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- PDB-9gvu: Human Rab27A in complex with cyclic peptide IMP-2660 -

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Basic information

Entry
Database: PDB / ID: 9gvu
TitleHuman Rab27A in complex with cyclic peptide IMP-2660
Components
  • Cyclic peptide IMP-2660
  • Ras-related protein Rab-27A
KeywordsEXOCYTOSIS / Macrocyclic peptides / mRNA display / Rab27A / PPI inhibitor
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 / exocytic vesicle / multivesicular body sorting pathway ...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 / exocytic vesicle / multivesicular body sorting pathway / melanocyte differentiation / myosin V binding / RAB geranylgeranylation / melanosome membrane / melanosome transport / multivesicular body membrane / RAB GEFs exchange GTP for GDP on RABs / complement-dependent cytotoxicity / Insulin processing / synaptic vesicle transport / antigen processing and presentation / positive regulation of reactive oxygen species biosynthetic process / exocytosis / Regulation of MITF-M-dependent genes involved in pigmentation / positive regulation of exocytosis / protein secretion / photoreceptor outer segment / positive regulation of phagocytosis / secretory granule / small monomeric GTPase / specific granule lumen / blood coagulation / GDP binding / melanosome / late endosome / 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 / cytosol
Similarity search - Function
Rab27a/b / : / 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-27A
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPetracca, R. / Tersa, M. / De Vita, E. / Morgan, M.R. / Cota, E. / Tate, E.W.
Funding support United Kingdom, European Union, 3items
OrganizationGrant numberCountry
Cancer Research UKC29637/A20781 United Kingdom
Cancer Research UKC29637/A26892 United Kingdom
H2020 Marie Curie Actions of the European Commission797995European Union
CitationJournal: To Be Published
Title: A potent macrocyclic peptide modulator of Rab27a identified by RaPID screening
Authors: Petracca, R. / Tersa, M. / De Vita, E. / Morgan, M.R. / Cota, E. / Tate, E.W.
History
DepositionSep 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-27A
B: Ras-related protein Rab-27A
D: Cyclic peptide IMP-2660
F: Cyclic peptide IMP-2660
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,73022
Polymers45,3474
Non-polymers2,38218
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9760 Å2
ΔGint-55 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.357, 72.714, 91.658
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABDF

#1: Protein Ras-related protein Rab-27A / Rab-27 / GTP-binding protein Ram


Mass: 20953.697 Da / Num. of mol.: 2 / Mutation: Q78L, C123S, C188S
Source method: isolated from a genetically manipulated source
Details: Missing hypervariable C-terminal (193-221) / Source: (gene. exp.) Homo sapiens (human) / Gene: RAB27A, RAB27
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P51159, small monomeric GTPase
#2: Protein/peptide Cyclic peptide IMP-2660


Mass: 1719.987 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)

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Non-polymers , 4 types, 193 molecules

#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.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 0.15 M NH4SO4, 0.1 MES, pH 6.0, 15% PEG 4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.097→56.97 Å / Num. obs: 28187 / % possible obs: 99.6 % / Redundancy: 12.5 % / CC1/2: 0.951 / Net I/σ(I): 4.39
Reflection shellResolution: 2.097→2.172 Å / Num. unique obs: 2727 / CC1/2: 0.821

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→56.97 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 1405 5 %
Rwork0.1865 --
obs0.189 28107 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→56.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2937 0 267 175 3379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083253
X-RAY DIFFRACTIONf_angle_d1.0984394
X-RAY DIFFRACTIONf_dihedral_angle_d18.205704
X-RAY DIFFRACTIONf_chiral_restr0.048449
X-RAY DIFFRACTIONf_plane_restr0.004542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.170.33161170.27052544X-RAY DIFFRACTION97
2.17-2.260.33631250.26122649X-RAY DIFFRACTION100
2.26-2.360.31350.23732643X-RAY DIFFRACTION100
2.36-2.490.30931360.22822647X-RAY DIFFRACTION100
2.49-2.640.28881390.22082644X-RAY DIFFRACTION100
2.64-2.850.29331430.20332673X-RAY DIFFRACTION100
2.85-3.130.23521300.18932681X-RAY DIFFRACTION100
3.13-3.590.21071450.16342691X-RAY DIFFRACTION100
3.59-4.520.19911720.14622691X-RAY DIFFRACTION100
4.52-56.970.20541630.18532839X-RAY DIFFRACTION100

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