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- PDB-6sur: The Rab33B-Atg16L1 crystal structure -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6sur
TitleThe Rab33B-Atg16L1 crystal structure
Components
  • Autophagy-related protein 16-1
  • Ras-related protein Rab-33B
KeywordsCELL CYCLE / Autophagy
Function / homology
Function and homology information


negative regulation of constitutive secretory pathway / regulation of retrograde vesicle-mediated transport, Golgi to ER / TBC/RABGAPs / RAB geranylgeranylation / Atg12-Atg5-Atg16 complex / Macroautophagy / Intra-Golgi traffic / vacuole-isolation membrane contact site / regulation of Golgi organization / Rab protein signal transduction ...negative regulation of constitutive secretory pathway / regulation of retrograde vesicle-mediated transport, Golgi to ER / TBC/RABGAPs / RAB geranylgeranylation / Atg12-Atg5-Atg16 complex / Macroautophagy / Intra-Golgi traffic / vacuole-isolation membrane contact site / regulation of Golgi organization / Rab protein signal transduction / microautophagy / protein localization to Golgi apparatus / xenophagy / regulation of exocytosis / corpus callosum development / protein localization to phagophore assembly site / intra-Golgi vesicle-mediated transport / phagophore assembly site membrane / negative stranded viral RNA replication / endolysosome membrane / skeletal system morphogenesis / axonal transport / axoneme / autophagosome membrane / autophagosome assembly / positive regulation of autophagy / protein-membrane adaptor activity / sperm midpiece / autophagosome / hippocampus development / macroautophagy / Golgi lumen / protein transport / GTPase binding / presynapse / defense response to virus / endosome / Golgi membrane / axon / GTPase activity / glutamatergic synapse / 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. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family ...Rab33A/B / Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rab-33B / Autophagy-related protein 16-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.467 Å
AuthorsMetje-Sprink, J. / Kuehnel, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB860 Germany
CitationJournal: Sci Rep / Year: 2020
Title: Crystal structure of the Rab33B/Atg16L1 effector complex.
Authors: Metje-Sprink, J. / Groffmann, J. / Neumann, P. / Barg-Kues, B. / Ficner, R. / Kuhnel, K. / Schalk, A.M. / Binotti, B.
History
DepositionSep 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-33B
B: Ras-related protein Rab-33B
C: Ras-related protein Rab-33B
D: Ras-related protein Rab-33B
E: Ras-related protein Rab-33B
F: Ras-related protein Rab-33B
I: Autophagy-related protein 16-1
J: Autophagy-related protein 16-1
K: Autophagy-related protein 16-1
L: Autophagy-related protein 16-1
M: Autophagy-related protein 16-1
N: Autophagy-related protein 16-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,80824
Polymers159,52312
Non-polymers3,28512
Water00
1
A: Ras-related protein Rab-33B
B: Ras-related protein Rab-33B
I: Autophagy-related protein 16-1
J: Autophagy-related protein 16-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2698
Polymers53,1744
Non-polymers1,0954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ras-related protein Rab-33B
D: Ras-related protein Rab-33B
K: Autophagy-related protein 16-1
L: Autophagy-related protein 16-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2698
Polymers53,1744
Non-polymers1,0954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Ras-related protein Rab-33B
F: Ras-related protein Rab-33B
M: Autophagy-related protein 16-1
N: Autophagy-related protein 16-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2698
Polymers53,1744
Non-polymers1,0954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.400, 204.900, 107.200
Angle α, β, γ (deg.)90.000, 92.600, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 31 through 56 or resid 58...
21(chain B and (resid 31 through 56 or resid 58...
31(chain C and (resid 31 through 56 or resid 58...
41(chain D and (resid 31 through 56 or resid 58...
51(chain E and (resid 31 through 56 or resid 58...
61(chain F and (resid 31 through 56 or resid 58...
12(chain I and (resid 160 through 166 or resid 168...
22(chain J and (resid 160 through 166 or resid 168...
32(chain K and (resid 160 through 166 or resid 168...
42(chain L and (resid 160 through 166 or resid 168...
52(chain M and (resid 160 through 166 or resid 168...
62(chain N and (resid 160 through 166 or resid 168...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 31 through 56 or resid 58...A31 - 56
121(chain A and (resid 31 through 56 or resid 58...A58 - 60
131(chain A and (resid 31 through 56 or resid 58...A62
141(chain A and (resid 31 through 56 or resid 58...A0
151(chain A and (resid 31 through 56 or resid 58...A989
161(chain A and (resid 31 through 56 or resid 58...A98 - 132
171(chain A and (resid 31 through 56 or resid 58...A31 - 201
181(chain A and (resid 31 through 56 or resid 58...A141 - 152
191(chain A and (resid 31 through 56 or resid 58...A31 - 201
1101(chain A and (resid 31 through 56 or resid 58...A154 - 164
1111(chain A and (resid 31 through 56 or resid 58...A31 - 201
1121(chain A and (resid 31 through 56 or resid 58...A187 - 197
1131(chain A and (resid 31 through 56 or resid 58...A300 - 301
211(chain B and (resid 31 through 56 or resid 58...B31 - 56
221(chain B and (resid 31 through 56 or resid 58...B58 - 60
231(chain B and (resid 31 through 56 or resid 58...B62
241(chain B and (resid 31 through 56 or resid 58...B64
251(chain B and (resid 31 through 56 or resid 58...B31 - 201
261(chain B and (resid 31 through 56 or resid 58...B82 - 96
271(chain B and (resid 31 through 56 or resid 58...B31 - 201
281(chain B and (resid 31 through 56 or resid 58...B141 - 152
291(chain B and (resid 31 through 56 or resid 58...B166 - 180
2101(chain B and (resid 31 through 56 or resid 58...B182 - 183
2111(chain B and (resid 31 through 56 or resid 58...B300 - 301
311(chain C and (resid 31 through 56 or resid 58...C31 - 56
321(chain C and (resid 31 through 56 or resid 58...C58 - 60
331(chain C and (resid 31 through 56 or resid 58...C62
341(chain C and (resid 31 through 56 or resid 58...C64
351(chain C and (resid 31 through 56 or resid 58...C31 - 201
361(chain C and (resid 31 through 56 or resid 58...C82 - 96
371(chain C and (resid 31 through 56 or resid 58...C31 - 201
381(chain C and (resid 31 through 56 or resid 58...C141 - 152
391(chain C and (resid 31 through 56 or resid 58...C166 - 180
3101(chain C and (resid 31 through 56 or resid 58...C182 - 183
3111(chain C and (resid 31 through 56 or resid 58...C300 - 301
411(chain D and (resid 31 through 56 or resid 58...D31 - 56
421(chain D and (resid 31 through 56 or resid 58...D58 - 60
431(chain D and (resid 31 through 56 or resid 58...D62
441(chain D and (resid 31 through 56 or resid 58...D64
451(chain D and (resid 31 through 56 or resid 58...D31 - 201
461(chain D and (resid 31 through 56 or resid 58...D82 - 96
471(chain D and (resid 31 through 56 or resid 58...D31 - 201
481(chain D and (resid 31 through 56 or resid 58...D141 - 152
491(chain D and (resid 31 through 56 or resid 58...D166 - 180
4101(chain D and (resid 31 through 56 or resid 58...D182 - 185
4111(chain D and (resid 31 through 56 or resid 58...D300 - 301
511(chain E and (resid 31 through 56 or resid 58...E31 - 56
521(chain E and (resid 31 through 56 or resid 58...E58 - 60
531(chain E and (resid 31 through 56 or resid 58...E62
541(chain E and (resid 31 through 56 or resid 58...E64
551(chain E and (resid 31 through 56 or resid 58...E31 - 201
561(chain E and (resid 31 through 56 or resid 58...E82 - 96
571(chain E and (resid 31 through 56 or resid 58...E31 - 201
581(chain E and (resid 31 through 56 or resid 58...E141 - 152
591(chain E and (resid 31 through 56 or resid 58...E166 - 180
5101(chain E and (resid 31 through 56 or resid 58...E182 - 183
5111(chain E and (resid 31 through 56 or resid 58...E300 - 301
611(chain F and (resid 31 through 56 or resid 58...F31 - 56
621(chain F and (resid 31 through 56 or resid 58...F58 - 60
631(chain F and (resid 31 through 56 or resid 58...F62
641(chain F and (resid 31 through 56 or resid 58...F64
651(chain F and (resid 31 through 56 or resid 58...F31 - 200
661(chain F and (resid 31 through 56 or resid 58...F82 - 96
671(chain F and (resid 31 through 56 or resid 58...F31 - 200
681(chain F and (resid 31 through 56 or resid 58...F141 - 152
691(chain F and (resid 31 through 56 or resid 58...F166 - 180
6101(chain F and (resid 31 through 56 or resid 58...F182 - 183
6111(chain F and (resid 31 through 56 or resid 58...F300 - 301
112(chain I and (resid 160 through 166 or resid 168...I160 - 166
122(chain I and (resid 160 through 166 or resid 168...I168 - 178
132(chain I and (resid 160 through 166 or resid 168...I180
142(chain I and (resid 160 through 166 or resid 168...I182 - 196
152(chain I and (resid 160 through 166 or resid 168...I199 - 208
212(chain J and (resid 160 through 166 or resid 168...J160 - 166
222(chain J and (resid 160 through 166 or resid 168...J168 - 178
232(chain J and (resid 160 through 166 or resid 168...J180
242(chain J and (resid 160 through 166 or resid 168...J182 - 196
252(chain J and (resid 160 through 166 or resid 168...J199 - 208
312(chain K and (resid 160 through 166 or resid 168...K160 - 166
322(chain K and (resid 160 through 166 or resid 168...K168 - 178
332(chain K and (resid 160 through 166 or resid 168...K180
342(chain K and (resid 160 through 166 or resid 168...K182 - 196
352(chain K and (resid 160 through 166 or resid 168...K199 - 208
412(chain L and (resid 160 through 166 or resid 168...L160 - 166
422(chain L and (resid 160 through 166 or resid 168...L168 - 178
432(chain L and (resid 160 through 166 or resid 168...L180
442(chain L and (resid 160 through 166 or resid 168...L182 - 196
452(chain L and (resid 160 through 166 or resid 168...L199 - 208
512(chain M and (resid 160 through 166 or resid 168...M160 - 166
522(chain M and (resid 160 through 166 or resid 168...M168 - 178
532(chain M and (resid 160 through 166 or resid 168...M180
542(chain M and (resid 160 through 166 or resid 168...M182 - 196
552(chain M and (resid 160 through 166 or resid 168...M199 - 208
612(chain N and (resid 160 through 166 or resid 168...N160 - 166
622(chain N and (resid 160 through 166 or resid 168...N168 - 178
632(chain N and (resid 160 through 166 or resid 168...N180
642(chain N and (resid 160 through 166 or resid 168...N182 - 196
652(chain N and (resid 160 through 166 or resid 168...N199 - 208

NCS ensembles :
ID
1
2

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Components

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


Mass: 19896.842 Da / Num. of mol.: 6 / Mutation: Q92L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rab33b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: O35963
#2: Protein
Autophagy-related protein 16-1 / APG16-like 1


Mass: 6690.304 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Atg16l1, Apg16l / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: Q8C0J2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: Mg
#4: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 63.99 % / Description: Needle like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES monohydrate pH 6.5, 0.2 M sodium chloride, 10 % (w/v) PEG 4 000 0.1 M spermine

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Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.467→48.35 Å / Num. obs: 25983 / % possible obs: 96.28 % / Redundancy: 3.466 % / Biso Wilson estimate: 52.051 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.194 / Rrim(I) all: 0.229 / Χ2: 0.868 / Net I/σ(I): 7.86
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.47-3.63.2820.752.27310278822270.7240.89279.9
3.6-3.83.5070.5593.3212412360635390.8090.6698.1
3.8-43.3840.3924.579889297529220.8820.46898.2
4-53.5010.2177.8729471857384180.9640.25698.2
5-63.4330.1698.3313064384638050.970.20198.9
6-103.5830.08812.4114513411240500.9950.10498.5
10-153.2940.04123.0725798077830.9960.04997
15-47.13.4640.03925.811573363340.9970.04699.4
47.1-48.351.6670.05814.2851130.08127.3

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
Cootmodel building
PHASERphasing
XSCALEdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z06

1z06


Resolution: 3.467→48.35 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 25.05
RfactorNum. reflection% reflection
Rfree0.2388 1298 5 %
Rwork0.2056 --
obs0.2073 25983 96.28 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 152.01 Å2 / Biso mean: 60.2656 Å2 / Biso min: 25.11 Å2
Refinement stepCycle: final / Resolution: 3.467→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10474 0 198 0 10672
Biso mean--47.89 --
Num. residues----1319
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2577X-RAY DIFFRACTION5.705TORSIONAL
12B2577X-RAY DIFFRACTION5.705TORSIONAL
13C2577X-RAY DIFFRACTION5.705TORSIONAL
14D2577X-RAY DIFFRACTION5.705TORSIONAL
15E2577X-RAY DIFFRACTION5.705TORSIONAL
16F2577X-RAY DIFFRACTION5.705TORSIONAL
21I714X-RAY DIFFRACTION5.705TORSIONAL
22J714X-RAY DIFFRACTION5.705TORSIONAL
23K714X-RAY DIFFRACTION5.705TORSIONAL
24L714X-RAY DIFFRACTION5.705TORSIONAL
25M714X-RAY DIFFRACTION5.705TORSIONAL
26N714X-RAY DIFFRACTION5.705TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.47-3.6060.39881170.3453223480
3.606-3.770.33761480.2805280698
3.77-3.96870.28171470.2428279798
3.9687-4.21720.26021410.2267269496
4.2172-4.54260.22591500.1902283999
4.5426-4.99930.21931480.1732282899
4.9993-5.72170.23011500.1895283299
5.7217-7.20490.22921480.2118280998
7.2049-48.350.1571490.1478284699
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)
13.00050.4792-0.46562.65460.33243.1381-0.08890.0791-0.0909-0.0412-0.0163-0.1167-0.00590.20910.12140.26910.0062-0.01530.28470.00910.301519.281415.506237.8894
23.5289-0.33090.55993.3931-0.12052.80680.02790.245-0.1793-0.0987-0.08030.30320.3141-0.26070.03590.3409-0.01080.02950.4168-0.03350.4898-9.3041-13.580617.499
31.555-0.33460.17623.8652-0.3130.9832-0.1611-0.01440.07790.16720.2176-0.1678-0.02160.0422-0.04670.3820.0692-0.03780.4737-0.05750.317815.2664-7.3057-5.642
42.2787-0.6019-0.20161.6948-1.01644.2664-0.0969-0.25030.40320.4205-0.0738-0.1232-0.71180.10580.17690.5522-0.0339-0.04850.5033-0.00750.4265-12.92418.0667-29.8671
52.40351.0786-0.47034.2362-2.37841.8036-0.07240.1545-0.3407-0.59370.16770.06970.30260.1579-0.08370.5346-0.01620.01150.41380.02760.553622.354556.16079.8227
63.0406-0.07530.52653.18570.32842.71060.02610.0463-0.10190.34150.03580.26830.015-0.2688-0.00490.41980.00390.11390.41170.07250.5473-5.701338.978141.2816
70.7970.4249-0.55323.4909-1.29693.3914-0.50170.1118-0.3099-0.7529-0.1227-0.63461.3382-0.0785-0.03140.4243-0.00940.03850.4290.12140.58889.2508-14.857244.7933
82.1325-0.50281.49922.714-1.7544.8619-0.42320.06190.33320.7586-0.5788-0.7203-0.69751.22460.52220.58790.0820.01350.46570.05690.53644.4967-8.9147.9397
90.93730.66550.74064.20931.97624.144-0.40070.17270.0858-0.50390.62050.3393-0.09390.6209-0.19130.5839-0.0264-0.04150.69550.06750.49883.1153-8.0366-36.7638
101.1242-0.9724-1.35183.27942.23613.3749-0.4582-0.2585-0.07740.64670.31620.09651.10140.3060.10.68840.0492-0.02290.51220.09550.4825-1.4929-12.4684-31.878
110.7654-0.0628-0.99272.57111.21621.9687-0.2924-0.0988-0.04720.49780.14230.10630.25560.43120.1970.67780.0308-0.09430.5783-0.00680.699212.880464.357539.6581
121.56320.99940.17783.98710.4162.5061-0.16270.38060.1373-0.01250.2405-0.075-0.29690.32640.02510.37730.08490.07890.61310.14790.83397.411367.115433.4916
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA31 - 201
2X-RAY DIFFRACTION2chain BB31 - 201
3X-RAY DIFFRACTION3chain CC31 - 201
4X-RAY DIFFRACTION4chain DD31 - 201
5X-RAY DIFFRACTION5chain EE31 - 201
6X-RAY DIFFRACTION6chain FF31 - 200
7X-RAY DIFFRACTION7chain II159 - 208
8X-RAY DIFFRACTION8chain JJ159 - 208
9X-RAY DIFFRACTION9chain KK159 - 208
10X-RAY DIFFRACTION10chain LL159 - 208
11X-RAY DIFFRACTION11chain MM159 - 208
12X-RAY DIFFRACTION12chain NN160 - 208

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  • 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

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