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- PDB-8a4a: Structure of human Rep15 in complex with bovine Rab3C. -

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Basic information

Entry
Database: PDB / ID: 8a4a
TitleStructure of human Rep15 in complex with bovine Rab3C.
Components
  • Rab15 effector protein
  • Ras-related protein Rab-3C
KeywordsENDOCYTOSIS / Rab GTPase
Function / homology
Function and homology information


transferrin transport / receptor recycling / GTP-dependent protein binding / myosin V binding / regulation of exocytosis / vesicle docking involved in exocytosis / antigen processing and presentation / protein secretion / protein localization to plasma membrane / recycling endosome ...transferrin transport / receptor recycling / GTP-dependent protein binding / myosin V binding / regulation of exocytosis / vesicle docking involved in exocytosis / antigen processing and presentation / protein secretion / protein localization to plasma membrane / recycling endosome / synaptic vesicle / early endosome membrane / endosome membrane / endosome / intracellular membrane-bounded organelle / GTPase activity / GTP binding / perinuclear region of cytoplasm / plasma membrane
Similarity search - Function
Rab15 effector / Rab15 effector / Rab3 / small GTPase Rab1 family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-3C / Rab15 effector protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 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-3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4714
Polymers52,9242
Non-polymers5472
Water72140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.290, 108.795, 172.027
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

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Components

#1: Protein Rab15 effector protein


Mass: 26800.125 Da / Num. of mol.: 1
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-3C / SMG P25C


Mass: 26124.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: RAB3C / Production host: Escherichia coli (E. coli) / References: UniProt: P10949
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES pH 6.0 10% w/v PEG 6000

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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: 2.52→45.97 Å / Num. obs: 18879 / % possible obs: 99.21 % / Redundancy: 13.3 % / Biso Wilson estimate: 58.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1095 / Rpim(I) all: 0.03114 / Rrim(I) all: 0.112 / Net I/σ(I): 18.83
Reflection shellResolution: 2.52→2.61 Å / Redundancy: 13.2 % / Rmerge(I) obs: 1.365 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 1827 / CC1/2: 0.713 / CC star: 0.913 / Rpim(I) all: 0.3864 / % possible all: 99.19

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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: 3RAB

3rab


Resolution: 2.52→45.97 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2544 941 5.01 %
Rwork0.2069 17860 -
obs0.2093 18801 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.11 Å2 / Biso mean: 74.0698 Å2 / Biso min: 39.21 Å2
Refinement stepCycle: final / Resolution: 2.52→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3058 0 33 40 3131
Biso mean--51.36 63.62 -
Num. residues----379
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.52-2.650.36981300.3112504263499
2.65-2.820.24511310.266124952626100
2.82-3.040.31851340.249825402674100
3.04-3.340.24761340.213525362670100
3.34-3.820.30171330.21632510264398
3.83-4.820.20071360.17152579271599
4.82-45.970.24511430.195126962839100
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)
10.92690.6138-0.25970.5752-0.02851.24130.0738-0.9583-0.37050.25580.6199-0.12640.34780.01590.00040.78990.0714-0.0990.60110.04360.385932.44837.753780.9012
20.0017-0.02580.0090.15610.06950.0404-0.31650.2944-0.3531-0.42170.30250.3237-0.13570.160900.6761-0.0555-0.03940.62580.09640.593616.841858.854669.2761
30.99380.2538-1.38920.8627-0.09841.99580.0079-0.1279-0.00720.11990.0594-0.3795-0.05870.1684-00.4310.0006-0.09140.4275-0.0250.471135.890739.367468.9618
40.7906-0.23470.44980.0288-0.12080.2741-0.11590.63350.7253-0.44950.5817-0.42550.66460.1067-00.7388-0.1584-0.0350.8525-0.07810.983724.374943.758250.2589
51.11331.16230.29951.8162-0.33540.93290.00150.2624-0.35130.0646-0.07530.28280.3282-0.4493-00.4797-0.0364-0.02070.6292-0.05020.446924.211735.124464.4221
61.46450.8976-1.07331.5718-0.23881.09420.12870.1826-0.21390.4572-0.10060.62610.2736-0.905500.623-0.07490.00520.77940.05030.671917.480729.865969.6756
70.34740.1219-0.29290.1636-0.18720.25310.36840.081-0.64350.338-0.3087-0.35410.3104-0.1197-00.7657-0.0812-0.00130.7270.07790.713425.543524.832772.8344
82.65050.4741-0.890.29960.19190.84640.02760.16450.41190.1069-0.03940.0561-0.2362-0.259400.4360.0578-0.01850.4499-0.03860.512843.840146.400345.9733
90.07970.0667-0.1470.374-0.05820.2674-0.32680.0899-0.22320.2204-0.1672-0.4910.14740.626-00.5834-0.03030.02390.5251-0.02920.726840.894730.514453.3885
100.7010.4082-0.05090.9360.70830.7784-0.0225-0.1358-0.61230.2131-0.0184-0.01890.2985-0.079100.5016-0.01610.02110.4516-0.09990.671850.472931.589345.2907
111.9047-1.6166-0.59252.2967-0.62212.34790.08750.5133-0.0147-0.1368-0.0158-0.4478-0.03620.253300.46070.02240.01320.4616-0.0770.648758.669338.130143.1037
120.47990.0578-0.32750.21730.03350.2506-0.08140.7390.7213-0.3241-0.1122-0.0362-0.32840.315800.6640.00250.00170.76590.05860.541648.238545.024432.9893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 37 )A15 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 51 )A38 - 51
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 113 )A52 - 113
4X-RAY DIFFRACTION4chain 'A' and (resid 114 through 143 )A114 - 143
5X-RAY DIFFRACTION5chain 'A' and (resid 144 through 174 )A144 - 174
6X-RAY DIFFRACTION6chain 'A' and (resid 175 through 217 )A175 - 217
7X-RAY DIFFRACTION7chain 'A' and (resid 218 through 235 )A218 - 235
8X-RAY DIFFRACTION8chain 'B' and (resid 26 through 86 )B26 - 86
9X-RAY DIFFRACTION9chain 'B' and (resid 87 through 99 )B87 - 99
10X-RAY DIFFRACTION10chain 'B' and (resid 100 through 131 )B100 - 131
11X-RAY DIFFRACTION11chain 'B' and (resid 132 through 179 )B132 - 179
12X-RAY DIFFRACTION12chain 'B' and (resid 180 through 197 )B180 - 197

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