[English] 日本語
Yorodumi
- PDB-6y09: Crystal structure of Atg16L in complex with GTP-bound Rab33B (Q92L) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y09
TitleCrystal structure of Atg16L in complex with GTP-bound Rab33B (Q92L)
Components
  • Autophagy-related protein 16-1
  • Ras-related protein Rab-33B
KeywordsPROTEIN TRANSPORT / ATG16L / autophagy / autophagosome formation / Rab33B
Function / homology
Function and homology information


negative regulation of constitutive secretory pathway / regulation of retrograde vesicle-mediated transport, Golgi to ER / Atg12-Atg5-Atg16 complex / Macroautophagy / regulation of Golgi organization / Rab protein signal transduction / vacuole-isolation membrane contact site / microautophagy / Intra-Golgi traffic / protein localization to Golgi apparatus ...negative regulation of constitutive secretory pathway / regulation of retrograde vesicle-mediated transport, Golgi to ER / Atg12-Atg5-Atg16 complex / Macroautophagy / regulation of Golgi organization / Rab protein signal transduction / vacuole-isolation membrane contact site / microautophagy / Intra-Golgi traffic / protein localization to Golgi apparatus / xenophagy / intra-Golgi vesicle-mediated transport / protein localization to phagophore assembly site / phagophore assembly site membrane / corpus callosum development / RAB geranylgeranylation / regulation of exocytosis / negative stranded viral RNA replication / endolysosome membrane / TBC/RABGAPs / skeletal system morphogenesis / axoneme / autophagosome membrane / autophagosome assembly / autophagosome / positive regulation of autophagy / protein-membrane adaptor activity / sperm midpiece / hippocampus development / macroautophagy / Golgi lumen / protein transport / presynapse / GTPase binding / defense response to virus / endosome / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Rab33A/B / Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / small GTPase Rab1 family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Small GTP-binding protein domain / G-protein beta WD-40 repeat ...Rab33A/B / Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / small GTPase Rab1 family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Small GTP-binding protein domain / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Autophagy-related protein 16-1 / Ras-related protein Rab-33B
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPantoom, S. / Wu, Y.W.
CitationJournal: Autophagy / Year: 2021
Title: RAB33B recruits the ATG16L1 complex to the phagophore via a noncanonical RAB binding protein.
Authors: Pantoom, S. / Konstantinidis, G. / Voss, S. / Han, H. / Hofnagel, O. / Li, Z. / Wu, Y.W.
History
DepositionFeb 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: 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: Ras-related protein Rab-33B
C: Autophagy-related protein 16-1
B: Ras-related protein Rab-33B
D: Autophagy-related protein 16-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,53923
Polymers72,9854
Non-polymers2,55419
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11440 Å2
ΔGint-53 kcal/mol
Surface area29190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.950, 132.420, 155.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein Ras-related protein Rab-33B


Mass: 21960.377 Da / Num. of mol.: 2 / Mutation: Q92L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB33B / Plasmid: pOPIN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H082
#2: Protein Autophagy-related protein 16-1 / APG16-like 1


Mass: 14532.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Atg16l1, Apg16l / Plasmid: pRSF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8C0J2

-
Non-polymers , 6 types, 233 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.01 Å3/Da / Density % sol: 69.31 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 14% PEG3350, 0.2 M Potassium thiocyanate and 0.1 M Sodium potassium phosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97714 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97714 Å / Relative weight: 1
ReflectionResolution: 2.4→48.17 Å / Num. obs: 46731 / % possible obs: 99.91 % / Redundancy: 12.9 % / Biso Wilson estimate: 40.26 Å2 / CC1/2: 0.871 / Net I/σ(I): 17.05
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 2.67 / Num. unique obs: 4618 / CC1/2: 0.871 / % possible all: 99.87

-
Processing

Software
NameVersionClassification
REFMAC1.9_1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q8T and 1Z06

3q8t

1z06


Resolution: 2.4→48.168 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 25.72
RfactorNum. reflection% reflection
Rfree0.2311 2330 5 %
Rwork0.1918 --
obs0.1937 46611 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 173.48 Å2 / Biso mean: 64.2674 Å2 / Biso min: 19.77 Å2
Refinement stepCycle: final / Resolution: 2.4→48.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4258 0 157 214 4629
Biso mean--66.77 53.93 -
Num. residues----523
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)
15.50080.03360.22653.54490.76364.88810.0802-0.3061-0.43450.33990.0771-0.32890.29280.351-0.13510.2706-0.0183-0.05190.2251-0.01620.362515.6816180.612543.3638
27.04661.0760.22534.2746-0.47537.2036-0.0903-0.4096-0.60040.40660.0607-0.51560.2930.18630.0440.30840.0525-0.06120.21830.03880.431217.7626177.371345.6177
32.5390.4076-0.64241.7741-0.43451.5774-0.08960.0284-0.0463-0.08850.08180.11480.0697-0.0854-0.0010.26790.0164-0.00470.2933-0.03990.315811.8455188.823735.5285
49.91876.2731-6.32643.9958-4.03444.04190.3059-0.73940.4421.0721-0.3732-0.1283-0.4831-0.12530.12510.4909-0.0001-0.01070.5173-0.05320.343614.3709189.482151.593
52.95451.8488-2.94892.0929-0.79426.954-0.7339-0.3930.12530.02110.4604-0.43510.71210.19780.39191.24380.31940.12831.00810.07370.972620.2029165.0014-22.7504
63.4638-2.0746-4.21525.84264.27163.8819-0.4156-0.1937-0.41350.3174-0.42680.62280.6169-0.05610.73510.3566-0.0499-0.01110.37910.01540.57115.9272167.089638.8617
75.65320.4607-0.20065.379-0.11455.2686-0.1336-0.45810.52710.3190.16150.2629-0.52-0.0637-0.01470.28630.01460.02960.2458-0.040.384811.6388145.878543.8811
88.23721.63983.18438.770.84636.0109-0.17560.40610.7309-0.3579-0.103-0.6833-0.380.26150.39490.3702-0.02920.04070.30020.04730.545822.8882149.731631.9717
93.0271-0.27650.15072.0811-0.31422.151-0.0247-0.06320.0776-0.09670.0157-0.06190.0406-0.00330.00650.20920.0074-0.00660.24530.03530.261415.3844133.302235.1704
104.66282.10284.47319.04941.37444.4175-0.1692-0.8764-0.16310.9427-0.0106-0.09880.2494-0.07460.04690.3622-0.01190.04320.5554-0.00850.299514.0312135.32450.7184
118.75172.3634-3.64123.4864-3.46793.67260.15360.43120.3597-0.2420.0288-0.30730.3265-0.4091-0.25941.36560.16040.16960.6745-0.17271.53740.175162.4034-39.4437
120.4634-0.11621.13630.0333-0.40063.1923-0.1548-0.6998-0.20180.0817-0.0226-0.17930.649-0.79530.05921.44220.14010.23841.09140.10980.86527.2212170.6665-25.7792
131.6466-1.74710.51443.6693-1.9414.2912-0.05460.01580.3902-0.0058-0.3809-0.5939-0.81570.22790.46570.4405-0.10110.01690.4057-0.07770.580321.4334159.608431.5093
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 55 )A30 - 55
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 89 )A56 - 89
3X-RAY DIFFRACTION3chain 'A' and (resid 90 through 187 )A90 - 187
4X-RAY DIFFRACTION4chain 'A' and (resid 188 through 202 )A188 - 202
5X-RAY DIFFRACTION5chain 'C' and (resid 140 through 173 )C140 - 173
6X-RAY DIFFRACTION6chain 'C' and (resid 174 through 225 )C174 - 225
7X-RAY DIFFRACTION7chain 'B' and (resid 30 through 89 )B30 - 89
8X-RAY DIFFRACTION8chain 'B' and (resid 90 through 104 )B90 - 104
9X-RAY DIFFRACTION9chain 'B' and (resid 105 through 187 )B105 - 187
10X-RAY DIFFRACTION10chain 'B' and (resid 188 through 202 )B188 - 202
11X-RAY DIFFRACTION11chain 'D' and (resid 140 through 144 )D140 - 144
12X-RAY DIFFRACTION12chain 'D' and (resid 145 through 163 )D145 - 163
13X-RAY DIFFRACTION13chain 'D' and (resid 164 through 225 )D164 - 225

+
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