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- PDB-5wyh: Crystal structure of RidL(1-200) complexed with VPS29 -

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Basic information

Entry
Database: PDB / ID: 5wyh
TitleCrystal structure of RidL(1-200) complexed with VPS29
Components
  • Interaptin
  • Vacuolar protein sorting-associated protein 29Vacuole
KeywordsMETAL BINDING PROTEIN/PROTEIN BINDING / Complex VPS29 RidL / METAL BINDING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / intracellular protein transport / late endosome / early endosome / endosome membrane / endosome ...retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / intracellular protein transport / late endosome / early endosome / endosome membrane / endosome / intracellular membrane-bounded organelle / metal ion binding / cytosol
Similarity search - Function
Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesHomo sapiens (human)
Legionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsYao, J. / Sun, Q. / Jia, D.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Mechanism of inhibition of retromer transport by the bacterial effector RidL.
Authors: Yao, J. / Yang, F. / Sun, X. / Wang, S. / Gan, N. / Liu, Q. / Liu, D. / Zhang, X. / Niu, D. / Wei, Y. / Ma, C. / Luo, Z.Q. / Sun, Q. / Jia, D.
History
DepositionJan 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation / citation_author
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
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 29
B: Interaptin
C: Vacuolar protein sorting-associated protein 29
D: Interaptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5135
Polymers87,4214
Non-polymers921
Water4,071226
1
A: Vacuolar protein sorting-associated protein 29
B: Interaptin


Theoretical massNumber of molelcules
Total (without water)43,7112
Polymers43,7112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Vacuolar protein sorting-associated protein 29
D: Interaptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8033
Polymers43,7112
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.312, 82.049, 87.332
Angle α, β, γ (deg.)101.73, 104.26, 104.77
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAPROPROAA-2 - 1821 - 185
21ALAALAPROPROCC-2 - 1821 - 185
12GLUGLULEULEUBB5 - 1993 - 197
22GLUGLULEULEUDD5 - 1993 - 197

NCS ensembles :
ID
1
2

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Components

#1: Protein Vacuolar protein sorting-associated protein 29 / Vacuole / hVPS29 / PEP11 homolog / Vesicle protein sorting 29


Mass: 20823.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS29, DC15, DC7, MDS007 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBQ0
#2: Protein Interaptin


Mass: 22886.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
Gene: lp12_2303 / Production host: Escherichia coli (E. coli) / References: UniProt: G8UZ99
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 3.26 Å3/Da / Density % sol: 62.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris pH8.0, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 0.9792 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Mar 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.816
11H, -H-K, -H-L20.184
ReflectionResolution: 2.5→50 Å / Num. obs: 37098 / % possible obs: 96.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.063 / Rrim(I) all: 0.116 / Χ2: 1.333 / Net I/σ(I): 10.3 / Num. measured all: 138440
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.5-2.543.70.89118050.7160.5341.36296.7
2.54-2.593.70.93419040.7440.5591.26697.2
2.59-2.643.70.75418500.8470.4531.21597.10.881
2.64-2.693.70.7218450.8270.431.32696.60.839
2.69-2.753.70.58118920.8840.3491.27296.70.679
2.75-2.823.70.48118390.9120.2881.27497.10.561
2.82-2.893.70.418490.9370.2391.32970.466
2.89-2.963.70.3418950.9470.2051.30496.60.398
2.96-3.053.70.26118210.9640.1561.26196.80.304
3.05-3.153.70.21818840.9720.1311.32960.254
3.15-3.263.70.18318150.9720.1091.31595.70.213
3.26-3.393.70.13318600.9830.081.31895.60.155
3.39-3.553.80.11218110.9860.0661.36395.60.13
3.55-3.733.70.09718470.9860.0581.37896.20.113
3.73-3.973.70.08818840.9880.0531.41297.30.103
3.97-4.273.70.07618410.9910.0461.38497.30.089
4.27-4.73.70.06718640.9930.041.29496.40.078
4.7-5.383.70.06818530.9920.0411.34597.10.079
5.38-6.783.90.0719130.9920.0411.41399.30.081
6.78-503.80.06718260.9930.041.594.80.078

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→31.86 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.918 / SU B: 14.37 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22494 1665 5 %RANDOM
Rwork0.18955 ---
obs0.19131 31351 81.81 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.801 Å2
Baniso -1Baniso -2Baniso -3
1--13.88 Å20.3 Å2-0.19 Å2
2--0.95 Å2-2.29 Å2
3---12.93 Å2
Refinement stepCycle: 1 / Resolution: 2.46→31.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6147 0 6 226 6379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196286
X-RAY DIFFRACTIONr_bond_other_d0.0020.025843
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9618488
X-RAY DIFFRACTIONr_angle_other_deg0.937313622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7745760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.4325.016309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.612151132
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.561528
X-RAY DIFFRACTIONr_chiral_restr0.0810.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026912
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021224
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_it1.9852.8123052
X-RAY DIFFRACTIONr_mcbond_other1.9832.8123051
X-RAY DIFFRACTIONr_mcangle_it3.1174.2153808
X-RAY DIFFRACTIONr_mcangle_other3.1174.2153809
X-RAY DIFFRACTIONr_scbond_it2.383.0943234
X-RAY DIFFRACTIONr_scbond_other2.3783.0953234
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7714.5374681
X-RAY DIFFRACTIONr_long_range_B_refined5.66333.7046969
X-RAY DIFFRACTIONr_long_range_B_other5.64433.5976946
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A11776
12C11776
21B12986
22D12986
LS refinement shellResolution: 2.455→2.519 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 24 -
Rwork0.243 400 -
obs--14.3 %
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)
13.97040.3382-0.47984.401-0.46842.7618-0.0296-0.34490.16180.27810.0795-0.1259-0.05850.0186-0.04990.02860.01220.00440.0341-0.00660.099622.6159-22.265915.3991
21.41510.06670.16812.5288-1.47413.83630.0886-0.5208-0.28570.4278-0.0642-0.03670.5574-0.092-0.02440.3462-0.05870.01240.20260.08390.11881.7037-59.368729.545
34.3276-0.19770.26834.5061-0.79912.4261-0.09720.3339-0.0946-0.25250.078-0.15970.03130.01260.01920.0475-0.01260.05390.0279-0.00910.07430.51850.40480.1521
41.678-0.4682-0.02663.2468-1.44973.66170.05540.58010.3407-0.5926-0.0874-0.0569-0.4567-0.14870.0320.34460.00610.0310.2260.08880.111-19.93237.5791-14.5043
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 182
2X-RAY DIFFRACTION2B5 - 200
3X-RAY DIFFRACTION3C-2 - 182
4X-RAY DIFFRACTION4D3 - 200

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