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- PDB-9pvg: Co-crystal structure of two CCM2 PTB domains bound to a KRIT1 pep... -

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Basic information

Entry
Database: PDB / ID: 9pvg
TitleCo-crystal structure of two CCM2 PTB domains bound to a KRIT1 peptide encompassing NPxF2 and NPxF3
Components
  • Krev interaction trapped protein 1
  • Malcavernin
KeywordsSIGNALING PROTEIN / PTB domain / NPxY / NPxF / Cerebral Cavernous Malformations / CCM / protein-protein
Function / homology
Function and homology information


endothelial cell development / venous blood vessel morphogenesis / pericardium development / blood vessel endothelial cell differentiation / GTPase regulator activity / endothelium development / endothelial tube morphogenesis / integrin activation / cell-cell junction organization / negative regulation of endothelial cell migration ...endothelial cell development / venous blood vessel morphogenesis / pericardium development / blood vessel endothelial cell differentiation / GTPase regulator activity / endothelium development / endothelial tube morphogenesis / integrin activation / cell-cell junction organization / negative regulation of endothelial cell migration / regulation of establishment of cell polarity / small GTPase-mediated signal transduction / negative regulation of endothelial cell proliferation / inner ear development / regulation of angiogenesis / negative regulation of endothelial cell apoptotic process / vasculogenesis / stress-activated MAPK cascade / phosphatidylinositol-4,5-bisphosphate binding / cell redox homeostasis / negative regulation of angiogenesis / integrin-mediated signaling pathway / multicellular organism growth / cell-cell junction / heart development / angiogenesis / microtubule binding / in utero embryonic development / cytoskeleton / protein-containing complex / mitochondrion / extracellular space / plasma membrane / cytoplasm
Similarity search - Function
Cerebral cavernous malformations 2 / Cerebral cavernous malformations 2, harmonin-homology domain / Cerebral cavernous malformation protein, harmonin-homology / 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 ankyrin-repeats domain ...Cerebral cavernous malformations 2 / Cerebral cavernous malformations 2, harmonin-homology domain / Cerebral cavernous malformation protein, harmonin-homology / 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 ankyrin-repeats domain / KRIT1/FRMD8, FERM domain C-lobe / Phosphotyrosine interaction domain (PID) profile. / PTB/PI domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Krev interaction trapped protein 1 / Cerebral cavernous malformations 2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFisher, O.S. / Boggon, T.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS134606 United States
American Heart Association961309 United States
CitationJournal: To Be Published
Title: Co-crystal structure of two CCM2 PTB domains bound to a KRIT1 peptide encompassing NPxF2 and NPxF3
Authors: Fisher, O.S. / Boggon, T.J.
History
DepositionAug 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malcavernin
B: Malcavernin
C: Malcavernin
E: Krev interaction trapped protein 1
F: Krev interaction trapped protein 1
D: Malcavernin


Theoretical massNumber of molelcules
Total (without water)84,7986
Polymers84,7986
Non-polymers00
Water00
1
A: Malcavernin
E: Krev interaction trapped protein 1
D: Malcavernin


Theoretical massNumber of molelcules
Total (without water)42,3993
Polymers42,3993
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-17 kcal/mol
Surface area14580 Å2
MethodPISA
2
B: Malcavernin
C: Malcavernin
F: Krev interaction trapped protein 1


Theoretical massNumber of molelcules
Total (without water)42,3993
Polymers42,3993
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-16 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.198, 120.441, 67.778
Angle α, β, γ (deg.)90.00, 102.73, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17E
27F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEPHEPHEAA63 - 21715 - 169
21ILEILEPHEPHEBB63 - 21715 - 169
12ASPASPGLNGLNAA61 - 21813 - 170
22ASPASPGLNGLNCC61 - 21813 - 170
13ASPASPGLNGLNAA61 - 21813 - 170
23ASPASPGLNGLNDF61 - 21813 - 170
14ILEILEPHEPHEBB63 - 21715 - 169
24ILEILEPHEPHECC63 - 21715 - 169
15ILEILEPHEPHEBB63 - 21715 - 169
25ILEILEPHEPHEDF63 - 21715 - 169
16PROPROTHRTHRCC55 - 2227 - 174
26PROPROTHRTHRDF55 - 2227 - 174
17THRTHRGLYGLYED227 - 2541 - 28
27THRTHRGLYGLYFE227 - 2541 - 28

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

#1: Protein
Malcavernin / Cerebral cavernous malformations 2 protein


Mass: 19523.039 Da / Num. of mol.: 4 / Fragment: PTB domain (UNP residues 51-228)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCM2, C7orf22, PP10187 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BSQ5
#2: Protein/peptide Krev interaction trapped protein 1 / Krev interaction trapped 1 / Cerebral cavernous malformations 1 protein


Mass: 3352.813 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O00522
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 42.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M TrisHCl pH 7, 20% PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2014
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 14580 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rpim(I) all: 0.135 / Net I/σ(I): 6.2
Reflection shellResolution: 3→3.11 Å / Num. unique obs: 743 / Rpim(I) all: 0.843

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.889 / SU B: 42.451 / SU ML: 0.685 / Cross valid method: THROUGHOUT / ESU R Free: 0.53 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29668 743 5.3 %RANDOM
Rwork0.24702 ---
obs0.24972 13397 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 86.628 Å2
Baniso -1Baniso -2Baniso -3
1-12.98 Å20 Å2-1.51 Å2
2---7.29 Å20 Å2
3----4.54 Å2
Refinement stepCycle: 1 / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4573 0 0 0 4573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194656
X-RAY DIFFRACTIONr_bond_other_d0.0060.024531
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9646330
X-RAY DIFFRACTIONr_angle_other_deg1.268310396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8795574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.13924.498209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44715782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5321524
X-RAY DIFFRACTIONr_chiral_restr0.0720.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025202
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021026
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.5818.3022326
X-RAY DIFFRACTIONr_mcbond_other5.5698.3022325
X-RAY DIFFRACTIONr_mcangle_it8.87512.442890
X-RAY DIFFRACTIONr_mcangle_other8.87612.4412891
X-RAY DIFFRACTIONr_scbond_it6.0249.1132330
X-RAY DIFFRACTIONr_scbond_other6.0219.112328
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.85513.3813440
X-RAY DIFFRACTIONr_long_range_B_refined15.64879.22118007
X-RAY DIFFRACTIONr_long_range_B_other15.64879.22418008
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A70430.12
12B70430.12
21A71570.14
22C71570.14
31A70970.15
32D70970.15
41B69590.14
42C69590.14
51B69030.15
52D69030.15
61C78710.15
62D78710.15
71E11670.12
72F11670.12
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 57 -
Rwork0.347 970 -
obs--98.85 %

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