[English] 日本語
Yorodumi
- PDB-3lh8: Crystal structure of mouse VPS26B in spacegroup P41 21 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lh8
TitleCrystal structure of mouse VPS26B in spacegroup P41 21 2
ComponentsVacuolar protein sorting-associated protein 26B
KeywordsPROTEIN TRANSPORT / arrestin / fibronectin / Membrane / Transport
Function / homology
Function and homology information


postsynaptic early endosome / postsynaptic recycling endosome / retromer complex / retrograde transport, endosome to Golgi / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / phagocytic vesicle / intracellular protein transport / cellular response to type II interferon / late endosome / early endosome ...postsynaptic early endosome / postsynaptic recycling endosome / retromer complex / retrograde transport, endosome to Golgi / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / phagocytic vesicle / intracellular protein transport / cellular response to type II interferon / late endosome / early endosome / glutamatergic synapse / cytosol
Similarity search - Function
Vacuolar protein sorting protein 26 related / Vacuolar protein sorting-associated protein 26 / Immunoglobulin-like - #640 / Arrestin-like, C-terminal / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 26B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCollins, B. / Shaw, D. / Norwood, S.
CitationJournal: Traffic / Year: 2011
Title: Assembly and solution structure of the core retromer protein complex.
Authors: Norwood, S.J. / Shaw, D.J. / Cowieson, N.P. / Owen, D.J. / Teasdale, R.D. / Collins, B.M.
History
DepositionJan 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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 26B
B: Vacuolar protein sorting-associated protein 26B


Theoretical massNumber of molelcules
Total (without water)79,2982
Polymers79,2982
Non-polymers00
Water3,819212
1
A: Vacuolar protein sorting-associated protein 26B


Theoretical massNumber of molelcules
Total (without water)39,6491
Polymers39,6491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Vacuolar protein sorting-associated protein 26B


Theoretical massNumber of molelcules
Total (without water)39,6491
Polymers39,6491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.157, 118.157, 193.815
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPROchain A and (resseq 9:57 or resseq 59:156 or resseq 160:216 or resseq 219:235 or resseq 242:296 )AA9 - 5713 - 61
12LYSLYSPROPROchain A and (resseq 9:57 or resseq 59:156 or resseq 160:216 or resseq 219:235 or resseq 242:296 )AA59 - 15663 - 160
13SERSERGLYGLYchain A and (resseq 9:57 or resseq 59:156 or resseq 160:216 or resseq 219:235 or resseq 242:296 )AA160 - 216164 - 220
14PROPROASPASPchain A and (resseq 9:57 or resseq 59:156 or resseq 160:216 or resseq 219:235 or resseq 242:296 )AA219 - 235223 - 239
15GLUGLUGLYGLYchain A and (resseq 9:57 or resseq 59:156 or resseq 160:216 or resseq 219:235 or resseq 242:296 )AA242 - 296246 - 300
21SERSERPROPROchain B and (resseq 9:57 or resseq 59:156 or resseq 160:216 or resseq 219:235 or resseq 242:296 )BB9 - 5713 - 61
22LYSLYSPROPROchain B and (resseq 9:57 or resseq 59:156 or resseq 160:216 or resseq 219:235 or resseq 242:296 )BB59 - 15663 - 160
23SERSERGLYGLYchain B and (resseq 9:57 or resseq 59:156 or resseq 160:216 or resseq 219:235 or resseq 242:296 )BB160 - 216164 - 220
24PROPROASPASPchain B and (resseq 9:57 or resseq 59:156 or resseq 160:216 or resseq 219:235 or resseq 242:296 )BB219 - 235223 - 239
25GLUGLUGLYGLYchain B and (resseq 9:57 or resseq 59:156 or resseq 160:216 or resseq 219:235 or resseq 242:296 )BB242 - 296246 - 300

-
Components

#1: Protein Vacuolar protein sorting-associated protein 26B / Vesicle protein sorting 26B


Mass: 39648.973 Da / Num. of mol.: 2 / Fragment: UNP residues 7-336 / Mutation: L197S,R199E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vps26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8C0E2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 4.27 Å3/Da / Density % sol: 71.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M sodium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95364 Å
DetectorDetector: CCD / Date: Nov 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95364 Å / Relative weight: 1
ReflectionResolution: 2.6→40.9 Å / Num. obs: 79550 / % possible obs: 98.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 60.1 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 21.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 3.3 / Num. unique all: 6970 / % possible all: 93.2

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R51

2r51


Resolution: 2.6→40.9 Å / SU ML: 0.42 / σ(F): 1.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2921 3972 4.99 %
Rwork0.2611 --
obs0.2627 79550 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.135 Å2 / ksol: 0.362 e/Å3
Refinement stepCycle: LAST / Resolution: 2.6→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4697 0 0 212 4909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094805
X-RAY DIFFRACTIONf_angle_d1.2956466
X-RAY DIFFRACTIONf_dihedral_angle_d20.0721810
X-RAY DIFFRACTIONf_chiral_restr0.079703
X-RAY DIFFRACTIONf_plane_restr0.005824
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2311X-RAY DIFFRACTIONPOSITIONAL
12B2311X-RAY DIFFRACTIONPOSITIONAL0.064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.69290.34453410.31126970X-RAY DIFFRACTION90
2.6929-2.80070.33273860.28577412X-RAY DIFFRACTION97
2.8007-2.92810.32644260.27017595X-RAY DIFFRACTION100
2.9281-3.08240.30744020.26517641X-RAY DIFFRACTION100
3.0824-3.27550.29193870.26067734X-RAY DIFFRACTION100
3.2755-3.52830.294350.25227564X-RAY DIFFRACTION100
3.5283-3.88310.28184360.2497629X-RAY DIFFRACTION100
3.8831-4.44440.27023860.23447672X-RAY DIFFRACTION100
4.4444-5.59720.25273900.23647675X-RAY DIFFRACTION100
5.5972-40.90740.29443830.28577686X-RAY DIFFRACTION100

+
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