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- PDB-2d4q: Crystal structure of the Sec-PH domain of the human neurofibromat... -

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Basic information

Entry
Database: PDB / ID: 2d4q
TitleCrystal structure of the Sec-PH domain of the human neurofibromatosis type 1 protein
ComponentsNeurofibromin
KeywordsSIGNALING PROTEIN / CRAL_TRIO / PH / TRITON x-100 / BETA HAIRPIN / Sec14
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 / gamma-aminobutyric acid secretion, neurotransmission / observational learning / Schwann cell migration / negative regulation of Schwann cell migration / vascular associated smooth muscle cell migration / amygdala development / mast cell apoptotic process ...positive regulation of mast cell apoptotic process / negative regulation of Rac protein signal transduction / regulation of glial cell differentiation / gamma-aminobutyric acid secretion, neurotransmission / observational learning / Schwann cell migration / negative regulation of Schwann cell migration / vascular associated smooth muscle cell migration / amygdala development / mast cell apoptotic process / negative regulation of mast cell proliferation / 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 vascular associated smooth muscle cell migration / positive regulation of adenylate cyclase activity / forebrain morphogenesis / regulation of cell-matrix adhesion / negative regulation of neurotransmitter secretion / hair follicle maturation / regulation of blood vessel endothelial cell migration / cell communication / camera-type eye morphogenesis / smooth muscle tissue development / negative regulation of oligodendrocyte differentiation / myelination in peripheral nervous system / sympathetic nervous system development / phosphatidylcholine binding / myeloid leukocyte migration / phosphatidylethanolamine binding / peripheral nervous system development / metanephros development / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / endothelial cell proliferation / artery morphogenesis / collagen fibril organization / regulation of bone resorption / regulation of long-term synaptic potentiation / neural tube development / regulation of postsynapse organization / forebrain astrocyte development / pigmentation / negative regulation of neuroblast proliferation / regulation of synaptic transmission, GABAergic / adrenal gland development / negative regulation of protein import into nucleus / negative regulation of cell-matrix adhesion / spinal cord development / regulation of GTPase activity / negative regulation of endothelial cell proliferation / negative regulation of MAPK cascade / Rac protein signal transduction / oligodendrocyte differentiation / negative regulation of osteoclast differentiation / RAS signaling downstream of NF1 loss-of-function variants / negative regulation of astrocyte differentiation / neuroblast proliferation / extrinsic apoptotic signaling pathway via death domain receptors / regulation of angiogenesis / Schwann cell development / skeletal muscle tissue development / negative regulation of fibroblast proliferation / negative regulation of stem cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of endothelial cell proliferation / GTPase activator activity / extracellular matrix organization / negative regulation of angiogenesis / osteoclast differentiation / regulation of ERK1 and ERK2 cascade / negative regulation of MAP kinase activity / negative regulation of cell migration / liver development / phosphatidylinositol 3-kinase/protein kinase B signal transduction / long-term synaptic potentiation / stem cell proliferation / regulation of long-term neuronal synaptic plasticity / brain development / negative regulation of protein kinase activity / visual learning / wound healing / cerebral cortex development / cognition / osteoblast differentiation / positive regulation of GTPase activity / protein import into nucleus / Regulation of RAS by GAPs / positive regulation of neuron apoptotic process / MAPK cascade / presynapse / cellular response to heat / heart development / fibroblast proliferation / actin cytoskeleton organization / regulation of gene expression / angiogenesis
Similarity search - Function
Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / 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 ...Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / 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
PYROPHOSPHATE 2- / Neurofibromin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.3 Å
AuthorsD'angelo, I. / Welti, S. / Bonneau, F. / Scheffzek, K.
Citation
Journal: Embo Rep. / Year: 2006
Title: A novel bipartite phospholipid-binding module in the neurofibromatosis type 1 protein
Authors: D'angelo, I. / Welti, S. / Bonneau, F. / Scheffzek, K.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Expression, purification and preliminary crystallographic characterization of a novel segment from the neurofibromatosis type 1 protein.
Authors: Bonneau, F. / D'angelo, I. / Welti, S. / Ylanne, J. / Stier, G. / Scheffzek, K.
History
DepositionOct 22, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurofibromin
B: Neurofibromin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5656
Polymers58,9202
Non-polymers1,6464
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.5, 113.5, 125.6
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 29459.754 Da / Num. of mol.: 2 / Fragment: Sec14 homology domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: neurofibromin / Plasmid: PETM11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21359
#2: Chemical ChemComp-OXN / OXTOXYNOL-10 / ALPHA-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENYL]-OMEGA-HYDROXYPOLY(OXY-1,2-ETHANEDIYL) / TRITON X-100 / Triton X-100


Mass: 646.849 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H62O11 / Comment: detergent*YM
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.260
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2911vapor diffusion, hanging drop6Na4P2O7, MES, PEG 4000, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
2912vapor diffusion, hanging drop6NaH2PO, NaCl, sodium acetate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 5, 2002 / Details: Toroidal Zerodur mirror, radii of 4.9km and 79mm
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. obs: 37204 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Rsym value: 0.07 / Net I/σ(I): 6.9
Reflection shellResolution: 2.3→2.48 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 17554 / Rsym value: 0.28 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.3→15 Å / Isotropic thermal model: overall / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Refmac, CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1722 -RANDOM
Rwork0.24 ---
all0.33 34893 --
obs0.33 34716 99.5 %-
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0 Å0 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4141 0 66 113 4320
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.011
X-RAY DIFFRACTIONc_bond_d1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d1.03
LS refinement shellResolution: 2.3→2.48 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.33 251 -
Rwork0.28 --
obs-4834 94 %

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