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- PDB-7opr: Rab27a fusion with Slp2a-RBDa1 effector covalent adduct with CB1 ... -

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Basic information

Entry
Database: PDB / ID: 7opr
TitleRab27a fusion with Slp2a-RBDa1 effector covalent adduct with CB1 in C123
ComponentsSynaptotagmin-like protein 2,Ras-related protein Rab-27A
KeywordsEXOCYTOSIS / GTPase / Exosome / Acrylamide / Cysteine-reactive
Function / homology
Function and homology information


multivesicular body organization / cytotoxic T cell degranulation / positive regulation of constitutive secretory pathway / positive regulation of regulated secretory pathway / melanosome localization / natural killer cell degranulation / exosomal secretion / melanosome transport / Weibel-Palade body / neurexin family protein binding ...multivesicular body organization / cytotoxic T cell degranulation / positive regulation of constitutive secretory pathway / positive regulation of regulated secretory pathway / melanosome localization / natural killer cell degranulation / exosomal secretion / melanosome transport / Weibel-Palade body / neurexin family protein binding / exocytic vesicle / melanocyte differentiation / melanosome membrane / multivesicular body sorting pathway / RAB geranylgeranylation / myosin V binding / multivesicular body membrane / RAB GEFs exchange GTP for GDP on RABs / Regulation of MITF-M-dependent genes involved in pigmentation / complement-dependent cytotoxicity / vesicle docking involved in exocytosis / positive regulation of reactive oxygen species biosynthetic process / synaptic vesicle transport / Insulin processing / phosphatidylserine binding / exocytosis / positive regulation of exocytosis / antigen processing and presentation / protein secretion / photoreceptor outer segment / phosphatase binding / positive regulation of phagocytosis / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / small monomeric GTPase / G protein activity / secretory granule / intracellular protein transport / small GTPase binding / specific granule lumen / GDP binding / blood coagulation / melanosome / late endosome / lysosome / apical plasma membrane / protein domain specific binding / GTPase activity / dendrite / Neutrophil degranulation / positive regulation of gene expression / GTP binding / Golgi apparatus / extracellular exosome / extracellular region / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Synaptotagmin-like 1-5, C2B domain / Rab27a/b / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / : / small GTPase Rab1 family profile. / C2 domain / Protein kinase C conserved region 2 (CalB) ...Synaptotagmin-like 1-5, C2B domain / Rab27a/b / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / : / small GTPase Rab1 family profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / C2 domain superfamily / 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
Chem-05Y / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-27A / Synaptotagmin-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsJamshidiha, M. / Tersa, M. / Lanyon-Hogg, T. / Perez-Dorado, I. / Sutherell, C.L. / De Vita, E. / Morgan, R.M.L. / Tate, E.W. / Cota, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC29637/A20781 United Kingdom
CitationJournal: Rsc Med Chem / Year: 2022
Title: Identification of the first structurally validated covalent ligands of the small GTPase RAB27A.
Authors: Jamshidiha, M. / Lanyon-Hogg, T. / Sutherell, C.L. / Craven, G.B. / Tersa, M. / De Vita, E. / Brustur, D. / Perez-Dorado, I. / Hassan, S. / Petracca, R. / Morgan, R.M. / Sanz-Hernandez, M. / ...Authors: Jamshidiha, M. / Lanyon-Hogg, T. / Sutherell, C.L. / Craven, G.B. / Tersa, M. / De Vita, E. / Brustur, D. / Perez-Dorado, I. / Hassan, S. / Petracca, R. / Morgan, R.M. / Sanz-Hernandez, M. / Norman, J.C. / Armstrong, A. / Mann, D.J. / Cota, E. / Tate, E.W.
History
DepositionJun 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 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: Synaptotagmin-like protein 2,Ras-related protein Rab-27A
B: Synaptotagmin-like protein 2,Ras-related protein Rab-27A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,22517
Polymers51,7142
Non-polymers2,51115
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-47 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.385, 76.663, 118.243
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -37 through -32 or (resid -31...
21(chain B and (resid -37 through 34 or resid 36...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid -37 through -32 or (resid -31...A-37 - -32
121(chain A and (resid -37 through -32 or (resid -31...A-31
131(chain A and (resid -37 through -32 or (resid -31...A-37 - 188
141(chain A and (resid -37 through -32 or (resid -31...A-37 - 188
151(chain A and (resid -37 through -32 or (resid -31...A-37 - 188
161(chain A and (resid -37 through -32 or (resid -31...A-37 - 188
211(chain B and (resid -37 through 34 or resid 36...B-37 - 34
221(chain B and (resid -37 through 34 or resid 36...B36 - 49
231(chain B and (resid -37 through 34 or resid 36...B51 - 89
241(chain B and (resid -37 through 34 or resid 36...B91 - 110
251(chain B and (resid -37 through 34 or resid 36...B119 - 138
261(chain B and (resid -37 through 34 or resid 36...B140 - 188
271(chain B and (resid -37 through 34 or resid 36...B194 - 501

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Synaptotagmin-like protein 2,Ras-related protein Rab-27A / Breast cancer-associated antigen SGA-72M / Exophilin-4 / Rab-27 / GTP-binding protein Ram


Mass: 25857.162 Da / Num. of mol.: 2 / Mutation: Q78L,C188S
Source method: isolated from a genetically manipulated source
Details: The ligand CB1 is covalently bound to cysteine123. I have modelled the ligand CB1 already covalently bound to Cys123 into the peptide chain, for this reason there is a mismatch in the ...Details: The ligand CB1 is covalently bound to cysteine123. I have modelled the ligand CB1 already covalently bound to Cys123 into the peptide chain, for this reason there is a mismatch in the sequence. I am not sure how to fix this mismatch. I hope this information is clear.,The ligand CB1 is covalently bound to cysteine123. I have modelled the ligand CB1 already covalently bound to Cys123 into the peptide chain, for this reason there is a mismatch in the sequence. I am not sure how to fix this mismatch. I hope this information is clear.
Source: (gene. exp.) Homo sapiens (human) / Gene: SYTL2, KIAA1597, SGA72M, SLP2, SLP2A, RAB27A, RAB27 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q9HCH5, UniProt: P51159, small monomeric GTPase

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Non-polymers , 5 types, 263 molecules

#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-05Y / ~{N}-[1-(2-pyridin-2-ylethyl)benzimidazol-2-yl]propanamide


Mass: 294.351 Da / Num. of mol.: 2 / Mutation: Q78L, C188S
Source method: isolated from a genetically manipulated source
Formula: C17H18N4O
Details: The ligand CB1 is covalently bound to cysteine123. I have modelled the ligand CB1 already covalently bound to Cys123 into the peptide chain, for this reason there is a mismatch in the ...Details: The ligand CB1 is covalently bound to cysteine123. I have modelled the ligand CB1 already covalently bound to Cys123 into the peptide chain, for this reason there is a mismatch in the sequence. I am not sure how to fix this mismatch. I hope this information is clear.
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB27A, RAB27 / Production host: Escherichia coli BL21 (bacteria) / Feature type: SUBJECT OF INVESTIGATION / References: small monomeric GTPase
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.15M Ammonium sulphate, 0.1M MES pH 6.0, 15% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.32→64.33 Å / Num. obs: 49537 / % possible obs: 99.82 % / Redundancy: 2 % / Biso Wilson estimate: 32.9 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.05896 / Rpim(I) all: 0.05896 / Rrim(I) all: 0.08338 / Net I/σ(I): 9.77
Reflection shellResolution: 2.32→2.403 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3254 / Mean I/σ(I) obs: 2.23 / Num. unique obs: 4902 / CC1/2: 0.832 / CC star: 0.953 / Rpim(I) all: 0.3254 / Rrim(I) all: 0.4602 / % possible all: 99.67

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
xia2data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BC1

3bc1


Resolution: 2.32→64.33 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2549 1212 4.87 %
Rwork0.1827 23673 -
obs0.1862 24885 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.06 Å2 / Biso mean: 36.1718 Å2 / Biso min: 11.48 Å2
Refinement stepCycle: final / Resolution: 2.32→64.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3422 0 120 248 3790
Biso mean--33.11 38.51 -
Num. residues----426
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1194X-RAY DIFFRACTION7.069TORSIONAL
12B1194X-RAY DIFFRACTION7.069TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.32-2.410.27861280.21012580100
2.41-2.520.30861410.2212599100
2.52-2.650.34091270.21712590100
2.65-2.820.26231440.19912582100
2.82-3.040.2911310.19972603100
3.04-3.340.31571320.18552633100
3.34-3.830.23711400.17282642100
3.83-4.820.19091240.14592662100
4.82-5.50.23391450.1884278299

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