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- PDB-6oq4: Crystal Structure of the Ternary Complex of KRIT1 bound to both t... -

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Basic information

Entry
Database: PDB / ID: 6oq4
TitleCrystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi1
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 / GTPase regulator activity / regulation of cell junction assembly / endothelium development / modification of postsynaptic structure / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / calcium-ion regulated exocytosis / negative regulation of synaptic vesicle exocytosis / integrin activation ...Rap protein signal transduction / GTPase regulator activity / regulation of cell junction assembly / endothelium development / modification of postsynaptic structure / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / calcium-ion regulated exocytosis / negative regulation of synaptic vesicle exocytosis / integrin activation / Rap1 signalling / establishment of endothelial barrier / MET activates RAP1 and RAC1 / negative regulation of endothelial cell migration / regulation of establishment of cell polarity / 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 / cellular response to cAMP / lipid droplet / phosphatidylinositol-4,5-bisphosphate binding / Integrin signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cell redox homeostasis / negative regulation of angiogenesis / small monomeric GTPase / establishment of localization in cell / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / 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 / G protein activity / microtubule binding / angiogenesis / cytoskeleton / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / GTPase activity / Neutrophil degranulation / protein-containing complex binding / GTP binding / glutamatergic synapse / 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 / KRIT1/FRMD8, FERM domain C-lobe / Ras-related protein Rap1 / Ankyrin repeats (many copies) / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein ...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 / KRIT1/FRMD8, FERM domain C-lobe / Ras-related protein Rap1 / Ankyrin repeats (many copies) / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH-domain like / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / 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 / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / PH-like domain superfamily / Roll / P-loop containing nucleotide triphosphate hydrolases / Roll / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Chem-N0G / Krev interaction trapped protein 1 / Ras-related protein Rap-1b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.754 Å
AuthorsGingras, A.R.
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. / Sun, H. / Gongol, B. / Shyy, J.Y. / Ballatore, C. / Sklar, L.A. / Gingras, A.R.
History
DepositionApr 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)57,3345
Polymers56,3932
Non-polymers9413
Water2,522140
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)57.350, 77.410, 58.620
Angle α, β, γ (deg.)90.000, 91.640, 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 / 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) / Variant (production host): Star / 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 (E. coli) / References: UniProt: P61224

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Non-polymers , 4 types, 143 molecules

#3: Chemical ChemComp-N0G / 2-{(Z)-[(2-hydroxynaphthalen-1-yl)methylidene]amino}-N-[(1S)-1-phenylethyl]benzamide / Sirtinol


Mass: 394.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H22N2O2 / 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
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / 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: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.75→58.6 Å / Num. obs: 51111 / % possible obs: 99.5 % / Redundancy: 4.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Net I/σ(I): 17.84
Reflection shellResolution: 1.75→1.86 Å / Rmerge(I) obs: 0.911 / Num. unique obs: 8192 / CC1/2: 0.773

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.754→58.596 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.264 / WRfactor Rwork: 0.225 / SU B: 4.23 / SU ML: 0.128 / Average fsc free: 0.8295 / Average fsc work: 0.8393 / Cross valid method: FREE R-VALUE / ESU R: 0.143 / ESU R Free: 0.136
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.264 2555 5.001 %
Rwork0.2268 48536 -
all0.229 --
obs-51091 99.498 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.448 Å2
Baniso -1Baniso -2Baniso -3
1--0.042 Å20 Å20.028 Å2
2--0.037 Å20 Å2
3---0.003 Å2
Refinement stepCycle: LAST / Resolution: 1.754→58.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3839 0 63 140 4042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133984
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173718
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.6445386
X-RAY DIFFRACTIONr_angle_other_deg1.1531.5768641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5795472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73623.286210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70215738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.121521
X-RAY DIFFRACTIONr_chiral_restr0.0430.2509
X-RAY DIFFRACTIONr_chiral_restr_other0.070.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024351
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02806
X-RAY DIFFRACTIONr_nbd_refined0.1820.2672
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.23354
X-RAY DIFFRACTIONr_nbtor_refined0.1530.21880
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21634
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2174
X-RAY DIFFRACTIONr_metal_ion_refined0.020.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2130.28
X-RAY DIFFRACTIONr_nbd_other0.1520.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.280.21
X-RAY DIFFRACTIONr_mcbond_it1.514.0361894
X-RAY DIFFRACTIONr_mcbond_other1.5074.0361893
X-RAY DIFFRACTIONr_mcangle_it2.6586.0412361
X-RAY DIFFRACTIONr_mcangle_other2.6586.0412362
X-RAY DIFFRACTIONr_scbond_it1.3734.2852090
X-RAY DIFFRACTIONr_scbond_other1.3734.2872091
X-RAY DIFFRACTIONr_scangle_it2.3726.3353024
X-RAY DIFFRACTIONr_scangle_other2.3726.3363025
X-RAY DIFFRACTIONr_lrange_it4.51345.9994339
X-RAY DIFFRACTIONr_lrange_other4.45545.8964316
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.754-1.80.4171890.38835860.3938150.4960.49998.95150.335
1.8-1.8490.3721820.35534720.35636790.6320.63199.32050.299
1.849-1.9020.3271770.31933590.31935550.7590.75699.46550.272
1.902-1.9610.3211730.29832840.29934740.8050.81299.51070.252
1.961-2.0250.2891690.2832050.2833870.8430.85799.61620.235
2.025-2.0960.3041630.27630970.27832700.8690.86899.69420.237
2.096-2.1750.3011560.26629720.26831360.8740.88299.74490.23
2.175-2.2640.3021520.25228870.25430480.8720.89299.70470.22
2.264-2.3640.2781450.23127470.23328980.9010.91799.7930.198
2.364-2.4790.3041390.24726410.2527920.8840.90899.57020.216
2.479-2.6130.2371310.23725030.23726470.9190.9299.50890.209
2.613-2.7710.2821270.2523970.25225280.8950.90999.84180.226
2.771-2.9620.2771160.24922160.25123450.8920.90699.44560.235
2.962-3.1990.3091100.23620810.2421990.8690.90399.63620.235
3.199-3.5030.2691000.21819020.22120170.9060.9299.25630.227
3.503-3.9150.222920.19517490.19618560.9320.94399.19180.213
3.915-4.5170.21810.18115310.18216240.9460.95499.26110.207
4.517-5.5240.218680.18212970.18313720.9520.95999.48980.22
5.524-7.7780.273530.21810200.2210780.9290.94299.53620.25
7.778-58.5960.206320.1785900.1796290.9530.96798.88710.217

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