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- PDB-4y5o: CCM2 HHD in complex with MEKK3 NPB1 -

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Basic information

Entry
Database: PDB / ID: 4y5o
TitleCCM2 HHD in complex with MEKK3 NPB1
Components
  • Malcavernin
  • Mitogen-activated protein kinase kinase kinase 3
KeywordsTRANSFERASE / Complex / kinase / scaffold
Function / homology
Function and homology information


endothelial cell development / venous blood vessel morphogenesis / positive regulation of cell proliferation in bone marrow / blood vessel endothelial cell differentiation / pericardium development / mitogen-activated protein kinase kinase kinase / endothelium development / endothelial tube morphogenesis / cell-cell junction organization / positive regulation of p38MAPK cascade ...endothelial cell development / venous blood vessel morphogenesis / positive regulation of cell proliferation in bone marrow / blood vessel endothelial cell differentiation / pericardium development / mitogen-activated protein kinase kinase kinase / endothelium development / endothelial tube morphogenesis / cell-cell junction organization / positive regulation of p38MAPK cascade / positive regulation of cell migration involved in sprouting angiogenesis / blood vessel development / negative regulation of cellular senescence / inner ear development / MAP kinase kinase kinase activity / vasculogenesis / regulation of angiogenesis / stress-activated MAPK cascade / integrin-mediated signaling pathway / multicellular organism growth / Interleukin-1 signaling / MAPK cascade / heart development / positive regulation of canonical NF-kappaB signal transduction / in utero embryonic development / protein autophosphorylation / protein kinase activity / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex / mitochondrion / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Cerebral cavernous malformations 2 / Cerebral cavernous malformations 2, harmonin-homology domain / Cerebral cavernous malformation protein, harmonin-homology / Paired amphipathic helix 2 (pah2 repeat) - #20 / Mitogen-activated protein kinase kinase kinase 2/3, PB1 domain / Paired amphipathic helix 2 (pah2 repeat) / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain ...Cerebral cavernous malformations 2 / Cerebral cavernous malformations 2, harmonin-homology domain / Cerebral cavernous malformation protein, harmonin-homology / Paired amphipathic helix 2 (pah2 repeat) - #20 / Mitogen-activated protein kinase kinase kinase 2/3, PB1 domain / Paired amphipathic helix 2 (pah2 repeat) / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Phosphotyrosine interaction domain (PID) profile. / PTB/PI domain / PH-like domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Mitogen-activated protein kinase kinase kinase 3 / Cerebral cavernous malformations 2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsFisher, O.S. / Boggon, T.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM007324 United States
National Science Foundation (NSF, United States) United States
CitationJournal: Nat Commun / Year: 2015
Title: Structure and vascular function of MEKK3-cerebral cavernous malformations 2 complex.
Authors: Fisher, O.S. / Deng, H. / Liu, D. / Zhang, Y. / Wei, R. / Deng, Y. / Zhang, F. / Louvi, A. / Turk, B.E. / Boggon, T.J. / Su, B.
History
DepositionFeb 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Refinement description
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malcavernin
B: Mitogen-activated protein kinase kinase kinase 3


Theoretical massNumber of molelcules
Total (without water)25,8432
Polymers25,8432
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-17 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.310, 45.349, 61.533
Angle α, β, γ (deg.)90.000, 94.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Malcavernin / Cerebral cavernous malformations 2 protein


Mass: 11162.600 Da / Num. of mol.: 1
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 (DE3) / References: UniProt: Q9BSQ5
#2: Protein Mitogen-activated protein kinase kinase kinase 3 / MAPK/ERK kinase kinase 3 / MEKK 3


Mass: 14680.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K3, MAPKKK3, MEKK3 / Plasmid: pCDF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q99759, mitogen-activated protein kinase kinase kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium phosphate and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 10025 / % possible obs: 97.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.115 / Χ2: 1.042 / Net I/av σ(I): 13.256 / Net I/σ(I): 11 / Num. measured all: 57461
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.35-2.435.50.68810091.03698.7
2.43-2.535.60.4610140.94499.1
2.53-2.655.60.3989941.05999.7
2.65-2.795.80.3510021.13399
2.79-2.965.90.22810211.04799
2.96-3.1960.17610131.07698.9
3.19-3.5160.1449961.07397.3
3.51-4.025.30.1179500.97192.7
4.02-5.065.80.07310030.99595.9
5.06-5060.06210231.07195.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
PHASERphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FQN, 2O2V

4fqn

2o2v


Resolution: 2.35→36.811 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2323 463 4.85 %
Rwork0.2075 9092 -
obs0.2087 9555 94.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.49 Å2 / Biso mean: 79.879 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.35→36.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1443 0 0 20 1463
Biso mean---60.69 -
Num. residues----181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071473
X-RAY DIFFRACTIONf_angle_d1.0181987
X-RAY DIFFRACTIONf_chiral_restr0.059229
X-RAY DIFFRACTIONf_plane_restr0.003258
X-RAY DIFFRACTIONf_dihedral_angle_d14.151556
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.690.32141600.24752870303091
2.69-3.38880.28621560.25963120327698
3.3888-36.81530.19771470.18123102324995
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)
15.141-3.036-6.17042.05643.17069.0120.3819-0.51950.43580.53190.5983-0.436-0.3951.3075-1.20240.4793-0.0283-0.08690.8934-0.13120.85116.1405-13.8073-15.6813
23.7589-5.3498-3.34989.34642.96837.5228-0.3281-1.077-0.29960.0436-0.34160.24370.2483-0.25250.80170.48070.0247-0.00620.6819-0.17820.7251.5109-14.9225-19.6581
34.97092.7866-0.23572.93733.22978.670.3063-2.8221-0.33440.9385-0.762-0.25450.6439-0.06870.42850.83640.0215-0.1031.70050.02530.60172.0976-18.7974-8.2265
42.1744-0.85680.50999.22692.91072.20110.322-0.59821.67-0.2567-0.5508-0.2412-0.8636-0.20870.22880.5233-0.1466-0.09110.6666-0.07620.96438.1194-10.4126-23.699
55.7779-0.03740.43585.1657-0.63324.97860.16880.5929-0.2916-0.15170.4394-0.769-0.1480.8904-0.5860.37960.04570.24430.2577-0.13660.6975-7.5301-14.2964-27.4276
69.4362-0.94182.6964.1989-2.66652.7393-0.1117-0.3908-0.373-0.11750.559-0.12450.50780.1452-0.39980.49520.07610.05530.3549-0.11360.4157-15.4595-19.5868-31.6787
75.8891.70581.32838.5474-2.75473.5832-0.0911-0.90740.28380.5121-0.07030.0715-0.21880.07010.12220.35970.04950.00470.4052-0.17220.4807-13.8608-16.2608-23.1072
84.80583.67760.12939.1274-3.13762.6568-0.0808-0.06380.9248-0.9069-0.00270.1376-1.08030.73140.01960.4604-0.0205-0.00410.36980.01090.6068-9.8632-7.5398-32.4448
92.8312-1.66842.2854.4825-4.28034.147-0.2915-1.257-0.63630.56010.3626-0.7862-0.25780.0862-0.16360.51120.05740.00660.460.0290.6766-9.6663-19.5304-20.7945
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 293 through 309 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 310 through 327 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 328 through 370 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 15 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 16 through 51 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 52 through 65 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 66 through 96 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 97 through 115 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 116 through 124 )B0

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