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- PDB-4wj7: CCM2 PTB domain in complex with KRIT1 NPxY/F3 -

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Basic information

Entry
Database: PDB / ID: 4wj7
TitleCCM2 PTB domain in complex with KRIT1 NPxY/F3
Components
  • KRIT1 NPxY/F3
  • Malcavernin
KeywordsPROTEIN BINDING / Complex / PTB domain / NPxY motif
Function / homology
Function and homology information


endothelial cell development / venous blood vessel morphogenesis / pericardium development / blood vessel endothelial cell differentiation / endothelial tube morphogenesis / endothelium development / cell-cell junction organization / inner ear development / regulation of angiogenesis / vasculogenesis ...endothelial cell development / venous blood vessel morphogenesis / pericardium development / blood vessel endothelial cell differentiation / endothelial tube morphogenesis / endothelium development / cell-cell junction organization / inner ear development / regulation of angiogenesis / vasculogenesis / stress-activated MAPK cascade / integrin-mediated signaling pathway / multicellular organism growth / heart development / in utero embryonic development / protein-containing complex / mitochondrion / cytoplasm
Similarity search - Function
Cerebral cavernous malformations 2 / Cerebral cavernous malformations 2, harmonin-homology domain / Cerebral cavernous malformation protein, harmonin-homology / Phosphotyrosine interaction domain (PID) profile. / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Cerebral cavernous malformations 2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.753 Å
AuthorsFisher, O.S. / Liu, W. / Zhang, R. / Stiegler, A.L. / Boggon, T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS085078 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for the Disruption of the Cerebral Cavernous Malformations 2 (CCM2) Interaction with Krev Interaction Trapped 1 (KRIT1) by Disease-associated Mutations.
Authors: Fisher, O.S. / Liu, W. / Zhang, R. / Stiegler, A.L. / Ghedia, S. / Weber, J.L. / Boggon, T.J.
History
DepositionSep 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.pdbx_ordinal / _struct_keywords.text
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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
D: Malcavernin
W: KRIT1 NPxY/F3
X: KRIT1 NPxY/F3
Y: KRIT1 NPxY/F3
Z: KRIT1 NPxY/F3


Theoretical massNumber of molelcules
Total (without water)83,7798
Polymers83,7798
Non-polymers00
Water18010
1
A: Malcavernin
W: KRIT1 NPxY/F3


Theoretical massNumber of molelcules
Total (without water)20,9452
Polymers20,9452
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-10 kcal/mol
Surface area7880 Å2
MethodPISA
2
B: Malcavernin
X: KRIT1 NPxY/F3


Theoretical massNumber of molelcules
Total (without water)20,9452
Polymers20,9452
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-11 kcal/mol
Surface area8040 Å2
MethodPISA
3
C: Malcavernin
Y: KRIT1 NPxY/F3


Theoretical massNumber of molelcules
Total (without water)20,9452
Polymers20,9452
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-8 kcal/mol
Surface area7710 Å2
MethodPISA
4
D: Malcavernin
Z: KRIT1 NPxY/F3


Theoretical massNumber of molelcules
Total (without water)20,9452
Polymers20,9452
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-8 kcal/mol
Surface area7320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.938, 110.938, 315.255
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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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 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9BSQ5
#2: Protein/peptide
KRIT1 NPxY/F3


Mass: 1421.660 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / 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: 3.37 Å3/Da / Density % sol: 63.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% (w/v) PEG 6000, 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 30768 / % possible obs: 100 % / Redundancy: 17.9 % / Biso Wilson estimate: 93.7 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.07 / Net I/σ(I): 23
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 19 % / Mean I/σ(I) obs: 1.21 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble search model of PDB IDs: 4JIF, 3SO6, 3G9W, 3HQC, 3DXE, 2EJ8, 2V76, 1J0W, 1WVH, 2CY4, 2DYQ, 1QQG, 1X11, and 1AQC

4jif

3so6

3g9w

3hqc

3dxe

2ej8

2v76

1j0w

1wvh

2cy4

2dyq

1qqg

1x11

1aqc


Resolution: 2.753→29.669 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 1809 6.51 %Random
Rwork0.2198 25967 --
obs0.2218 27776 90.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 244.97 Å2 / Biso mean: 102.7045 Å2 / Biso min: 45.2 Å2
Refinement stepCycle: final / Resolution: 2.753→29.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4418 0 0 10 4428
Biso mean---69.16 -
Num. residues----566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044496
X-RAY DIFFRACTIONf_angle_d0.8686110
X-RAY DIFFRACTIONf_chiral_restr0.046731
X-RAY DIFFRACTIONf_plane_restr0.003772
X-RAY DIFFRACTIONf_dihedral_angle_d12.6921617
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.753-2.82690.44511060.36061424153066
2.8269-2.91010.35661010.34731552165371
2.9101-3.00390.36881110.34711651176277
3.0039-3.11120.37041210.31591729185081
3.1112-3.23560.31851440.28121983212792
3.2356-3.38260.27181460.25012083222996
3.3826-3.56070.25281520.22792171232399
3.5607-3.78340.25031480.22052156230499
3.7834-4.07480.2511500.20512132228296
4.0748-4.48360.20471500.16612166231698
4.4836-5.12950.181520.16132224237699
5.1295-6.45170.25911590.23122772436100
6.4517-29.67090.24011690.21582419258899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.09231.25062.75336.02550.30943.75380.4224-0.0169-0.2614-0.32630.1301-0.037-0.06970.2918-0.41610.62090.09280.09080.8026-0.09510.443831.625663.1281178.856
24.7571.35761.6338.69121.9376.47470.0852-0.80430.6590.4704-0.1899-0.338-1.05490.49150.14250.8506-0.04680.06170.7624-0.17090.555932.459375.3627190.798
39.16012.52842.00187.57334.20016.81460.62340.61.26060.0678-0.4233-0.894-1.4742-0.04480.13541.1511-0.00280.20960.87160.06990.62230.143373.5944172.9655
47.95272.16290.49493.26742.85696.947-0.97813.07970.9231-2.27260.5612-0.0075-0.6339-0.6319-0.21680.9416-0.05930.21261.1611-0.20180.429935.039867.9983169.4008
53.86660.773-0.53544.9123-1.99435.8703-0.0812-0.4666-0.00420.1461-0.04580.1397-0.29220.29390.01630.4957-0.0140.05330.7319-0.21490.367931.093465.0053182.0305
67.57080.118-0.84814.97030.17865.5788-0.2141-0.4395-0.4018-0.132-0.0473-0.12160.3139-0.37530.290.5542-0.03960.1060.7437-0.1150.392129.374560.6244180.1096
76.59833.40271.54558.88484.61013.27070.07820.853-0.1189-1.3322-0.3692-0.2747-0.2424-0.5340.02360.80020.14740.11910.93160.0740.430148.158758.8475147.0628
85.52520.0146-2.41658.15520.78677.84720.1972-0.61580.59120.2521-0.00020.2172-0.9449-0.0868-0.05790.5328-0.08440.14880.7827-0.02540.488748.796163.1208160.1507
95.6688-1.46562.23052.9427-2.33191.9595-0.69312.34780.5368-0.7372-0.0540.9945-2.5814-1.03810.77471.49540.0720.03781.23110.14020.615750.39164.7634143.0079
106.4065-1.4417-1.62334.9080.68455.65510.1966-0.17020.043-0.1403-0.31650.00490.00880.2620.17140.488-0.01880.13670.7986-0.03330.378450.373854.7718154.6196
114.98910.11261.82122.1803-1.35376.2797-0.28930.52990.2764-0.76660.2586-0.1442-0.57740.39270.24390.82620.0217-0.03840.91220.12650.665316.08274.0318147.5862
120.685-0.1020.45231.2874-0.05890.4980.2393-0.6477-0.83610.57970.27540.9394-0.5784-1.3846-0.62021.0056-0.164-0.08931.0916-0.00150.7185.620761.3654160.3661
132.8938-1.53221.66119.5506-1.69066.48350.44830.295-0.1972-1.1615-0.6865-0.00590.1390.70990.00370.67420.0745-0.04290.90890.01240.494416.465260.4304149.216
146.9407-3.3085-1.92965.18240.830.5337-0.34690.5064-0.1704-0.6662-0.56220.1092-1.693-1.18681.04121.29090.2449-0.10780.7430.10180.589110.187177.877146.6882
156.0364-6.4963-5.89477.01076.32035.75091.96452.69490.3009-2.0857-0.5175-0.8196-1.46840.00190.68371.5421-0.0105-0.01951.50910.40710.990517.202674.8149136.1138
167.28550.52120.09424.8657-3.13755.36630.4961-0.15060.5740.2275-0.4159-0.012-0.9067-0.3351-0.07610.68870.1245-0.12930.7173-0.08120.5879.973571.7336153.4695
172.32813.0966-1.62539.10040.53168.05040.3453-0.3759-0.45310.0722-0.2543-0.1243-0.3054-0.28450.21650.68970.1315-0.0360.67390.0790.397412.221164.5958155.4741
188.2997-5.80131.2546.833-0.40617.3169-0.0018-0.05361.3340.612-0.1592-1.2099-1.73740.0927-0.0310.9204-0.1264-0.04640.5661-0.0260.622216.42174.4726157.0206
192.1032-1.10310.05285.25393.0646.0025-1.0928-1.8016-0.97590.30230.967-0.2880.40230.40810.1041.6030.5532-0.07511.21720.18811.154526.676150.7119132.3023
206.7392-2.2501-4.99983.63210.0989.3771-0.18430.7109-0.70960.896-0.10221.85260.5839-1.80770.19571.67660.1139-0.061.16220.16141.029110.908753.6001124.0002
213.0954-3.09520.39354.45372.64726.588-0.109-1.5214-0.01971.36850.07590.7944-0.4502-1.6699-0.75331.62930.18220.16681.22290.05140.887119.752562.7836132.4585
226.8825-0.4134-3.21753.84690.57354.1952-0.6181-1.8733-0.6527-0.3330.3-0.03131.52072.1340.04452.26030.5874-0.29681.870.29321.431129.109348.4859137.3298
234.6287-0.96090.00927.8374-2.15074.38740.3802-0.1366-0.8092-0.0291-0.1809-0.15681.71750.6691-0.32861.79870.49450.02441.05280.10741.083322.854446.5772126.4942
249.7468-2.72222.05262.44520.46167.74791.09951.9741-0.5115-0.2182-1.10640.1084-0.2913-0.3385-0.07880.6211-0.0170.14950.53180.00480.403929.4255.02185.4908
255.1171-6.0408-4.53248.15595.05634.36730.07820.9435-0.8001-0.0256-0.30430.25050.3435-0.29650.0620.5650.09690.08370.72190.18060.429654.46347.7003158.3362
266.57222.27293.11645.27781.79089.1420.8939-0.20872.1657-0.0224-1.196-0.5119-1.97950.52490.73971.0505-0.19990.16230.98450.01040.48339.544972.603163.5324
272.19772.7342-0.26847.6641-1.01795.53710.16460.2005-3.87210.1037-1.7821-1.68691.60730.97450.40521.98630.0718-0.1110.905-0.15271.485718.313139.4499121.1728
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 55 through 84 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 106 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 115 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 129 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 130 through 157 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 158 through 221 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 60 through 73 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 74 through 118 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 119 through 129 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 130 through 221 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 61 through 73 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 74 through 84 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 85 through 115 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 116 through 124 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 125 through 129 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 130 through 146 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 147 through 193 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 194 through 220 )C0
19X-RAY DIFFRACTION19chain 'D' and (resid 63 through 73 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 74 through 97 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 98 through 106 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 107 through 129 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 130 through 217 )D0
24X-RAY DIFFRACTION24chain 'W' and (resid 244 through 254 )W0
25X-RAY DIFFRACTION25chain 'X' and (resid 244 through 255 )X0
26X-RAY DIFFRACTION26chain 'Y' and (resid 244 through 254 )Y0
27X-RAY DIFFRACTION27chain 'Z' and (resid 244 through 254 )Z0

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