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- PDB-8a4b: Structure of human Rep15:Rab3B_Q81L complex. -

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Basic information

Entry
Database: PDB / ID: 8a4b
TitleStructure of human Rep15:Rab3B_Q81L complex.
Components
  • Rab15 effector protein
  • Ras-related protein Rab-3B
KeywordsENDOCYTOSIS / Rab GTPase / Effector
Function / homology
Function and homology information


positive regulation of dopamine uptake involved in synaptic transmission / receptor recycling / transferrin transport / regulation of vesicle size / myosin V binding / RAB geranylgeranylation / dopaminergic synapse / regulation of synaptic vesicle cycle / antigen processing and presentation / exocytosis ...positive regulation of dopamine uptake involved in synaptic transmission / receptor recycling / transferrin transport / regulation of vesicle size / myosin V binding / RAB geranylgeranylation / dopaminergic synapse / regulation of synaptic vesicle cycle / antigen processing and presentation / exocytosis / small monomeric GTPase / recycling endosome / synaptic vesicle membrane / GDP binding / synaptic vesicle / protein transport / early endosome membrane / vesicle / endosome / endosome membrane / GTPase activity / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / plasma membrane / cytoplasm
Similarity search - Function
Rab15 effector / Rab15 effector / Rab3 / : / Small GTPase Rab domain 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 ...Rab15 effector / Rab15 effector / Rab3 / : / Small GTPase Rab domain 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rab-3B / Rab15 effector protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRai, A. / Vetter, I.R. / Goody, R.S.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)grant GO 284/10-1 Germany
CitationJournal: Nat Commun / Year: 2022
Title: Rep15 interacts with several Rab GTPases and has a distinct fold for a Rab effector.
Authors: Rai, A. / Singh, A.K. / Bleimling, N. / Posern, G. / Vetter, I.R. / Goody, R.S.
History
DepositionJun 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rab15 effector protein
B: Ras-related protein Rab-3B
C: Rab15 effector protein
D: Ras-related protein Rab-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6618
Polymers90,5664
Non-polymers1,0954
Water37821
1
A: Rab15 effector protein
B: Ras-related protein Rab-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8314
Polymers45,2832
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Rab15 effector protein
D: Ras-related protein Rab-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8314
Polymers45,2832
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.840, 107.960, 91.100
Angle α, β, γ (deg.)90.000, 106.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Rab15 effector protein


Mass: 25184.314 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REP15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6BDI9
#2: Protein Ras-related protein Rab-3B


Mass: 20098.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB3B / Production host: Escherichia coli (E. coli) / References: UniProt: P20337
#3: Chemical ChemComp-GTP / GUANOSINE-5'-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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.13 Å3/Da / Density % sol: 60.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Bis-Tris pH 8.5, 0.2 M KNa-tartrate and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97793 Å / Relative weight: 1
ReflectionResolution: 2.8→49.54 Å / Num. obs: 27424 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 75.21 Å2 / CC1/2: 0.999 / CC star: 1 / Rpim(I) all: 0.03751 / Rrim(I) all: 0.097 / Net I/σ(I): 15.26
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.28 / Num. unique obs: 2719 / CC1/2: 0.719 / CC star: 0.915 / Rpim(I) all: 0.5676 / % possible all: 99.49

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8A4A

8a4a


Resolution: 2.8→49.54 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2689 1370 5 %
Rwork0.2231 26006 -
obs0.2254 27376 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 170.41 Å2 / Biso mean: 93.9224 Å2 / Biso min: 51.11 Å2
Refinement stepCycle: final / Resolution: 2.8→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6058 0 66 21 6145
Biso mean--69.08 76.97 -
Num. residues----752
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.90.39951360.37552577271399
2.9-3.020.36511370.325426032740100
3.02-3.150.33731380.300326072745100
3.15-3.320.33561350.267225612696100
3.32-3.530.29311370.236725972734100
3.53-3.80.29291370.237125942731100
3.8-4.180.2541360.206925862722100
4.18-4.790.23351380.193626102748100
4.79-6.030.25911380.212226252763100
6.03-49.540.22961380.19242646278499
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)
10.4496-0.17671.01753.73871.13132.8619-0.05290.5086-0.0488-0.81570.3331-0.2822-0.06650.0246-0.26960.8753-0.10550.09430.96870.0450.7706-11.76522.7151-28.4455
22.5409-1.9244-0.29012.6365-0.82460.95080.2233-0.760.46480.0720.2225-0.06130.9228-0.9637-0.54280.9849-0.19050.05911.08450.08181.0596-19.63630.6076-8.3306
33.7529-1.56731.57642.857-0.16943.0695-0.1681-0.12230.6951-0.04080.11191.0043-0.1923-0.78550.01930.7088-0.0555-0.03230.95980.160.8752-21.705211.9506-21.6349
41.59780.0991-0.47551.74310.60433.36450.0754-0.12470.509-0.408-0.15510.074-0.74240.52680.2261.2782-0.0158-0.16041.35580.26961.4502-22.542616.373-29.2953
55.0552-1.66411.04794.87513.66123.96440.08380.0535-0.5404-0.17550.09170.08090.4184-0.3856-0.25960.6026-0.0403-0.04420.58620.12190.72141.8313-1.3099-5.2948
64.55430.45271.36692.9288-1.10033.8322-0.1638-0.31850.3407-0.1195-0.2211-0.4479-0.0554-0.08590.40150.52920.048-0.04260.69690.00260.9098-2.3135.769-3.4083
72.9802-1.6944-0.18964.01350.92763.7923-0.0013-0.05790.6375-0.2408-0.2705-0.001-0.5812-0.1280.27980.6464-0.0114-0.02920.61380.07630.92987.787113.3694-3.1521
87.879-0.81940.53935.0224-2.45222.0388-0.4824-0.5828-0.43031.17380.00830.5609-0.1634-1.27540.73290.81850.06530.0380.91880.00440.69785.29869.51914.3928
92.3990.7553-0.15752.85510.03531.32290.0463-0.4101-0.03560.23560.0117-0.0419-0.02010.2465-0.05560.55960.019-0.04220.61530.02030.940714.79273.78540.6467
103.15370.2495-1.36445.7024-0.01911.33770.34090.08930.1902-0.8388-0.3797-0.4983-0.40890.2427-0.02421.4183-0.1030.00031.2204-0.120.4619-16.9665-24.0482-38.0417
115.9137-0.3343-0.52514.7322-2.63332.00980.0162-0.77290.89181.0796-1.2341-1.14511.00481.43571.2010.7362-0.12330.05771.196-0.04180.7034-3.6007-6.6219-27.051
121.0358-0.4875-1.09663.8545-1.24663.5594-0.15050.39010.0294-0.60210.25950.46080.0976-0.1035-0.12790.7539-0.1025-0.07920.8327-0.0340.6495-21.6989-24.1572-26.1485
131.6719-0.36790.60632.13671.26721.1589-0.38630.09880.11440.05730.04640.3221-0.5088-0.29660.07880.9668-0.11750.0881.3314-0.18941.2161-9.6273-19.5163-9.5525
142.6202-0.8785-1.60521.8005-0.49182.4843-0.3852-0.0022-0.6709-0.11690.1204-0.94290.22150.51980.15650.7229-0.04380.0290.9362-0.09160.8314-8.2008-31.0929-21.7619
150.49010.11380.35090.8507-0.02040.41240.1693-0.109-0.7155-0.65060.02480.05820.5685-0.47190.14891.37860.02150.10141.3796-0.32281.1749-7.2387-35.634-29.2092
163.8908-1.1849-0.89583.978-2.52933.51360.09890.2480.4076-0.10280.0298-0.0887-0.23260.5856-0.09150.592-0.047-0.00730.6555-0.08730.8835-32.0206-18.0344-5.5801
173.7363-0.4237-1.07082.6691.50314.2592-0.3122-0.2058-0.1275-0.1424-0.25540.2929-0.1081-0.01010.63860.60740.0444-0.05910.6606-0.03780.9253-27.5662-24.8822-3.5098
183.5319-2.19590.15272.8910.75823.19490.0793-0.1117-0.556-0.1483-0.10870.31030.58830.03150.07690.6512-0.03730.00470.55980.01630.8838-37.6335-32.5669-3.2794
193.377-0.7018-2.74752.95451.49992.7325-0.52750.27420.0970.8901-0.4066-0.62930.15961.14270.54070.65040.0225-0.06370.79950.11790.9148-33.9491-28.74893.5954
204.7915-0.0568-0.81074.0844-0.18921.4399-0.1879-0.41110.35230.25660.20170.0451-0.1944-0.2430.05340.56130.0402-0.04410.5601-0.01570.8253-44.7058-22.98670.5377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 114 )A18 - 114
2X-RAY DIFFRACTION2chain 'A' and (resid 115 through 143 )A115 - 143
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 190 )A144 - 190
4X-RAY DIFFRACTION4chain 'A' and (resid 191 through 236 )A191 - 236
5X-RAY DIFFRACTION5chain 'B' and (resid 18 through 66 )B18 - 66
6X-RAY DIFFRACTION6chain 'B' and (resid 67 through 92 )B67 - 92
7X-RAY DIFFRACTION7chain 'B' and (resid 93 through 123 )B93 - 123
8X-RAY DIFFRACTION8chain 'B' and (resid 124 through 135 )B124 - 135
9X-RAY DIFFRACTION9chain 'B' and (resid 136 through 187 )B136 - 187
10X-RAY DIFFRACTION10chain 'C' and (resid 18 through 37 )C18 - 37
11X-RAY DIFFRACTION11chain 'C' and (resid 38 through 51 )C38 - 51
12X-RAY DIFFRACTION12chain 'C' and (resid 52 through 114 )C52 - 114
13X-RAY DIFFRACTION13chain 'C' and (resid 115 through 143 )C115 - 143
14X-RAY DIFFRACTION14chain 'C' and (resid 144 through 190 )C144 - 190
15X-RAY DIFFRACTION15chain 'C' and (resid 191 through 235 )C191 - 235
16X-RAY DIFFRACTION16chain 'D' and (resid 19 through 66 )D19 - 66
17X-RAY DIFFRACTION17chain 'D' and (resid 67 through 92 )D67 - 92
18X-RAY DIFFRACTION18chain 'D' and (resid 93 through 123 )D93 - 123
19X-RAY DIFFRACTION19chain 'D' and (resid 124 through 135 )D124 - 135
20X-RAY DIFFRACTION20chain 'D' and (resid 136 through 187 )D136 - 187

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