[English] 日本語
Yorodumi
- PDB-5wyh: Crystal structure of RidL(1-200) complexed with VPS29 -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / intracellular protein transport / late endosome / early endosome / endosome / endosome membrane ...WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / intracellular protein transport / late endosome / early endosome / endosome / endosome membrane / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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: _ / Refine code: _

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

-
Components

#1: Protein Vacuolar protein sorting-associated protein 29 / 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


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


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more