[English] 日本語
Yorodumi
- PDB-7xfr: Crystal structure of WIPI2b in complex with the second site of ATG16L1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xfr
TitleCrystal structure of WIPI2b in complex with the second site of ATG16L1
Components
  • Autophagy-related protein 16-1
  • Isoform 2 of WD repeat domain phosphoinositide-interacting protein 2
KeywordsPROTEIN BINDING / WIPI2b / ATG16L1
Function / homology
Function and homology information


C-terminal protein lipidation / Atg12-Atg5-Atg16 complex / vacuole-isolation membrane contact site / ubiquitin-like protein transferase activity / microautophagy / xenophagy / corpus callosum development / protein localization to phagophore assembly site / phagophore assembly site membrane / negative stranded viral RNA replication ...C-terminal protein lipidation / Atg12-Atg5-Atg16 complex / vacuole-isolation membrane contact site / ubiquitin-like protein transferase activity / microautophagy / xenophagy / corpus callosum development / protein localization to phagophore assembly site / phagophore assembly site membrane / negative stranded viral RNA replication / endolysosome membrane / Macroautophagy / axoneme / autophagosome membrane / autophagosome assembly / autophagosome / positive regulation of autophagy / protein-membrane adaptor activity / sperm midpiece / hippocampus development / macroautophagy / protein transport / GTPase binding / defense response to virus / identical protein binding / cytosol
Similarity search - Function
Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats ...Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Autophagy-related protein 16-1 / Isoform 2 of WD repeat domain phosphoinositide-interacting protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsGong, X.Y. / Pan, L.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21822705 China
CitationJournal: Sci Adv / Year: 2023
Title: ATG16L1 adopts a dual-binding site mode to interact with WIPI2b in autophagy.
Authors: Gong, X. / Wang, Y. / Tang, Y. / Wang, Y. / Zhang, M. / Li, M. / Zhang, Y. / Pan, L.
History
DepositionApr 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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: Isoform 2 of WD repeat domain phosphoinositide-interacting protein 2
B: Autophagy-related protein 16-1
C: Isoform 2 of WD repeat domain phosphoinositide-interacting protein 2
D: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)86,2534
Polymers86,2534
Non-polymers00
Water7,638424
1
A: Isoform 2 of WD repeat domain phosphoinositide-interacting protein 2
B: Autophagy-related protein 16-1

C: Isoform 2 of WD repeat domain phosphoinositide-interacting protein 2
D: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)86,2534
Polymers86,2534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Unit cell
Length a, b, c (Å)74.199, 80.630, 76.755
Angle α, β, γ (deg.)90.000, 97.326, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Isoform 2 of WD repeat domain phosphoinositide-interacting protein 2 / WIPI-2 / WIPI49-like protein 2


Mass: 35310.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WIPI2, CGI-50 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y4P8-2
#2: Protein Autophagy-related protein 16-1 / APG16-like 1


Mass: 7815.774 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG16L1, APG16L, UNQ9393/PRO34307 / Production host: Escherichia coli (E. coli) / References: UniProt: Q676U5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES monohydrate(pH 6.5), 12% w/v Polyethylene glycol 20000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.76→73.59 Å / Num. obs: 83257 / % possible obs: 93.71 % / Redundancy: 6.7 % / Biso Wilson estimate: 31.73 Å2 / Rrim(I) all: 0.037 / Net I/av σ(I): 24.4 / Net I/σ(I): 24.71
Reflection shellResolution: 1.76→1.79 Å / Num. unique obs: 4440 / Rrim(I) all: 0.748

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LTG

5ltg


Resolution: 1.76→24.99 Å / SU ML: 0.1383 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.7137
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1928 4058 4.88 %
Rwork0.1645 79140 -
obs0.1659 83198 93.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.27 Å2
Refinement stepCycle: LAST / Resolution: 1.76→24.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5932 0 0 424 6356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086110
X-RAY DIFFRACTIONf_angle_d0.97228269
X-RAY DIFFRACTIONf_chiral_restr0.0584963
X-RAY DIFFRACTIONf_plane_restr0.00791070
X-RAY DIFFRACTIONf_dihedral_angle_d15.50692305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.780.25491620.22752879X-RAY DIFFRACTION99.97
1.78-1.80.25961510.21482884X-RAY DIFFRACTION99.97
1.8-1.830.20561370.19582942X-RAY DIFFRACTION100
1.83-1.850.2261560.1942870X-RAY DIFFRACTION100
1.85-1.880.23971680.18922891X-RAY DIFFRACTION100
1.88-1.90.24741710.18612850X-RAY DIFFRACTION100
1.9-1.930.199820.19161652X-RAY DIFFRACTION56.83
1.93-1.960.22121430.172926X-RAY DIFFRACTION100
1.96-1.990.21071480.1672914X-RAY DIFFRACTION100
1.99-2.030.20051670.16862861X-RAY DIFFRACTION99.97
2.03-2.060.21381320.17172689X-RAY DIFFRACTION96.21
2.09-2.10.2108560.1611350X-RAY DIFFRACTION99.58
2.1-2.150.21311510.16012886X-RAY DIFFRACTION100
2.15-2.190.20641610.16692910X-RAY DIFFRACTION100
2.19-2.240.18921340.16692659X-RAY DIFFRACTION98.62
2.26-2.30.2177850.16991766X-RAY DIFFRACTION98.98
2.3-2.360.17711620.17212912X-RAY DIFFRACTION99.97
2.36-2.430.21311440.16852929X-RAY DIFFRACTION99.93
2.43-2.510.21631350.16622914X-RAY DIFFRACTION100
2.51-2.60.18031450.17072900X-RAY DIFFRACTION100
2.6-2.70.21871480.17972902X-RAY DIFFRACTION100
2.7-2.830.21681500.17562925X-RAY DIFFRACTION99.94
2.83-2.980.21591360.1722946X-RAY DIFFRACTION99.87
2.98-3.160.19191610.17582893X-RAY DIFFRACTION99.97
3.16-3.410.20931440.17232911X-RAY DIFFRACTION99.9
3.41-3.750.18491040.15612299X-RAY DIFFRACTION78.04
3.75-4.290.17551300.1482767X-RAY DIFFRACTION93.27
4.29-5.390.13391490.12832947X-RAY DIFFRACTION99.87
5.39-24.990.20011460.17982966X-RAY DIFFRACTION98.61

+
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://pdbjlvh1.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