[English] 日本語
Yorodumi
- PDB-8ttt: Structure of SNX27 FERM complexed with Fam21A repeat 15 (1124-1140) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ttt
TitleStructure of SNX27 FERM complexed with Fam21A repeat 15 (1124-1140)
Components
  • Fam21A repeat 15 peptide
  • Sorting nexin-27
KeywordsTRANSPORT PROTEIN / SNX27 / FAM21 / WASH / sorting nexin / endosome / protein transport
Function / homology
Function and homology information


establishment of natural killer cell polarity / WASH complex / retromer complex binding / phosphatidylinositol phosphate binding / regulation of Arp2/3 complex-mediated actin nucleation / protein localization to endosome / regulation of synapse maturation / endocytic recycling / phosphatidylinositol-3-phosphate binding / retrograde transport, endosome to Golgi ...establishment of natural killer cell polarity / WASH complex / retromer complex binding / phosphatidylinositol phosphate binding / regulation of Arp2/3 complex-mediated actin nucleation / protein localization to endosome / regulation of synapse maturation / endocytic recycling / phosphatidylinositol-3-phosphate binding / retrograde transport, endosome to Golgi / endosomal transport / endosome to lysosome transport / regulation of postsynaptic membrane neurotransmitter receptor levels / immunological synapse / phosphatidylinositol binding / intracellular protein transport / Schaffer collateral - CA1 synapse / protein transport / early endosome membrane / endosome / early endosome / intracellular membrane-bounded organelle / glutamatergic synapse / nucleolus / signal transduction / plasma membrane / cytosol
Similarity search - Function
FAM21/CAPZIP domain / WASH complex subunit CAP-Z interacting, central region / SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / PhoX homologous domain, present in p47phox and p40phox. ...FAM21/CAPZIP domain / WASH complex subunit CAP-Z interacting, central region / SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / WASH complex subunit 2A / Sorting nexin-27
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsGuo, Q. / Chen, K.-E. / Collins, B.M.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1156493 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1136021 Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Structural basis for coupling of the WASH subunit FAM21 with the endosomal SNX27-Retromer complex.
Authors: Guo, Q. / Chen, K.E. / Gimenez-Andres, M. / Jellett, A.P. / Gao, Y. / Simonetti, B. / Liu, M. / Danson, C.M. / Heesom, K.J. / Cullen, P.J. / Collins, B.M.
History
DepositionAug 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sorting nexin-27
B: Fam21A repeat 15 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1336
Polymers32,7372
Non-polymers3964
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-1 kcal/mol
Surface area14330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.567, 74.371, 105.229
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Sorting nexin-27


Mass: 30947.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX27 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96L92
#2: Protein/peptide Fam21A repeat 15 peptide


Mass: 1788.846 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q641Q2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M Sodium Cacodylate pH 6.0 and 22.5% PEG4000 / PH range: 6.0 -6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.33→42.95 Å / Num. obs: 12909 / % possible obs: 97.6 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.083 / Rrim(I) all: 0.22 / Χ2: 0.44 / Net I/σ(I): 7.9 / Num. measured all: 88510
Reflection shellResolution: 2.33→2.41 Å / % possible obs: 75.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 1.524 / Num. measured all: 5906 / Num. unique obs: 940 / CC1/2: 0.379 / Rpim(I) all: 0.632 / Rrim(I) all: 1.656 / Χ2: 0.31 / Net I/σ(I) obs: 1.1

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→42.95 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2509 1271 9.99 %
Rwork0.1908 --
obs0.1968 12721 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 26 45 2251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092265
X-RAY DIFFRACTIONf_angle_d1.0543056
X-RAY DIFFRACTIONf_dihedral_angle_d8.837301
X-RAY DIFFRACTIONf_chiral_restr0.056323
X-RAY DIFFRACTIONf_plane_restr0.008384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.440.33521220.26891113X-RAY DIFFRACTION89
2.44-2.550.30711390.23941252X-RAY DIFFRACTION100
2.55-2.690.29891420.22391277X-RAY DIFFRACTION100
2.69-2.860.28131410.21871274X-RAY DIFFRACTION100
2.86-3.080.30851400.22181255X-RAY DIFFRACTION100
3.08-3.390.2471440.19011290X-RAY DIFFRACTION100
3.39-3.880.23631420.17391287X-RAY DIFFRACTION100
3.88-4.880.19741460.15571307X-RAY DIFFRACTION100
4.88-42.950.24581550.18311395X-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://pdbjlc1.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