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- PDB-8ij9: Crystal structure of the ELKS1/Rab6B complex -

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Basic information

Entry
Database: PDB / ID: 8ij9
TitleCrystal structure of the ELKS1/Rab6B complex
Components
  • ELKS/Rab6-interacting/CAST family member 1
  • Ras-related protein Rab-6B
KeywordsPROTEIN BINDING / small GTPase / scaffold protein / protein complex
Function / homology
Function and homology information


regulation of calcium-dependent activation of synaptic vesicle fusion / structural constituent of presynaptic active zone / Retrograde transport at the Trans-Golgi-Network / maintenance of presynaptic active zone structure / TBC/RABGAPs / cytoskeleton of presynaptic active zone / protein localization to Golgi membrane / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / COPI-independent Golgi-to-ER retrograde traffic ...regulation of calcium-dependent activation of synaptic vesicle fusion / structural constituent of presynaptic active zone / Retrograde transport at the Trans-Golgi-Network / maintenance of presynaptic active zone structure / TBC/RABGAPs / cytoskeleton of presynaptic active zone / protein localization to Golgi membrane / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / COPI-independent Golgi-to-ER retrograde traffic / IkappaB kinase complex / neuromuscular synaptic transmission / regulation of presynaptic cytosolic calcium ion concentration / presynaptic active zone cytoplasmic component / intra-Golgi vesicle-mediated transport / myosin V binding / presynaptic cytosol / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / retrograde transport, endosome to Golgi / synaptic vesicle priming / Golgi organization / endoplasmic reticulum-Golgi intermediate compartment / GABA-ergic synapse / endomembrane system / small monomeric GTPase / ciliary basal body / PDZ domain binding / intracellular protein transport / regulation of synaptic plasticity / small GTPase binding / synaptic vesicle / protein transport / presynapse / cytoplasmic vesicle / postsynaptic density / Golgi membrane / GTPase activity / centrosome / glutamatergic synapse / synapse / regulation of DNA-templated transcription / GTP binding / Golgi apparatus / membrane / cytosol / cytoplasm
Similarity search - Function
Active zone protein ELKS / RIM-binding protein of the cytomatrix active zone / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / TRIETHYLENE GLYCOL / Ras-related protein Rab-6B / ELKS/Rab6-interacting/CAST family member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsJin, G. / Wei, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971131 China
National Natural Science Foundation of China (NSFC)32170697 China
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural basis of ELKS/Rab6B interaction and its role in vesicle capturing enhanced by liquid-liquid phase separation.
Authors: Jin, G. / Lin, L. / Li, K. / Li, J. / Yu, C. / Wei, Z.
History
DepositionFeb 26, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein Rab-6B
B: Ras-related protein Rab-6B
C: ELKS/Rab6-interacting/CAST family member 1
D: ELKS/Rab6-interacting/CAST family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3789
Polymers57,1334
Non-polymers1,2455
Water4,071226
1
A: Ras-related protein Rab-6B
C: ELKS/Rab6-interacting/CAST family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1144
Polymers28,5672
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-21 kcal/mol
Surface area12090 Å2
MethodPISA
2
B: Ras-related protein Rab-6B
D: ELKS/Rab6-interacting/CAST family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2645
Polymers28,5672
Non-polymers6983
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-24 kcal/mol
Surface area12430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.193, 93.227, 53.077
Angle α, β, γ (deg.)90.00, 103.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Ras-related protein Rab-6B


Mass: 19641.350 Da / Num. of mol.: 2 / Mutation: Q72L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rab6b, D9Bwg0185e / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61294, small monomeric GTPase
#2: Protein ELKS/Rab6-interacting/CAST family member 1 / ERC-1 / CAZ-associated structural protein 2 / CAST2 / Rab6-interacting protein 2


Mass: 8925.161 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Erc1, Cast2, Elks, Rab6ip2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q811U3

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Non-polymers , 4 types, 231 molecules

#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5 and 42 % v/v Polyethylene glycol 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.04→51.56 Å / Num. obs: 26796 / % possible obs: 90.2 % / Redundancy: 2.2 % / CC1/2: 0.989 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.06 / Rrim(I) all: 0.098 / Χ2: 0.93 / Net I/σ(I): 7.2 / Num. measured all: 59879
Reflection shellResolution: 2.04→2.15 Å / % possible obs: 61.6 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.294 / Num. measured all: 4710 / Num. unique obs: 2644 / CC1/2: 0.8 / Rpim(I) all: 0.254 / Rrim(I) all: 0.39 / Χ2: 0.79 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIXv1.19.2refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→51.56 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 1273 4.78 %
Rwork0.1719 --
obs0.1745 26635 89.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→51.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3806 0 76 226 4108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013945
X-RAY DIFFRACTIONf_angle_d1.1295320
X-RAY DIFFRACTIONf_dihedral_angle_d18.1861519
X-RAY DIFFRACTIONf_chiral_restr0.062615
X-RAY DIFFRACTIONf_plane_restr0.008663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.120.3241810.21311595X-RAY DIFFRACTION51
2.12-2.220.22781530.19652923X-RAY DIFFRACTION95
2.22-2.340.24321130.19122357X-RAY DIFFRACTION75
2.34-2.480.26871670.18282976X-RAY DIFFRACTION97
2.48-2.670.26751410.18383097X-RAY DIFFRACTION98
2.67-2.940.27021470.19173099X-RAY DIFFRACTION99
2.94-3.370.2351460.18133095X-RAY DIFFRACTION99
3.37-4.240.21361580.15123074X-RAY DIFFRACTION98
4.24-51.560.17741670.15643146X-RAY DIFFRACTION99
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)
11.1589-0.3940.29331.48310.08861.11720.0523-0.0656-0.06810.1052-0.07170.06870.0716-0.11630.0350.1716-0.02670.02340.2277-0.01470.217911.638-24.779518.3856
23.33040.06921.36284.24143.79558.6662-0.1029-0.12460.15320.19960.1862-0.2753-0.28530.4116-0.07430.21710.005-0.02610.19660.02440.26499.6659-15.643923.2496
32.8664-0.47870.12090.73250.37621.41240.09140.27810.1289-0.2358-0.0884-0.046-0.119-0.02930.00490.24170.01150.01560.20880.01320.186615.8237-22.1866.4183
43.1925-2.07480.84663.0705-0.38013.03810.16420.31650.3701-0.3557-0.1346-0.2682-0.140.33230.05580.1791-0.01820.02010.22130.03160.269726.7511-20.712711.1192
55.2905-2.09620.61348.308-0.85133.8669-0.2239-0.27810.41960.58280.0046-0.1691-0.54160.3870.21950.2098-0.026-0.04590.25620.00350.25819.7791-15.114321.5267
68.0641.5383.55765.01152.11558.0803-0.353-0.18070.76370.54750.24260.0399-0.43210.43630.09930.30560.0431-0.01040.2213-0.0360.27741.065-32.303539.3708
71.5776-0.05560.3531.21230.31942.1846-0.0078-0.065-0.02380.1010.0238-0.02690.0606-0.072-0.00810.1760.00240.0040.15320.01440.1724-5.049-41.58834.1126
83.4801-0.59620.18781.8362-0.34491.6211-0.07450.07390.14270.0471-0.00130.0427-0.0842-0.01490.08260.1974-0.01770.00390.18690.02810.1756-5.7447-36.363322.8872
94.0033-0.06022.44283.49030.75492.0903-0.03140.42830.1482-0.4035-0.04860.0066-0.29910.3024-0.01060.26410.01680.06410.2149-0.00840.3349-3.9993-14.312314.9227
102.13460.30390.7872.2873-0.30779.70370.1051-0.0072-0.22720.12630.02710.07630.3551-0.4944-0.06660.2259-0.02320.06450.22990.01210.3942-6.3494-22.144619.6416
114.3844-0.1493-0.38761.73980.154.2807-0.0541-0.0389-0.11770.13320.0160.05010.1141-0.18850.07710.2754-0.0268-0.02650.1452-0.00980.1335-3.5748-38.632352.186
125.9486-0.86322.25851.56491.1472.78541.0268-0.5529-0.83450.2337-0.3529-0.21220.3533-0.0353-0.60980.5480.0159-0.04130.23120.05030.35664.4847-46.763350.0437
133.37972.7766-0.9112.58190.29253.80930.3393-1.0098-0.00080.7753-1.1660.4187-0.11730.38030.70460.8555-0.21090.10140.5374-0.06450.8709-24.0924-51.491750.794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 69 )
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 137 )
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 162 )
5X-RAY DIFFRACTION5chain 'A' and (resid 163 through 175 )
6X-RAY DIFFRACTION6chain 'B' and (resid 10 through 19 )
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 115 )
8X-RAY DIFFRACTION8chain 'B' and (resid 116 through 175 )
9X-RAY DIFFRACTION9chain 'C' and (resid 849 through 880 )
10X-RAY DIFFRACTION10chain 'C' and (resid 881 through 919 )
11X-RAY DIFFRACTION11chain 'D' and (resid 846 through 880 )
12X-RAY DIFFRACTION12chain 'D' and (resid 881 through 914 )
13X-RAY DIFFRACTION13chain 'D' and (resid 915 through 919 )

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