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- PDB-8t7v: Co-crystal structure of KRIT1 with a 1-hydroxy 2-naphthaldehyde d... -

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Basic information

Entry
Database: PDB / ID: 8t7v
TitleCo-crystal structure of KRIT1 with a 1-hydroxy 2-naphthaldehyde derivative (6-(furan-2-yl)-2-hydroxy-1-naphthaldehyde)
Components
  • Krev interaction trapped protein 1
  • Ras-related protein Rap-1b
KeywordsCELL ADHESION / Complex / Inhibitor
Function / homology
Function and homology information


Rap protein signal transduction / GTPase regulator activity / modification of postsynaptic structure / regulation of cell junction assembly / endothelium development / positive regulation of integrin activation / negative regulation of calcium ion-dependent exocytosis / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / integrin activation ...Rap protein signal transduction / GTPase regulator activity / modification of postsynaptic structure / regulation of cell junction assembly / endothelium development / positive regulation of integrin activation / negative regulation of calcium ion-dependent exocytosis / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / integrin activation / Rap1 signalling / establishment of endothelial barrier / MET activates RAP1 and RAC1 / regulation of establishment of cell polarity / negative regulation of endothelial cell migration / azurophil granule membrane / small GTPase-mediated signal transduction / p130Cas linkage to MAPK signaling for integrins / negative regulation of endothelial cell proliferation / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of angiogenesis / negative regulation of endothelial cell apoptotic process / phosphatidylinositol-4,5-bisphosphate binding / cellular response to cAMP / Integrin signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of angiogenesis / cell redox homeostasis / lipid droplet / small monomeric GTPase / establishment of localization in cell / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / G protein activity / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / GDP binding / Signaling by BRAF and RAF1 fusions / cell-cell junction / microtubule binding / angiogenesis / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / cytoskeleton / GTPase activity / glutamatergic synapse / Neutrophil degranulation / protein-containing complex binding / GTP binding / protein-containing complex / extracellular space / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
KRIT, N-terminal NPxY motif-rich region / Krev interaction trapped protein 1, FERM domain C-lobe / KRIT, N-terminal NPxY motif-rich domain superfamily / : / NUDIX, or N-terminal NPxY motif-rich, region of KRIT / Ras-related protein Rap1 / Ankyrin repeats (many copies) / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain ...KRIT, N-terminal NPxY motif-rich region / Krev interaction trapped protein 1, FERM domain C-lobe / KRIT, N-terminal NPxY motif-rich domain superfamily / : / NUDIX, or N-terminal NPxY motif-rich, region of KRIT / Ras-related protein Rap1 / Ankyrin repeats (many copies) / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / Small GTPase, Ras-type / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / small GTPase Ras family 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 / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Rab subfamily of small GTPases / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Chem-ZTA / Krev interaction trapped protein 1 / Ras-related protein Rap-1b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBruystens, J.G.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM130389 United States
CitationJournal: Acs Pharmacol Transl Sci / Year: 2023
Title: Targeted Reversible Covalent Modification of a Noncatalytic Lysine of the Krev Interaction Trapped 1 Protein Enables Site-Directed Screening for Protein-Protein Interaction Inhibitors.
Authors: Francisco, K.R. / Bruystens, J. / Varricchio, C. / McCurdy, S. / Wu, J. / Lopez-Ramirez, M.A. / Ginsberg, M. / Caffrey, C.R. / Brancale, A. / Gingras, A.R. / Hixon, M.S. / Ballatore, C.
History
DepositionJun 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Krev interaction trapped protein 1
B: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0495
Polymers56,2652
Non-polymers7853
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.546, 77.805, 58.827
Angle α, β, γ (deg.)90.000, 92.194, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Krev interaction trapped protein 1 / Krev interaction trapped 1 / Cerebral cavernous malformations 1 protein


Mass: 37244.219 Da / Num. of mol.: 1 / Fragment: FERM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRIT1, CCM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00522
#2: Protein Ras-related protein Rap-1b / GTP-binding protein smg p21B


Mass: 19020.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAP1B, OK/SW-cl.11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61224, small monomeric GTPase

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Non-polymers , 4 types, 29 molecules

#3: Chemical ChemComp-ZTA / (7M)-7-(furan-2-yl)-2-hydroxynaphthalene-1-carbaldehyde


Mass: 238.238 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 20% PEG 3350, 100mM Tris, pH 8.5, 100mM KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.2→58.79 Å / Num. obs: 24783 / % possible obs: 90.93 % / Redundancy: 3.1 % / Biso Wilson estimate: 39.57 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.58
Reflection shellResolution: 2.25→2.29 Å / Rmerge(I) obs: 0.514 / Num. unique obs: 644

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→46.24 Å / SU ML: 0.3171 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.0628
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2502 1096 4.87 %
Rwork0.2021 21412 -
obs0.2045 22508 90.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.75 Å2
Refinement stepCycle: LAST / Resolution: 2.25→46.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 50 26 3910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023993
X-RAY DIFFRACTIONf_angle_d0.48825410
X-RAY DIFFRACTIONf_chiral_restr0.0394601
X-RAY DIFFRACTIONf_plane_restr0.0036683
X-RAY DIFFRACTIONf_dihedral_angle_d5.3115530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.350.3514680.29951717X-RAY DIFFRACTION58.18
2.35-2.470.35811150.27882248X-RAY DIFFRACTION76.35
2.47-2.630.331410.25952724X-RAY DIFFRACTION93.44
2.63-2.830.32011550.25692899X-RAY DIFFRACTION99.38
2.83-3.120.271520.24532954X-RAY DIFFRACTION99.84
3.12-3.570.3091320.21292953X-RAY DIFFRACTION99.84
3.57-4.490.23811320.16842972X-RAY DIFFRACTION99.58
4.5-46.240.19232010.16552945X-RAY DIFFRACTION99.59

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