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- PDB-7opq: Rab27a fusion with Slp2a-RBDa1 effector covalent adduct with CA1 ... -

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Basic information

Entry
Database: PDB / ID: 7opq
TitleRab27a fusion with Slp2a-RBDa1 effector covalent adduct with CA1 in C188
ComponentsSynaptotagmin-like protein 2,Ras-related protein Rab-27A
KeywordsEXOCYTOSIS / GTPase / 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 / Weibel-Palade body / melanosome transport / 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 / Weibel-Palade body / melanosome transport / neurexin family protein binding / exocytic vesicle / melanocyte differentiation / multivesicular body sorting pathway / myosin V binding / RAB geranylgeranylation / melanosome membrane / multivesicular body membrane / RAB GEFs exchange GTP for GDP on RABs / complement-dependent cytotoxicity / vesicle docking involved in exocytosis / synaptic vesicle transport / phosphatidylserine binding / positive regulation of reactive oxygen species biosynthetic process / Insulin processing / antigen processing and presentation / exocytosis / Regulation of MITF-M-dependent genes involved in pigmentation / positive regulation of exocytosis / protein secretion / photoreceptor outer segment / phosphatase binding / positive regulation of phagocytosis / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / secretory granule / small monomeric GTPase / intracellular protein transport / small GTPase binding / specific granule lumen / blood coagulation / GDP binding / late endosome / melanosome / G protein activity / 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 / cytosol / cytoplasm
Similarity search - Function
Synaptotagmin-like 1-5, C2B domain / Rab27a/b / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain / Rab-binding domain profile. / : / small GTPase Rab1 family profile. / Protein kinase C conserved region 2 (CalB) / C2 domain ...Synaptotagmin-like 1-5, C2B domain / Rab27a/b / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain / Rab-binding domain profile. / : / small GTPase Rab1 family profile. / Protein kinase C conserved region 2 (CalB) / C2 domain / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-06D / 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: 2.23 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
Revision 1.2Nov 20, 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

Downloads & links

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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)54,01116
Polymers51,7142
Non-polymers2,29614
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-44 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.710, 76.816, 117.818
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 -35 through -31 or (resid -30...
21(chain B and (resid -35 through -32 or (resid -31...
12chain D
22chain F
13chain I
23chain J
33chain K
43chain M
53chain N
63chain O

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid -35 through -31 or (resid -30...A-35 - -31
121(chain A and (resid -35 through -31 or (resid -30...A-30
131(chain A and (resid -35 through -31 or (resid -30...A-37 - 188
141(chain A and (resid -35 through -31 or (resid -30...A-37 - 188
151(chain A and (resid -35 through -31 or (resid -30...A-37 - 188
161(chain A and (resid -35 through -31 or (resid -30...A-37 - 188
211(chain B and (resid -35 through -32 or (resid -31...B-35 - -32
221(chain B and (resid -35 through -32 or (resid -31...B-31 - -30
231(chain B and (resid -35 through -32 or (resid -31...B-35 - 188
241(chain B and (resid -35 through -32 or (resid -31...B-35 - 188
251(chain B and (resid -35 through -32 or (resid -31...B-35 - 188
261(chain B and (resid -35 through -32 or (resid -31...B-35 - 188
112chain DA204
212chain FB202
113chain IA204
213chain JA205
313chain KA206
413chain MA209 - 901
513chain NB204
613chain OB205

NCS ensembles :
ID
1
2
3

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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,C123S
Source method: isolated from a genetically manipulated source
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, 193 molecules

#2: Chemical ChemComp-06D / 1-[(2~{S})-2-(4-methoxyphenyl)pyrrolidin-1-yl]propan-1-one


Mass: 233.306 Da / Num. of mol.: 2 / Mutation: Q78L, C123S
Source method: isolated from a genetically manipulated source
Formula: C14H19NO2 / Source: (gene. exp.) Homo sapiens (human) / Gene: RAB27A, RAB27 / Production host: Escherichia coli BL21 (bacteria) / Feature type: SUBJECT OF INVESTIGATION / References: small monomeric GTPase
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.7 Å3/Da / Density % sol: 54.42 %
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: May 30, 2017
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.23→36.52 Å / Num. obs: 54026 / % possible obs: 96.86 % / Redundancy: 2 % / Biso Wilson estimate: 41.61 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.03394 / Rpim(I) all: 0.03394 / Rrim(I) all: 0.048 / Net I/σ(I): 13.67
Reflection shellResolution: 2.23→2.31 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3596 / Mean I/σ(I) obs: 2.01 / Num. unique obs: 2005 / CC1/2: 0.76 / CC star: 0.929 / Rpim(I) all: 0.3596 / Rrim(I) all: 0.5086 / % possible all: 72.64

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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: 2.23→36.52 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 1343 4.95 %
Rwork0.177 25809 -
obs0.1794 27152 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.67 Å2 / Biso mean: 46.7312 Å2 / Biso min: 22.81 Å2
Refinement stepCycle: final / Resolution: 2.23→36.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3269 0 160 179 3608
Biso mean--51.7 50.94 -
Num. residues----414
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1220X-RAY DIFFRACTION11.576TORSIONAL
12B1220X-RAY DIFFRACTION11.576TORSIONAL
21A8X-RAY DIFFRACTION11.576TORSIONAL
22B8X-RAY DIFFRACTION11.576TORSIONAL
31A12X-RAY DIFFRACTION11.576TORSIONAL
32A12X-RAY DIFFRACTION11.576TORSIONAL
33A12X-RAY DIFFRACTION11.576TORSIONAL
34A12X-RAY DIFFRACTION11.576TORSIONAL
35B12X-RAY DIFFRACTION11.576TORSIONAL
36B12X-RAY DIFFRACTION11.576TORSIONAL
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 (%)
2.23-2.310.2849990.25381914201373
2.31-2.40.29721370.227526122749100
2.4-2.510.2641380.215226192757100
2.51-2.640.27261350.204326322767100
2.64-2.810.23861320.194226322764100
2.81-3.030.26671410.189726372778100
3.03-3.330.23061410.176226622803100
3.33-3.810.20611360.16182575271196
3.81-4.80.18591340.142326982832100
4.8-37.260.21071500.181828282978100

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