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- PDB-7opp: Crystal structure of the Rab27a fusion with Slp2a-RBDa1 effector ... -

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Basic information

Entry
Database: PDB / ID: 7opp
TitleCrystal structure of the Rab27a fusion with Slp2a-RBDa1 effector for SF4 pocket drug targeting
ComponentsSynaptotagmin-like protein 2,Ras-related protein Rab-27A
KeywordsEXOCYTOSIS / Rab27 / GTPase / Slp2a / exosome
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 / 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) / C2 domain ...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
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

Downloads & links

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Assembly

Deposited unit
A: Synaptotagmin-like protein 2,Ras-related protein Rab-27A
C: Synaptotagmin-like protein 2,Ras-related protein Rab-27A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0056
Polymers51,9122
Non-polymers1,0934
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-43 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.710, 117.710, 115.670
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid -37 through -31 or (resid -30...A-37 - -10
121(chain 'A' and (resid -37 through -31 or (resid -30...A6 - 33
131(chain 'A' and (resid -37 through -31 or (resid -30...A36 - 55
141(chain 'A' and (resid -37 through -31 or (resid -30...A65 - 88
151(chain 'A' and (resid -37 through -31 or (resid -30...A91 - 102
161(chain 'A' and (resid -37 through -31 or (resid -30...A105 - 109
171(chain 'A' and (resid -37 through -31 or (resid -30...A112 - 114
181(chain 'A' and (resid -37 through -31 or (resid -30...A119 - 187
211(chain 'C' and (resid -37 through -9 or resid 5...C-37 - -10
221(chain 'C' and (resid -37 through -9 or resid 5...C6 - 33
231(chain 'C' and (resid -37 through -9 or resid 5...C36 - 55
241(chain 'C' and (resid -37 through -9 or resid 5...C65 - 88
251(chain 'C' and (resid -37 through -9 or resid 5...C91 - 102
261(chain 'C' and (resid -37 through -9 or resid 5...C105 - 109
271(chain 'C' and (resid -37 through -9 or resid 5...C112 - 114
281(chain 'C' and (resid -37 through -9 or resid 5...C119 - 187
192chain 'D'D194
292chain 'E'E194

NCS ensembles :
ID
1
2

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Components

#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: 25956.184 Da / Num. of mol.: 2 / Mutation: Q78L,C123S,C188S
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
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 4.47 Å3/Da / Density % sol: 72.51 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.5 M Sodium phosphate monobasic monohydrate, 0.1 M Sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.32→58.85 Å / Num. obs: 40486 / % possible obs: 99.96 % / Redundancy: 2 % / Biso Wilson estimate: 36.64 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02731 / Rpim(I) all: 0.02731 / Rrim(I) all: 0.03862 / Net I/σ(I): 20.04
Reflection shellResolution: 2.32→2.403 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2401 / Mean I/σ(I) obs: 3.29 / Num. unique obs: 3976 / CC1/2: 0.844 / CC star: 0.957 / Rpim(I) all: 0.2401 / Rrim(I) all: 0.3395 / % possible all: 99.95

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Processing

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

3bc1


Resolution: 2.32→58.85 Å / SU ML: 0.227 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.4598
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1945 4.8 %1945
Rwork0.1615 38539 --
obs0.1634 40484 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.05 Å2
Refinement stepCycle: LAST / Resolution: 2.32→58.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 66 382 3767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00743510
X-RAY DIFFRACTIONf_angle_d0.874751
X-RAY DIFFRACTIONf_chiral_restr0.0489522
X-RAY DIFFRACTIONf_plane_restr0.0045605
X-RAY DIFFRACTIONf_dihedral_angle_d22.9499478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.380.27821670.21792666X-RAY DIFFRACTION99.93
2.38-2.440.27441370.20262719X-RAY DIFFRACTION100
2.44-2.510.25741460.18582716X-RAY DIFFRACTION100
2.51-2.60.20931380.16662709X-RAY DIFFRACTION100
2.6-2.690.21431480.16712716X-RAY DIFFRACTION100
2.69-2.80.251200.18232783X-RAY DIFFRACTION99.97
2.8-2.920.27721400.19092698X-RAY DIFFRACTION99.96
2.92-3.080.20721360.17392760X-RAY DIFFRACTION100
3.08-3.270.20971120.17112754X-RAY DIFFRACTION99.9
3.27-3.520.20211330.15822764X-RAY DIFFRACTION100
3.52-3.880.17241580.14112729X-RAY DIFFRACTION100
3.88-4.440.16321170.12962813X-RAY DIFFRACTION100
4.44-5.590.16871650.1452775X-RAY DIFFRACTION100

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