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- PDB-4hdq: Crystal Structure of the Ternary Complex of KRIT1 bound to both t... -

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Basic information

Entry
Database: PDB / ID: 4hdq
TitleCrystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and the Heart of Glass (HEG1) cytoplasmic tail
Components
  • Krev interaction trapped protein 1
  • Protein HEG homolog 1
  • Ras-related protein Rap-1b
KeywordsSIGNALING PROTEIN / RA binding motif / GTPase / HEG1 cytoplasmic tail / PTD domain / Rap1 effector / transmembrane protein / Rap1 / HEG1 / Cell-cell junctions / plasma membrane / nucleus
Function / homology
Function and homology information


lymph circulation / cardiac muscle tissue growth / negative regulation of membrane permeability / negative regulation of Rho-dependent protein serine/threonine kinase activity / venous blood vessel morphogenesis / regulation of body fluid levels / Rap protein signal transduction / protein localization to cell junction / positive regulation of fibroblast growth factor production / modification of postsynaptic structure ...lymph circulation / cardiac muscle tissue growth / negative regulation of membrane permeability / negative regulation of Rho-dependent protein serine/threonine kinase activity / venous blood vessel morphogenesis / regulation of body fluid levels / Rap protein signal transduction / protein localization to cell junction / positive regulation of fibroblast growth factor production / modification of postsynaptic structure / GTPase regulator activity / pericardium development / regulation of cell junction assembly / endothelium development / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / cardiac atrium morphogenesis / endothelial cell morphogenesis / lymph vessel development / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / integrin activation / cell-cell junction organization / ventricular trabecula myocardium morphogenesis / Rap1 signalling / negative regulation of endothelial cell migration / establishment of endothelial barrier / regulation of establishment of cell polarity / MET activates RAP1 and RAC1 / negative regulation of Rho protein signal transduction / azurophil granule membrane / ventricular septum development / 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 / vasculogenesis / 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 / Integrin signaling / negative regulation of angiogenesis / post-embryonic development / cell redox homeostasis / small monomeric GTPase / G protein activity / establishment of localization in cell / lung development / Signaling by high-kinase activity BRAF mutants / multicellular organism growth / 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 / heart development / microtubule binding / angiogenesis / in utero embryonic development / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / cytoskeleton / external side of plasma membrane / GTPase activity / glutamatergic synapse / calcium ion binding / Neutrophil degranulation / protein-containing complex binding / GTP binding / protein-containing complex / extracellular space / extracellular exosome / extracellular region / 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) / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein / Calcium-binding EGF domain / 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) / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein / Calcium-binding EGF domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Small GTPase, Ras-type / FERM superfamily, second domain / Aspartic acid and asparagine hydroxylation site. / small GTPase Ras family profile. / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Epidermal growth factor-like domain. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / 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 / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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 / Protein HEG homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,2026
Polymers59,5633
Non-polymers6393
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-22 kcal/mol
Surface area22030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.310, 77.410, 58.570
Angle α, β, γ (deg.)90.00, 95.56, 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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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Protein HEG homolog 1 / HEG1


Mass: 3170.456 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 1356-1381) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9ULI3

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Non-polymers , 4 types, 96 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.17 Å3/Da / Density % sol: 43.34 %
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: I24 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 36963 / Num. obs: 36963 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 20.99
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 3.9 / Num. unique all: 16656 / % possible all: 96.8

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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 4HDO

4hdo


Resolution: 1.95→29.15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.33 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26278 1848 5 %RANDOM
Rwork0.20044 ---
all0.20342 ---
obs0.20342 35112 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.365 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å20.97 Å2
2--1.27 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3877 0 39 93 4009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023996
X-RAY DIFFRACTIONr_bond_other_d0.0010.022721
X-RAY DIFFRACTIONr_angle_refined_deg1.9321.9745401
X-RAY DIFFRACTIONr_angle_other_deg1.03836657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4555478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.75224.815189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.13715740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0531521
X-RAY DIFFRACTIONr_chiral_restr0.1180.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024343
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02786
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 126 -
Rwork0.255 2398 -
obs--93.97 %

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