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- PDB-3peg: Crystal structure of Neurofibromins Sec14-PH module containing a ... -

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Basic information

Entry
Database: PDB / ID: 3peg
TitleCrystal structure of Neurofibromins Sec14-PH module containing a patient derived duplication (TD)
ComponentsNeurofibromin
KeywordsLIPID BINDING PROTEIN / Sec14 domain / pleckstrin homology domain / PH domain / Phosphatidylethanolamin Binding / Lipid Binding
Function / homology
Function and homology information


positive regulation of mast cell apoptotic process / negative regulation of Rac protein signal transduction / regulation of glial cell differentiation / observational learning / Schwann cell migration / negative regulation of Schwann cell migration / vascular associated smooth muscle cell migration / amygdala development / negative regulation of mast cell proliferation / gamma-aminobutyric acid secretion, neurotransmission ...positive regulation of mast cell apoptotic process / negative regulation of Rac protein signal transduction / regulation of glial cell differentiation / observational learning / Schwann cell migration / negative regulation of Schwann cell migration / vascular associated smooth muscle cell migration / amygdala development / negative regulation of mast cell proliferation / gamma-aminobutyric acid secretion, neurotransmission / mast cell apoptotic process / Schwann cell proliferation / vascular associated smooth muscle cell proliferation / mast cell proliferation / glutamate secretion, neurotransmission / negative regulation of Schwann cell proliferation / negative regulation of leukocyte migration / negative regulation of neurotransmitter secretion / negative regulation of vascular associated smooth muscle cell migration / positive regulation of adenylate cyclase activity / forebrain morphogenesis / hair follicle maturation / regulation of cell-matrix adhesion / regulation of blood vessel endothelial cell migration / smooth muscle tissue development / camera-type eye morphogenesis / cell communication / negative regulation of oligodendrocyte differentiation / peripheral nervous system development / sympathetic nervous system development / myeloid leukocyte migration / myelination in peripheral nervous system / phosphatidylcholine binding / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / metanephros development / negative regulation of Ras protein signal transduction / phosphatidylethanolamine binding / regulation of bone resorption / collagen fibril organization / regulation of long-term synaptic potentiation / neural tube development / endothelial cell proliferation / forebrain astrocyte development / artery morphogenesis / pigmentation / regulation of postsynapse organization / negative regulation of neuroblast proliferation / negative regulation of protein import into nucleus / regulation of synaptic transmission, GABAergic / adrenal gland development / negative regulation of cell-matrix adhesion / regulation of GTPase activity / spinal cord development / Rac protein signal transduction / negative regulation of osteoclast differentiation / negative regulation of endothelial cell proliferation / oligodendrocyte differentiation / RAS signaling downstream of NF1 loss-of-function variants / negative regulation of astrocyte differentiation / extrinsic apoptotic signaling pathway via death domain receptors / neuroblast proliferation / negative regulation of MAPK cascade / regulation of angiogenesis / Schwann cell development / negative regulation of stem cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of fibroblast proliferation / negative regulation of MAP kinase activity / positive regulation of vascular associated smooth muscle cell proliferation / skeletal muscle tissue development / positive regulation of endothelial cell proliferation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of ERK1 and ERK2 cascade / GTPase activator activity / extracellular matrix organization / negative regulation of angiogenesis / osteoclast differentiation / liver development / positive regulation of GTPase activity / negative regulation of cell migration / stem cell proliferation / long-term synaptic potentiation / negative regulation of protein kinase activity / wound healing / regulation of long-term neuronal synaptic plasticity / brain development / visual learning / cerebral cortex development / cognition / osteoblast differentiation / Regulation of RAS by GAPs / protein import into nucleus / positive regulation of neuron apoptotic process / MAPK cascade / heart development / presynapse / cellular response to heat / actin cytoskeleton organization / fibroblast proliferation / regulation of gene expression
Similarity search - Function
Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / : / PH domain-like / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases ...Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / : / PH domain-like / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Rho GTPase activation protein / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Armadillo-type fold / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-PEV / Neurofibromin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.524 Å
AuthorsWelti, S. / Kuen, S. / D'Angelo, I. / Scheffzek, K.
CitationJournal: Hum.Mutat. / Year: 2011
Title: Structural and biochemical consequences of NF1 associated nontruncating mutations in the Sec14-PH module of neurofibromin.
Authors: Welti, S. / Kuhn, S. / D'Angelo, I. / Brugger, B. / Kaufmann, D. / Scheffzek, K.
History
DepositionOct 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software / Item: _software.classification
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neurofibromin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3398
Polymers33,1151
Non-polymers1,2257
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Neurofibromin
hetero molecules

A: Neurofibromin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,67916
Polymers66,2302
Non-polymers2,44914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+2/31
Buried area6850 Å2
ΔGint-199 kcal/mol
Surface area24790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.600, 104.600, 116.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Neurofibromin / Neurofibromatosis-related protein NF-1 / Neurofibromin truncated


Mass: 33114.852 Da / Num. of mol.: 1 / Mutation: insertion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P21359
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PEV / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLETHANOLAMINE / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 720.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H78NO8P / Comment: POPE, phospholipid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF RESIDUES 1699D-1712D CORRESPOND TO AN INSERTION BETWEEN RESIDUES 1712 AND 1713 OF ...THE SEQUENCE OF RESIDUES 1699D-1712D CORRESPOND TO AN INSERTION BETWEEN RESIDUES 1712 AND 1713 OF THE NATIVE PROTEIN. THIS INSERTION IS NEARLY A DUPLICATION OF RESIDUES 1699-1712 OF THE NATIVE PROTEIN WITH ONLY THE FIRST RESIDUE GLY BEING DIFFERENT FROM THE CORRESPONDING GLU 1699.

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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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05M HEPES, 39% PEG 400, 0.2M (NH4)2SO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC / Detector: CCD / Date: Sep 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.52→19.57 Å / Num. all: 13236 / Num. obs: 12507 / % possible obs: 94.5 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.52→2.67 Å / % possible all: 75.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.2_432)refinement
CNSrefinement
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.524→19.57 Å / SU ML: 0.22 / σ(F): 1.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 626 5.01 %5% of reflections
Rwork0.2233 ---
obs0.2254 12502 --
all-13236 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.499 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0878 Å2-0 Å2-0 Å2
2--0.0878 Å2-0 Å2
3----0.1755 Å2
Refinement stepCycle: LAST / Resolution: 2.524→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 73 15 2051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032077
X-RAY DIFFRACTIONf_angle_d0.6132809
X-RAY DIFFRACTIONf_dihedral_angle_d13.845765
X-RAY DIFFRACTIONf_chiral_restr0.042312
X-RAY DIFFRACTIONf_plane_restr0.002342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.524-2.77760.34731360.29732584X-RAY DIFFRACTION85
2.7776-3.17810.30281590.25793006X-RAY DIFFRACTION98
3.1781-3.99840.27851600.22613057X-RAY DIFFRACTION98
3.9984-19.57030.23621710.2033229X-RAY DIFFRACTION99
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)
11.3620.09720.6672.8745-1.2010.9549-0.04860.23340.0275-0.0407-0.11270.10380.16610.14520.09750.39290.0079-0.03910.4165-0.00540.355378.0958-9.510925.141
21.52850.58730.81150.34150.4651.8268-0.56320.508-0.377-0.47650.05380.3462-0.499-0.36320.29450.5526-0.0544-0.18590.5835-0.13810.463175.89612.573519.7403
30.566-0.53890.07720.9748-0.67570.8930.01540.1398-0.2170.37940.0733-0.2331-0.39780.2131-0.11430.5011-0.0509-0.06220.34430.01670.521671.626212.759128.3455
40.88820.1424-0.15692.1255-1.14220.8655-0.0468-0.16670.06640.8790.24980.643-0.6245-0.1465-0.26830.60470.05490.14740.4402-0.01450.542757.95514.729431.2336
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1566:1683)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 1684:1709D)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 1710D:1765)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 1766:1816)

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