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- PDB-8a4c: Structure of human Rep15:Rab3B complex. -

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Basic information

Entry
Database: PDB / ID: 8a4c
TitleStructure of human Rep15:Rab3B 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 / regulation of vesicle size / regulation of exocytosis / myosin V binding / GTP-dependent protein binding / RAB geranylgeranylation / dopaminergic synapse / regulation of synaptic vesicle cycle / antigen processing and presentation ...positive regulation of dopamine uptake involved in synaptic transmission / receptor recycling / regulation of vesicle size / regulation of exocytosis / myosin V binding / GTP-dependent protein binding / RAB geranylgeranylation / dopaminergic synapse / regulation of synaptic vesicle cycle / antigen processing and presentation / exocytosis / secretory granule / transferrin transport / small monomeric GTPase / recycling endosome / synaptic vesicle / GDP binding / synaptic vesicle membrane / protein transport / early endosome membrane / vesicle / endosome membrane / endosome / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-3B / Rab15 effector protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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

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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)104,6498
Polymers103,5564
Non-polymers1,0934
Water68538
1
A: Rab15 effector protein
B: Ras-related protein Rab-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3254
Polymers51,7782
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)52,3254
Polymers51,7782
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)188.810, 59.220, 109.020
Angle α, β, γ (deg.)90.000, 111.900, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Rab15 effector protein


Mass: 26800.125 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: 24978.064 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-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*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.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Bis-Tris pH 7.5, 0.2 M NaI and 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999961 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2017
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999961 Å / Relative weight: 1
ReflectionResolution: 2.75→47.1 Å / Num. obs: 29437 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 67.73 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rpim(I) all: 0.05485 / Rrim(I) all: 0.144 / Net I/σ(I): 14.13
Reflection shellResolution: 2.75→2.848 Å / Mean I/σ(I) obs: 1.98 / Num. unique obs: 2888 / CC1/2: 0.615 / CC star: 0.873 / Rpim(I) all: 0.6729

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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: 8A4B

8a4b


Resolution: 2.75→47.1 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2659 1472 5 %
Rwork0.2177 27942 -
obs0.22 29414 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.3 Å2 / Biso mean: 77.695 Å2 / Biso min: 36.14 Å2
Refinement stepCycle: final / Resolution: 2.75→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5989 0 66 38 6093
Biso mean--51.62 69.94 -
Num. residues----744
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.75-2.840.40951310.381924992630100
2.84-2.940.37571340.308325272661100
2.94-3.060.32831310.268124992630100
3.06-3.20.31511340.271125442678100
3.2-3.370.33841320.241525112643100
3.37-3.580.26431340.222925282662100
3.58-3.850.25321330.210125342667100
3.85-4.240.25371340.19725482682100
4.24-4.850.23261350.167425522687100
4.85-6.110.24321340.200725592693100
6.11-47.10.24261400.21742641278199
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)
11.2686-0.202-0.67990.77950.20732.7790.0174-0.1336-0.0890.1657-0.11060.0392-0.09690.134200.4443-0.028-0.0810.46940.08380.4962-35.05730.51445.9813
20.3341-0.62260.03871.0924-0.13550.0045-1.26960.32250.1661-0.24890.36430.9488-0.21820.3853-0.00070.89980.11330.02950.7824-0.00250.7248-54.10316.979138.6589
31.5169-0.68710.1091.38761.51762.75950.3204-0.28130.60210.9276-0.35650.3683-0.8191-0.28360.00290.5965-0.0062-0.08540.4406-0.00450.5841-44.93499.384253.7358
40.4967-0.2989-0.02531.69720.22870.7537-0.4784-0.21040.71360.6330.2695-0.2315-0.57550.007100.9674-0.048-0.14990.8015-0.03470.6884-39.381410.237960.4386
52.09970.045-0.28062.46960.98210.84830.03920.29910.1359-0.2806-0.016-0.32-0.07680.345400.4148-0.01230.02210.45960.01370.3952-54.8804-14.952236.6464
60.0467-0.16020.18610.4663-0.09520.1925-0.00580.7320.24060.10510.04220.0144-0.25780.152800.7588-0.126-0.01830.7270.01970.5383-61.6882-10.899127.8395
70.84820.3755-0.1080.90080.74280.6751-0.043-0.21040.20540.2121-0.2224-0.26090.28820.372300.42790.02240.00550.4655-0.02440.5165-57.8371-9.490543.9504
80.75050.30810.44731.87720.94480.4901-0.0813-0.32070.20950.20860.0301-0.36960.11840.0555-00.5569-0.01160.06430.4422-0.0340.4649-62.9883-19.62447.9585
90.28140.0701-0.62750.0203-0.2431.3958-0.35170.19870.301-0.0081-0.0520.46110.7824-0.8385-0.1260.22910.0612-0.02760.6923-0.03210.6731-68.4826-17.446441.8918
100.11480.17380.13710.27450.17260.2339-0.0090.1718-0.0327-0.4696-0.2392-0.2171-0.1254-0.121800.6265-0.00420.15560.5940.08440.518-53.3162-34.854142.2345
110.83330.51990.31540.869-0.33050.53820.22730.2544-0.0922-0.2851-0.03660.16070.1023-0.028200.4892-0.01550.09580.4397-0.01140.5627-63.8337-29.118939.7964
120.49920.12090.11781.20450.1680.37130.45890.0581-0.2991-1.3973-0.33970.49910.0408-0.4918-0.02650.5130.081-0.1580.6188-0.00720.5618-68.291-18.126430.9685
130.0034-0.0672-0.09870.81310.5560.4133-0.2222-0.7371-0.33060.5914-0.0264-0.0674-0.66750.614-00.5186-0.0228-0.09850.97390.14670.8273-16.42045.057926.454
140.0779-0.0599-0.1080.04750.0870.1922-0.05320.0592-0.7366-1.1604-0.4164-0.48380.7517-0.31700.6737-0.0779-0.00060.60070.130.7851-34.4803-9.62238.9112
150.08170.11990.52350.07670.50181.6202-0.10520.14390.1798-0.0283-0.13230.2055-0.3116-0.059-00.5029-0.0556-0.03690.51860.06380.6133-28.03699.733524.9856
160.9882-0.5210.62220.64530.130.9376-0.2190.1050.4023-0.7072-0.048-0.5711-0.58140.815900.8696-0.09750.01650.74350.09980.8009-25.100413.375815.5344
170.40330.72760.57490.97710.3291.23790.2161-0.0902-0.22330.2827-0.2598-0.04510.0222-0.1173-00.8036-0.0260.04220.57910.03220.6205-36.07732.163617.8941
180.7229-0.39410.15920.59840.07540.09110.00440.4251-0.7391-0.8178-0.38-0.2890.07790.094800.7154-0.0532-0.03170.6978-0.10540.7156-35.74631.91719.5673
190.94560.53410.30641.09681.10171.0942-0.07110.1498-0.3758-0.41330.2248-0.36330.49810.0549-0.00050.43260.14010.00550.60620.06320.822-25.5583-4.035419.4904
200.5526-0.50810.59251.0882-1.05930.847-0.2380.0526-0.7655-0.6225-0.01270.07230.6180.296300.79350.14850.16860.736-0.02370.8623-24.132-9.431912.1141
210.05740.00780.15550.06560.03460.31910.10091.04540.49040.04220.3764-0.17540.77720.41950.01031.0134-0.18870.43161.3701-0.04011.1766-15.38998.06847.851
220.2270.2265-0.05470.19830.02660.2276-0.61780.4612-0.2440.07050.262-1.55841.24171.38360.00230.81990.05650.11240.851-0.01070.9945-18.9115-4.772711.2758
231.0531-1.10470.65542.25980.72091.90010.1922-0.1622-0.0610.411-0.08030.1046-0.1264-0.2689-00.46080.01780.02290.46-0.01350.4219-50.942619.473317.2164
240.0032-0.1016-0.01920.7977-0.09420.15820.0486-0.1981-0.1865-0.17830.2181-0.15380.11440.240100.5158-0.01640.06690.8234-0.09290.5826-39.260623.393722.905
251.322-0.96750.47870.5491-0.08260.80710.2281-0.3703-0.3319-0.0628-0.0547-0.1233-0.12720.145600.5426-0.0240.04260.4578-0.02040.5112-50.027115.496614.8976
260.0851-0.5335-0.05251.58840.1151-0.02960.37680.16440.1625-0.0247-0.135-0.3038-0.20050.130500.53510.03080.0460.4562-0.01190.4288-45.741525.70655.1895
270.47820.5718-0.68140.7338-0.50480.77760.14840.15840.0627-0.02630.0040.03520.3478-0.616-00.5748-0.0593-0.03850.5115-0.07170.4431-52.728721.19175.1247
280.3543-0.3854-0.0620.38230.01620.1175-0.141-0.55170.3140.7064-0.3161-0.6309-0.3018-0.293300.7262-0.06860.00780.61740.00610.5041-42.815540.527115.786
291.7761-0.7473-0.81231.51540.66450.54650.0297-0.04750.0653-0.0907-0.17260.4922-0.3876-0.2886-00.5749-0.0029-0.01750.5039-0.03720.5164-55.786830.314111.6185
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 56 )B18 - 56
6X-RAY DIFFRACTION6chain 'B' and (resid 57 through 69 )B57 - 69
7X-RAY DIFFRACTION7chain 'B' and (resid 70 through 91 )B70 - 91
8X-RAY DIFFRACTION8chain 'B' and (resid 92 through 123 )B92 - 123
9X-RAY DIFFRACTION9chain 'B' and (resid 124 through 135 )B124 - 135
10X-RAY DIFFRACTION10chain 'B' and (resid 136 through 146 )B136 - 146
11X-RAY DIFFRACTION11chain 'B' and (resid 147 through 171 )B147 - 171
12X-RAY DIFFRACTION12chain 'B' and (resid 172 through 187 )B172 - 187
13X-RAY DIFFRACTION13chain 'C' and (resid 18 through 37 )C18 - 37
14X-RAY DIFFRACTION14chain 'C' and (resid 38 through 51 )C38 - 51
15X-RAY DIFFRACTION15chain 'C' and (resid 52 through 89 )C52 - 89
16X-RAY DIFFRACTION16chain 'C' and (resid 90 through 103 )C90 - 103
17X-RAY DIFFRACTION17chain 'C' and (resid 104 through 143 )C104 - 143
18X-RAY DIFFRACTION18chain 'C' and (resid 144 through 155 )C144 - 155
19X-RAY DIFFRACTION19chain 'C' and (resid 156 through 174 )C156 - 174
20X-RAY DIFFRACTION20chain 'C' and (resid 175 through 214 )C175 - 214
21X-RAY DIFFRACTION21chain 'C' and (resid 215 through 224 )C215 - 224
22X-RAY DIFFRACTION22chain 'C' and (resid 225 through 235 )C225 - 235
23X-RAY DIFFRACTION23chain 'D' and (resid 18 through 44 )D18 - 44
24X-RAY DIFFRACTION24chain 'D' and (resid 45 through 56 )D45 - 56
25X-RAY DIFFRACTION25chain 'D' and (resid 57 through 91 )D57 - 91
26X-RAY DIFFRACTION26chain 'D' and (resid 92 through 122 )D92 - 122
27X-RAY DIFFRACTION27chain 'D' and (resid 123 through 135 )D123 - 135
28X-RAY DIFFRACTION28chain 'D' and (resid 136 through 146 )D136 - 146
29X-RAY DIFFRACTION29chain 'D' and (resid 147 through 187 )D147 - 187

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