[English] 日本語
Yorodumi
- PDB-7e0b: The crystal structure of sorting nexin 27 and PBM complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7e0b
TitleThe crystal structure of sorting nexin 27 and PBM complex
Components
  • PBM
  • Sorting nexin-27
KeywordsCYTOSOLIC PROTEIN / sorting nexin 27
Function / homology
Function and homology information


establishment of natural killer cell polarity / regulation of synapse maturation / endocytic recycling / phosphatidylinositol-3-phosphate binding / endosomal transport / endosome to lysosome transport / regulation of postsynaptic membrane neurotransmitter receptor levels / immunological synapse / phosphatidylinositol binding / intracellular protein transport ...establishment of natural killer cell polarity / regulation of synapse maturation / endocytic recycling / phosphatidylinositol-3-phosphate binding / endosomal transport / endosome to lysosome transport / regulation of postsynaptic membrane neurotransmitter receptor levels / immunological synapse / phosphatidylinositol binding / intracellular protein transport / Schaffer collateral - CA1 synapse / early endosome membrane / early endosome / endosome / intracellular membrane-bounded organelle / glutamatergic synapse / signal transduction / cytosol
Similarity search - Function
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 ...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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsShang, G.J. / Qi, J.X.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: SNX27 suppresses SARS-CoV-2 infection by inhibiting viral lysosome/late endosome entry.
Authors: Yang, B. / Jia, Y. / Meng, Y. / Xue, Y. / Liu, K. / Li, Y. / Liu, S. / Li, X. / Cui, K. / Shang, L. / Cheng, T. / Zhang, Z. / Hou, Y. / Yang, X. / Yan, H. / Duan, L. / Tong, Z. / Wu, C. / ...Authors: Yang, B. / Jia, Y. / Meng, Y. / Xue, Y. / Liu, K. / Li, Y. / Liu, S. / Li, X. / Cui, K. / Shang, L. / Cheng, T. / Zhang, Z. / Hou, Y. / Yang, X. / Yan, H. / Duan, L. / Tong, Z. / Wu, C. / Liu, Z. / Gao, S. / Zhuo, S. / Huang, W. / Gao, G.F. / Qi, J. / Shang, G.
History
DepositionJan 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sorting nexin-27
B: PBM


Theoretical massNumber of molelcules
Total (without water)11,0352
Polymers11,0352
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-3 kcal/mol
Surface area5770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.550, 88.550, 43.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

-
Components

#1: Protein Sorting nexin-27


Mass: 10224.640 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX27, KIAA0488, My014 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q96L92
#2: Protein/peptide PBM


Mass: 810.806 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli K-12 (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M sodium sulfate, 20 % w/v PEG 3350.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.29→22.14 Å / Num. obs: 30746 / % possible obs: 97.8 % / Redundancy: 8.6 % / Biso Wilson estimate: 19.04 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.3
Reflection shellResolution: 1.29→1.32 Å / Num. unique obs: 6895 / CC1/2: 0.519

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z8J

4z8j


Resolution: 1.29→20.82 Å / SU ML: 0.1724 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.131
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1906 1507 4.9 %
Rwork0.1842 29239 -
obs0.1845 30746 96.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28 Å2
Refinement stepCycle: LAST / Resolution: 1.29→20.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms776 0 0 122 898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032806
X-RAY DIFFRACTIONf_angle_d0.54351091
X-RAY DIFFRACTIONf_chiral_restr0.4636126
X-RAY DIFFRACTIONf_plane_restr0.0041146
X-RAY DIFFRACTIONf_dihedral_angle_d22.8978308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.330.4421070.41462126X-RAY DIFFRACTION75.72
1.33-1.380.32911370.32022501X-RAY DIFFRACTION92.59
1.38-1.430.25891320.24872696X-RAY DIFFRACTION96.62
1.43-1.50.24071430.21382684X-RAY DIFFRACTION98.36
1.5-1.580.21271250.19162768X-RAY DIFFRACTION99.55
1.58-1.680.19561240.18732761X-RAY DIFFRACTION99.62
1.68-1.810.19181650.18612697X-RAY DIFFRACTION99.72
1.81-1.990.20091560.18312735X-RAY DIFFRACTION99.86
1.99-2.280.18471460.17352766X-RAY DIFFRACTION99.97
2.28-2.870.17611350.18752749X-RAY DIFFRACTION99.83
2.87-20.820.17491370.16762756X-RAY DIFFRACTION99.79
Refinement TLS params.Method: refined / Origin x: 16.2903886193 Å / Origin y: -3.58930360279 Å / Origin z: -5.19257281078 Å
111213212223313233
T0.171066136234 Å20.000101336297923 Å2-0.00435805356498 Å2-0.178776652077 Å2-0.00441841102942 Å2--0.172569711975 Å2
L2.01838440938 °2-0.291537557431 °2-0.735634589877 °2-0.686255276825 °2-0.00887944746894 °2--1.0376527113 °2
S-0.0326343227582 Å °0.0199613607667 Å °-0.0770157519413 Å °-0.0394293488995 Å °-0.0160998965195 Å °-0.00751349320768 Å °0.0219250689764 Å °-0.00963199863089 Å °4.55321128807E-9 Å °
Refinement TLS groupSelection details: all

+
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