(chain A and resseq 591:702)A591 - 702
7X-RAY DIFFRACTION7(chain B and resseq 20:144)B20 - 144
8X-RAY DIFFRACTION8(chain B and resseq 145:261)B145 - 261
9X-RAY DIFFRACTION9(chain B and resseq 262:372)B262 - 372
10X-RAY DIFFRACTION10(chain B and resseq 373:488)B373 - 488
11X-RAY DIFFRACTION11(chain B and resseq 489:590)B489 - 590
12X-RAY DIFFRACTION12(chain B and resseq 591:702)B591 - 702

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