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- PDB-6uzk: Crystal Structure of the Ternary Complex of KRIT1 bound to both t... -

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Basic information

Entry
Database: PDB / ID: 6uzk
TitleCrystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi6
Components
  • Krev interaction trapped protein 1
  • Ras-related protein Rap-1b
KeywordsCELL ADHESION / Complex / Small molecules / GTPase / KRIT1
Function / homology
Function and homology information


Rap protein signal transduction / modification of postsynaptic structure / GTPase regulator activity / regulation of cell junction assembly / endothelium development / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / integrin activation ...Rap protein signal transduction / modification of postsynaptic structure / GTPase regulator activity / regulation of cell junction assembly / endothelium development / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / integrin activation / Rap1 signalling / negative regulation of endothelial cell migration / establishment of endothelial barrier / regulation of establishment of cell polarity / MET activates RAP1 and RAC1 / azurophil granule membrane / small GTPase-mediated signal transduction / negative regulation of endothelial cell proliferation / p130Cas linkage to MAPK signaling for integrins / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of angiogenesis / negative regulation of endothelial cell apoptotic process / cellular response to cAMP / phosphatidylinositol-4,5-bisphosphate binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / negative regulation of angiogenesis / Integrin signaling / cell redox homeostasis / small monomeric GTPase / G protein activity / establishment of localization in cell / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / GDP binding / 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 / cell-cell junction / Signaling by BRAF and RAF1 fusions / 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 / Small GTPase, Ras-type ...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 / Small GTPase, Ras-type / FERM superfamily, second domain / small GTPase Ras family profile. / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / 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 / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / 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 / 2-hydroxy-6-methoxynaphthalene-1-carbaldehyde / Krev interaction trapped protein 1 / Ras-related protein Rap-1b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.924 Å
AuthorsGingras, A.R.
Funding support United States, 2items
OrganizationGrant numberCountry
Other governmentMRP-17-454909 United States
Other governmentDE-AC02-05CH11231 United States
CitationJournal: Faseb Bioadv / Year: 2021
Title: Inhibition of the HEG1-KRIT1 interaction increases KLF4 and KLF2 expression in endothelial cells.
Authors: Lopez-Ramirez, M.A. / McCurdy, S. / Li, W. / Haynes, M.K. / Hale, P. / Francisco, K. / Oukoloff, K. / Bautista, M. / Choi, C.H.J. / Sun, H. / Gongol, B. / Shyy, J.Y. / Ballatore, C. / Sklar, L.A. / Gingras, A.R.
History
DepositionNov 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)57,1425
Polymers56,3932
Non-polymers7493
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.204, 77.089, 58.410
Angle α, β, γ (deg.)90.000, 91.558, 90.000
Int Tables number4
Space group name H-MP1211

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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: 37372.348 Da / Num. of mol.: 1
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

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Non-polymers , 4 types, 78 molecules

#3: Chemical ChemComp-QMA / 2-hydroxy-6-methoxynaphthalene-1-carbaldehyde


Mass: 202.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O3 / 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 / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20-25% PEG 3,350, 100 mM Tris, pH 8.5, 100 mM KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.999995 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 36147 / % possible obs: 94 % / Redundancy: 3 % / CC1/2: 0.991 / Net I/σ(I): 16.33
Reflection shellResolution: 1.92→1.95 Å / Num. unique obs: 1384 / CC1/2: 0.486

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4hdo

4hdo


Resolution: 1.924→36.514 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.579 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / ESU R: 0.203 / ESU R Free: 0.194
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2861 1772 4.905 %
Rwork0.2201 --
all0.223 --
obs-36123 93.712 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.081 Å2
Baniso -1Baniso -2Baniso -3
1--0.834 Å20 Å22.847 Å2
2---1.463 Å20 Å2
3---2.139 Å2
Refinement stepCycle: LAST / Resolution: 1.924→36.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 48 75 3932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0123942
X-RAY DIFFRACTIONr_angle_refined_deg1.0691.6375331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0565470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31523.349209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.0115733
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4721521
X-RAY DIFFRACTIONr_chiral_restr0.0840.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022949
X-RAY DIFFRACTIONr_nbd_refined0.2160.21790
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22670
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2182
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1830.23
X-RAY DIFFRACTIONr_mcbond_it1.7774.7031880
X-RAY DIFFRACTIONr_mcangle_it3.3097.0422344
X-RAY DIFFRACTIONr_scbond_it1.5394.9162062
X-RAY DIFFRACTIONr_scangle_it2.7687.2822985
X-RAY DIFFRACTIONr_lrange_it6.19762.4725967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.924-1.9740.3781480.3191888X-RAY DIFFRACTION72.173
1.974-2.0280.3441020.3112203X-RAY DIFFRACTION83.123
2.028-2.0870.3331200.3122261X-RAY DIFFRACTION88.4144
2.087-2.1510.355980.3022270X-RAY DIFFRACTION91.2524
2.151-2.2210.295960.3122231X-RAY DIFFRACTION92.5617
2.221-2.2990.3351350.3092179X-RAY DIFFRACTION93.6842
2.299-2.3860.3381180.2632134X-RAY DIFFRACTION95.5452
2.386-2.4830.3421250.2672114X-RAY DIFFRACTION97.6024
2.483-2.5930.3331200.2612049X-RAY DIFFRACTION99.0411
2.593-2.7190.3291020.2611943X-RAY DIFFRACTION98.7923
2.719-2.8660.299840.251893X-RAY DIFFRACTION99.0481
2.866-3.040.31870.2491785X-RAY DIFFRACTION99.3631
3.04-3.2490.3331060.241666X-RAY DIFFRACTION99.5506
3.249-3.5080.253790.2091568X-RAY DIFFRACTION99.5166
3.508-3.8420.217620.1841461X-RAY DIFFRACTION99.1536
3.842-4.2930.223590.1731301X-RAY DIFFRACTION99.6337
4.293-4.9520.233450.1661171X-RAY DIFFRACTION99.5905
4.952-6.0550.265270.1881016X-RAY DIFFRACTION100
6.055-8.5170.278500.178764X-RAY DIFFRACTION100

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