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- PDB-3p7z: Crystal structure of the Neurofibromin Sec14-PH module containing... -

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Basic information

Entry
Database: PDB / ID: 3p7z
TitleCrystal structure of the Neurofibromin Sec14-PH module containing the patient derived mutation I1584V
ComponentsNeurofibromin
KeywordsLIPID BINDING PROTEIN / Sec14 homolgy domain / pleckstrin homology domain / binding of glycerophospholipids / glycerophospholipids / cytoplasmatic
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 / regulation of cell-matrix adhesion / forebrain morphogenesis / negative regulation of neurotransmitter secretion / hair follicle maturation / cell communication / regulation of blood vessel endothelial cell migration / camera-type eye morphogenesis / smooth muscle tissue development / negative regulation of oligodendrocyte differentiation / sympathetic nervous system development / myelination in peripheral nervous system / myeloid leukocyte migration / phosphatidylcholine binding / peripheral nervous system development / phosphatidylethanolamine binding / metanephros development / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of Ras protein signal transduction / collagen fibril organization / regulation of bone resorption / regulation of long-term synaptic potentiation / neural tube development / endothelial cell proliferation / forebrain astrocyte development / pigmentation / artery morphogenesis / regulation of postsynapse organization / regulation of synaptic transmission, GABAergic / negative regulation of neuroblast proliferation / negative regulation of MAPK cascade / adrenal gland development / negative regulation of protein import into nucleus / negative regulation of cell-matrix adhesion / spinal cord development / regulation of GTPase activity / Rac protein signal transduction / oligodendrocyte differentiation / negative regulation of osteoclast differentiation / negative regulation of endothelial cell proliferation / RAS signaling downstream of NF1 loss-of-function variants / negative regulation of astrocyte differentiation / extrinsic apoptotic signaling pathway via death domain receptors / neuroblast proliferation / regulation of angiogenesis / Schwann cell development / negative regulation of stem cell proliferation / negative regulation of fibroblast proliferation / skeletal muscle tissue development / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of endothelial cell proliferation / extracellular matrix organization / negative regulation of angiogenesis / GTPase activator activity / negative regulation of cell migration / osteoclast differentiation / regulation of ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / liver development / negative regulation of MAP kinase activity / stem cell proliferation / long-term synaptic potentiation / regulation of long-term neuronal synaptic plasticity / negative regulation of protein kinase activity / wound healing / brain development / visual learning / cerebral cortex development / cognition / positive regulation of GTPase activity / osteoblast differentiation / Regulation of RAS by GAPs / protein import into nucleus / MAPK cascade / positive regulation of neuron apoptotic process / presynapse / heart development / cellular response to heat / fibroblast proliferation / actin cytoskeleton organization / regulation of gene expression
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
Chem-PEV / PYROPHOSPHATE 2- / Neurofibromin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsWelti, S. / 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 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / 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
B: Neurofibromin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0957
Polymers63,2802
Non-polymers1,8155
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.061, 113.061, 124.612
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1817-

NA

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Components

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


Mass: 31640.160 Da / Num. of mol.: 2 / Mutation: I1584V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NF1 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon+RIL / References: UniProt: P21359
#2: Chemical ChemComp-PEV / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLETHANOLAMINE / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 720.012 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H78NO8P / Comment: POPE, phospholipid*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


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


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES, 7.5% PEG 4000, 0.2M Na4P207, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.65→49.144 Å / Num. obs: 24081 / % possible obs: 100 % / Observed criterion σ(I): 3
Reflection shellResolution: 2.65→2.87 Å / Mean I/σ(I) obs: 3.83 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
CNSrefinement
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→49 Å / SU ML: 0.12 / σ(F): 1.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2664 1228 5.1 %RANDOM
Rwork0.2161 ---
obs0.2186 24081 --
all-24081 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.557 Å2 / ksol: 0.339 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.0807 Å2-0 Å20 Å2
2---2.0807 Å20 Å2
3---2.723 Å2
Refinement stepCycle: LAST / Resolution: 2.65→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 117 166 4659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024599
X-RAY DIFFRACTIONf_angle_d0.5386219
X-RAY DIFFRACTIONf_dihedral_angle_d15.1011699
X-RAY DIFFRACTIONf_chiral_restr0.039680
X-RAY DIFFRACTIONf_plane_restr0.002771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.75620.39441400.35442494X-RAY DIFFRACTION100
2.7562-2.88160.32931370.31442471X-RAY DIFFRACTION100
2.8816-3.03350.32821330.27122503X-RAY DIFFRACTION100
3.0335-3.22350.27881360.25372501X-RAY DIFFRACTION100
3.2235-3.47230.28731370.21212512X-RAY DIFFRACTION100
3.4723-3.82170.22521350.19072521X-RAY DIFFRACTION100
3.8217-4.37440.21961430.16512533X-RAY DIFFRACTION100
4.3744-5.51010.21951460.16172576X-RAY DIFFRACTION100
5.5101-49.15240.26831210.21682742X-RAY DIFFRACTION100
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)
11.7002-1.05310.57760.603-0.6410.9970.0737-0.8139-1.7985-0.6885-0.16661.09640.912-0.15860.09490.5331-0.14770.0390.49270.13260.7441-34.8082-0.719418.724
21.78830.16160.28263.1684-0.56222.46440.0604-0.2266-0.0730.02310.13440.07430.1334-0.00920.00020.2840.1092-0.02550.35970.00030.351-24.347614.816815.7817
31.69260.0301-0.38210.7183-0.27571.25120.15050.11090.135-0.0119-0.0139-0.11670.0161-0.17310.00010.25570.02460.05060.2279-0.03410.168-19.32825.8899-6.9192
41.5714-0.0894-0.52872.4706-0.5112.4012-0.19730.2045-0.0359-0.05520.2560.35360.1153-0.333-00.1778-0.0637-0.05850.19160.06420.248-29.3063-2.8019-34.497
50.551-0.9725-0.05960.5799-0.47121.4715-0.21130.08310.2272-0.04330.2045-0.3407-0.06740.5078-0.00030.45-0.0021-0.02890.39170.01140.3747-11.3272-7.7578-23.2342
60.8311.1144-0.4991.06840.4181.26460.2031-0.0283-0.08630.5835-0.2324-0.1670.2257-0.1194-0.00010.41910.1607-0.03560.2987-0.03270.1516-13.145-8.1337-6.4808
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1547:1572)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 1573:1715)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 1716:1816)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 1547:1697)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 1698:1762)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 1763:1816)

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