[English] 日本語
Yorodumi
- PDB-6zay: Crystal structure of Atg16L in complex with GDP-bound Rab33B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zay
TitleCrystal structure of Atg16L in complex with GDP-bound Rab33B
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'-DIPHOSPHATE / 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
DepositionJun 6, 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)75,31023
Polymers73,0154
Non-polymers2,29519
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
ΔGint-75 kcal/mol
Surface area29470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.010, 132.110, 154.370
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: 21975.348 Da / Num. of mol.: 2
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, 198 molecules

#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 3.88 Å3/Da / Density % sol: 68.3 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 6.2
Details: 22% PEG3350, 0.2M potassium thiocyanate and 0.1M 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-F / Detector: PIXEL / Date: Jun 29, 2013
RadiationMonochromator: si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97714 Å / Relative weight: 1
ReflectionResolution: 2.4→49.572 Å / Num. obs: 46452 / % possible obs: 99.96 % / Redundancy: 13.1 % / Biso Wilson estimate: 38.92 Å2 / Rmerge(I) obs: 0.1169 / Net I/σ(I): 16.22
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 13.7 % / Num. unique obs: 4577 / CC1/2: 0.971 / % possible all: 99.89

-
Processing

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

1z06

3q8t


Resolution: 2.4→49.572 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2114 2317 5.01 %
Rwork0.1851 --
obs0.1865 46278 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.21 Å2 / Biso mean: 69.6901 Å2 / Biso min: 22.12 Å2
Refinement stepCycle: final / Resolution: 2.4→49.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4252 0 141 179 4572
Biso mean--75.88 56.03 -
Num. residues----522
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)
15.2335-0.2883-0.71573.6298-0.74343.84070.12950.3703-0.5874-0.3020.01210.46390.2222-0.3495-0.09810.31920.016-0.09930.26130.00060.5001-15.713448.1911-43.0456
28.1099-5.63796.6678.4098-7.05689.10570.8878-0.2316-1.2429-0.2034-0.02341.72311.0916-0.5136-0.76010.5156-0.0381-0.03690.37510.01260.8816-23.853442.2333-35.1159
32.9703-1.26911.33533.934-1.77067.9709-0.0160.0738-0.3415-0.07250.05720.11380.3815-0.01270.010.3455-0.0224-0.00060.2359-0.04710.5576-10.836344.7977-42.7768
43.7706-1.5221-1.79612.45291.23794.4592-0.1556-0.2249-0.12430.22110.1498-0.43140.2130.359-0.00470.2461-0.0382-0.04060.31280.04930.4215-7.893455.3006-33.6887
53.6475-0.3985-0.61411.1873-0.32081.49010.0490.07780.26870.00770.04380.1496-0.1031-0.062-0.07610.2648-0.02520.01190.27170.00740.4457-16.346161.6481-37.1715
69.4188-6.7267-5.78234.90874.15433.52310.4920.88930.3426-1.4903-0.37030.3625-0.6562-0.3863-0.22740.5436-0.0609-0.00140.51780.06520.4161-13.549157.1797-51.7232
74.3868-1.427-3.35642.90982.11333.0411-0.80380.2593-0.3782-0.9262-0.02620.71040.10560.09790.92191.4136-0.15940.1120.8559-0.0910.9359-20.375932.652724.3
83.24171.9574-3.46035.591-4.03043.5892-0.33530.1822-0.3606-0.355-0.2951-0.23270.97310.00670.69890.36090.0630.0010.3849-0.04750.5805-6.191134.3821-37.1237
97.3167-0.28431.37355.63260.47273.094-0.09390.56790.8192-0.2604-0.0285-0.2735-0.56730.09040.11740.32070.03250.00780.27720.03350.5486-12.871711.4994-42.2648
105.6607-5.52990.41415.82640.69632.71610.2888-0.7340.4755-0.24080.1986-1.4511-0.65060.4777-0.98680.4708-0.03130.06570.4523-0.06510.7834-4.808517.9325-34.4462
118.115-5.1767-5.66624.97815.12755.3409-0.08250.59950.1411-0.3935-0.4251-0.2025-0.5065-0.12950.47950.56720.02980.03610.39540.0950.492-12.00314.8367-48.42
129.8701-4.2525-4.70845.53415.94796.4680.05791.6120.6434-0.7609-0.64930.1855-0.3741-0.86590.43320.5448-0.00570.07550.47550.05040.5873-15.322112.6461-50.49
139.0952-4.13035.23459.3979-3.65933.2668-0.461-0.70370.15410.97710.11840.2541-0.3335-0.68970.22170.41870.01530.01250.3708-0.01980.7441-22.758218.0941-31.0389
147.219-1.25164.67956.725-2.90733.7676-0.4556-0.42910.22660.17930.690.7842-0.7138-0.6533-0.25040.31530.0544-0.00580.43490.00730.4733-20.71498.0255-39.417
153.8661-1.16911.66262.8021-0.41121.87360.0721-0.057-0.16050.0570.00540.35370.0399-0.1403-0.08280.2243-0.00890.01160.2683-0.02480.3709-17.0281-0.3888-33.277
168.499-4.03326.49543.4175-2.7098.80770.35420.3941-0.4682-0.3077-0.0097-0.08850.33460.2964-0.32280.28150.02010.04270.37890.01420.4728-9.59232.3132-46.4349
170.4767-0.1242-0.56860.03680.13821.0241-1.1355-0.33550.0294-0.21690.1811-0.94350.1363-0.46020.83861.8725-0.02730.14191.0058-0.05371.1622-9.399436.666320.516
182.86042.03772.16177.67275.76683.831-0.30750.25920.3778-0.8084-0.3130.6892-1.0816-0.30920.62160.46650.0832-0.05340.47390.11220.7885-22.756324.8851-39.565
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 67 )A56 - 67
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 104 )A68 - 104
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 135 )A105 - 135
5X-RAY DIFFRACTION5chain 'A' and (resid 136 through 187 )A136 - 187
6X-RAY DIFFRACTION6chain 'A' and (resid 188 through 202 )A188 - 202
7X-RAY DIFFRACTION7chain 'C' and (resid 140 through 171 )C140 - 171
8X-RAY DIFFRACTION8chain 'C' and (resid 172 through 225 )C172 - 225
9X-RAY DIFFRACTION9chain 'B' and (resid 30 through 55 )B30 - 55
10X-RAY DIFFRACTION10chain 'B' and (resid 56 through 67 )B56 - 67
11X-RAY DIFFRACTION11chain 'B' and (resid 68 through 77 )B68 - 77
12X-RAY DIFFRACTION12chain 'B' and (resid 78 through 89 )B78 - 89
13X-RAY DIFFRACTION13chain 'B' and (resid 90 through 103 )B90 - 103
14X-RAY DIFFRACTION14chain 'B' and (resid 104 through 115 )B104 - 115
15X-RAY DIFFRACTION15chain 'B' and (resid 116 through 176 )B116 - 176
16X-RAY DIFFRACTION16chain 'B' and (resid 177 through 202 )B177 - 202
17X-RAY DIFFRACTION17chain 'D' and (resid 140 through 175 )D140 - 175
18X-RAY DIFFRACTION18chain 'D' and (resid 176 through 225 )D176 - 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