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- PDB-3u7d: Crystal structure of the KRIT1/CCM1 FERM domain in complex with t... -

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Basic information

Entry
Database: PDB / ID: 3u7d
TitleCrystal structure of the KRIT1/CCM1 FERM domain in complex with the heart of glass (HEG1) cytoplasmic tail
Components
  • Krev interaction trapped protein 1
  • Protein HEG homolog 1
KeywordsPROTEIN BINDING / PSI-Biology / Assembly / Dynamics and Evolution of Cell-Cell and Cell-Matrix Adhesions / CELLMAT / FERM domain / Rap1 effector / membrane protein cytoplasmic tail / Structural Genomics
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 / protein localization to cell junction / positive regulation of fibroblast growth factor production / GTPase regulator activity / pericardium development ...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 / protein localization to cell junction / positive regulation of fibroblast growth factor production / GTPase regulator activity / pericardium development / endothelium development / cardiac atrium morphogenesis / endothelial cell morphogenesis / lymph vessel development / integrin activation / cell-cell junction organization / ventricular trabecula myocardium morphogenesis / negative regulation of endothelial cell migration / regulation of establishment of cell polarity / negative regulation of Rho protein signal transduction / ventricular septum development / small GTPase-mediated signal transduction / negative regulation of endothelial cell proliferation / vasculogenesis / regulation of angiogenesis / negative regulation of endothelial cell apoptotic process / phosphatidylinositol-4,5-bisphosphate binding / negative regulation of angiogenesis / post-embryonic development / cell redox homeostasis / lung development / multicellular organism growth / cell-cell junction / heart development / microtubule binding / angiogenesis / in utero embryonic development / cytoskeleton / external side of plasma membrane / calcium ion binding / protein-containing complex / extracellular space / extracellular region / plasma membrane / 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 / 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 ...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 / 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. / FERM superfamily, second domain / Aspartic acid and asparagine hydroxylation site. / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / 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 / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ubiquitin-like (UB roll) / PH-like domain superfamily / Roll / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Krev interaction trapped protein 1 / Protein HEG homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsGingras, A.R. / Liu, J.J. / Ginsberg, M.H. / Assembly, Dynamics and Evolution of Cell-Cell and Cell-Matrix Adhesions (CELLMAT)
CitationJournal: J.Cell Biol. / Year: 2012
Title: Structural basis of the junctional anchorage of the cerebral cavernous malformations complex.
Authors: Gingras, A.R. / Liu, J.J. / Ginsberg, M.H.
History
DepositionOct 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Feb 27, 2013Group: Other
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Krev interaction trapped protein 1
B: Protein HEG homolog 1
C: Krev interaction trapped protein 1
D: Protein HEG homolog 1


Theoretical massNumber of molelcules
Total (without water)81,0864
Polymers81,0864
Non-polymers00
Water18010
1
A: Krev interaction trapped protein 1
B: Protein HEG homolog 1


Theoretical massNumber of molelcules
Total (without water)40,5432
Polymers40,5432
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-5 kcal/mol
Surface area15890 Å2
MethodPISA
2
C: Krev interaction trapped protein 1
D: Protein HEG homolog 1


Theoretical massNumber of molelcules
Total (without water)40,5432
Polymers40,5432
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-4 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.050, 76.820, 79.180
Angle α, β, γ (deg.)90.00, 113.62, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThere is two complexes of the KRIT1 FERM domain with the HEG1 cytoplasmic tail in the asymmetric unit.

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Components

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


Mass: 37372.348 Da / Num. of mol.: 2 / Fragment: FERM domain, residues 417-736
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CCM1, Cerebral cavernous malformations 1 protein, Krev interaction trapped protein 1 or CCM1, KRIT1
Plasmid: pLEICS-07 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star / References: UniProt: O00522
#2: Protein/peptide Protein HEG homolog 1


Mass: 3170.456 Da / Num. of mol.: 2 / Fragment: C-terminal cytoplasmic tail, residues 1356-1381 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9ULI3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 10% PEG 4000 and 100mM Citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: Mar/Rayonix 3x3 Mosaic 225 / Detector: CCD / Date: Jun 18, 2010 / Details: Pt coated mirrors
RadiationMonochromator: horizontally diffracting Si (111) monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.49→72.55 Å / Num. all: 26768 / Num. obs: 26420 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 5.3
Reflection shellResolution: 2.49→2.62 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 2.3 / % possible all: 97.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→72.55 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.875 / SU B: 10.816 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30878 1407 5.1 %RANDOM
Rwork0.23354 ---
all0.23745 26768 --
obs0.23745 26420 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.326 Å2
Baniso -1Baniso -2Baniso -3
1-3.01 Å20 Å20.75 Å2
2---1.42 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.49→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5120 0 0 10 5130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225241
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.967077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1335619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.23924.089247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.62415985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3141530
X-RAY DIFFRACTIONr_chiral_restr0.120.2786
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213876
X-RAY DIFFRACTIONr_mcbond_it1.0331.53106
X-RAY DIFFRACTIONr_mcangle_it1.91225036
X-RAY DIFFRACTIONr_scbond_it2.34432135
X-RAY DIFFRACTIONr_scangle_it3.7094.52040
LS refinement shellResolution: 2.49→2.555 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 89 -
Rwork0.296 1934 -
obs--96.47 %

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