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- PDB-4hdo: Crystal structure of the binary Complex of KRIT1 bound to the Rap... -

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Basic information

Entry
Database: PDB / ID: 4hdo
TitleCrystal structure of the binary Complex of KRIT1 bound to the Rap1 GTPase
Components
  • Krev interaction trapped protein 1
  • Ras-related protein Rap-1b
KeywordsSIGNALING PROTEIN / RA binding motif / PTB fold / GTPase / GTP / Rap effector / Rap1 / HEG1 / Cell-cell junctions / nucleus
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 domain 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 / Krev interaction trapped protein 1 / Ras-related protein Rap-1b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsGingras, A.R.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The Structure of the Ternary Complex of Krev Interaction Trapped 1 (KRIT1) Bound to Both the Rap1 GTPase and the Heart of Glass (HEG1) Cytoplasmic Tail.
Authors: Gingras, A.R. / Puzon-McLaughlin, W. / Ginsberg, M.H.
History
DepositionOct 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Sep 4, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)57,0315
Polymers56,3932
Non-polymers6393
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.850, 77.750, 58.850
Angle α, β, γ (deg.)90.00, 91.20, 90.00
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 / KRIT1 / Krev interaction trapped 1 / Cerebral cavernous malformations 1 protein


Mass: 37372.348 Da / Num. of mol.: 1 / Fragment: FERM domain (UNP residues 417-736)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRIT1, CCM1 / Plasmid: pLEICS-07 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: O00522
#2: Protein Ras-related protein Rap-1b / Rap1B / GTP-binding protein smg p21B


Mass: 19020.508 Da / Num. of mol.: 1 / Fragment: UNP residues 1-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAP1B, OK/SW-cl.11 / Plasmid: pTAC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P61224

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Non-polymers , 4 types, 271 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 268 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15% PEG2000 MME, 100 mM Tris, 100 mM potassium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. all: 57913 / Num. obs: 57913 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 31.27
Reflection shellResolution: 1.67→1.77 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.37 / Num. unique all: 21549 / % possible all: 80

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Processing

Software
NameVersionClassification
dlsbeamline softwaredata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C1Y

1c1y


Resolution: 1.67→32.43 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.1 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23142 2896 5 %RANDOM
Rwork0.21153 ---
all0.21253 ---
obs0.21253 55017 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.771 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20.32 Å2
2--0.62 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.67→32.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3830 0 39 268 4137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.023976
X-RAY DIFFRACTIONr_bond_other_d0.0010.022718
X-RAY DIFFRACTIONr_angle_refined_deg1.0061.9745379
X-RAY DIFFRACTIONr_angle_other_deg0.76836653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6665479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02224.817191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61915744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3671522
X-RAY DIFFRACTIONr_chiral_restr0.0560.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024326
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02780
LS refinement shellResolution: 1.67→1.715 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 161 -
Rwork0.28 3061 -
obs--73.26 %

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