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- PDB-3pg7: Crystal structure of the H. sapiens NF1 SEC-PH domain (del1750 mutant) -

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Basic information

Entry
Database: PDB / ID: 3pg7
TitleCrystal structure of the H. sapiens NF1 SEC-PH domain (del1750 mutant)
ComponentsNeurofibromin
KeywordsLIPID BINDING PROTEIN / SEC lipid binding domain / PH domain
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 / negative regulation of Schwann cell migration / Schwann cell migration / vascular associated smooth muscle cell migration / amygdala development / Schwann cell proliferation / negative regulation of mast cell proliferation ...positive regulation of mast cell apoptotic process / negative regulation of Rac protein signal transduction / regulation of glial cell differentiation / observational learning / negative regulation of Schwann cell migration / Schwann cell migration / vascular associated smooth muscle cell migration / amygdala development / Schwann cell proliferation / negative regulation of mast cell proliferation / mast cell apoptotic process / gamma-aminobutyric acid secretion, neurotransmission / 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 / forebrain morphogenesis / regulation of cell-matrix adhesion / 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 / myeloid leukocyte migration / sympathetic nervous system development / peripheral nervous system development / myelination in peripheral nervous system / phosphatidylcholine binding / negative regulation of Ras protein signal transduction / metanephros development / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / phosphatidylethanolamine binding / collagen fibril organization / endothelial cell proliferation / regulation of long-term synaptic potentiation / regulation of bone resorption / regulation of postsynapse organization / neural tube development / artery morphogenesis / forebrain astrocyte development / negative regulation of neuroblast proliferation / adrenal gland development / negative regulation of protein import into nucleus / pigmentation / spinal cord development / regulation of synaptic transmission, GABAergic / Rac protein signal transduction / negative regulation of vascular associated smooth muscle cell migration / negative regulation of osteoclast differentiation / negative regulation of endothelial cell proliferation / oligodendrocyte differentiation / negative regulation of astrocyte differentiation / RAS signaling downstream of NF1 loss-of-function variants / extrinsic apoptotic signaling pathway via death domain receptors / neuroblast proliferation / negative regulation of cell-matrix adhesion / regulation of angiogenesis / negative regulation of MAPK cascade / regulation of ERK1 and ERK2 cascade / Schwann cell development / negative regulation of stem cell proliferation / skeletal muscle tissue development / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of endothelial cell proliferation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / extracellular matrix organization / GTPase activator activity / osteoclast differentiation / positive regulation of GTPase activity / negative regulation of angiogenesis / liver development / negative regulation of cell migration / stem cell proliferation / long-term synaptic potentiation / regulation of long-term neuronal synaptic plasticity / wound healing / visual learning / brain development / cerebral cortex development / cognition / protein import into nucleus / Regulation of RAS by GAPs / osteoblast differentiation / MAPK cascade / positive regulation of neuron apoptotic process / presynapse / heart development / cellular response to heat / regulation of gene expression / actin cytoskeleton organization / fibroblast proliferation / angiogenesis / neuron apoptotic process / Ras protein signal transduction / response to hypoxia
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
PYROPHOSPHATE 2- / PHOSPHATIDYLETHANOLAMINE / Neurofibromin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.189 Å
AuthorsWelti, 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 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Neurofibromin
B: Neurofibromin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4816
Polymers58,6612
Non-polymers1,8204
Water4,342241
1
A: Neurofibromin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0652
Polymers29,3311
Non-polymers7341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neurofibromin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4174
Polymers29,3311
Non-polymers1,0863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.440, 113.440, 124.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 29330.574 Da / Num. of mol.: 2 / Mutation: K1771 deletion 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-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


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


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.41 Å3/Da / Density % sol: 63.97 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å
DetectorDetector: CCD
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→36.857 Å / Num. all: 77235 / Num. obs: 74716 / % possible obs: 93.44 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.189→36 Å / SU ML: 1.7 / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 3792 5.08 %0.05
Rwork0.2083 ---
obs0.2104 74716 93.44 %-
all-77235 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.838 Å2 / ksol: 0.349 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8285 Å2-0 Å2-0 Å2
2---0.8285 Å2-0 Å2
3----7.0229 Å2
Refinement stepCycle: LAST / Resolution: 2.189→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4011 0 110 241 4362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044218
X-RAY DIFFRACTIONf_angle_d0.8975735
X-RAY DIFFRACTIONf_dihedral_angle_d16.991502
X-RAY DIFFRACTIONf_chiral_restr0.061645
X-RAY DIFFRACTIONf_plane_restr0.003713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.189-2.21670.31041500.28732287X-RAY DIFFRACTION83
2.2167-2.24590.34841370.27472409X-RAY DIFFRACTION86
2.2459-2.27660.30551050.25182439X-RAY DIFFRACTION86
2.2766-2.30920.28911520.25722409X-RAY DIFFRACTION86
2.3092-2.34360.28811500.24062373X-RAY DIFFRACTION86
2.3436-2.38020.2421020.22572473X-RAY DIFFRACTION87
2.3802-2.41930.30721340.23392569X-RAY DIFFRACTION90
2.4193-2.4610.24571400.24062533X-RAY DIFFRACTION91
2.461-2.50570.31181310.23032554X-RAY DIFFRACTION91
2.5057-2.55390.26881290.2332545X-RAY DIFFRACTION91
2.5539-2.6060.26241530.22482593X-RAY DIFFRACTION93
2.606-2.66270.26191630.22712615X-RAY DIFFRACTION94
2.6627-2.72460.31321360.2342669X-RAY DIFFRACTION95
2.7246-2.79270.31611400.23512669X-RAY DIFFRACTION95
2.7927-2.86820.27681370.21122725X-RAY DIFFRACTION96
2.8682-2.95250.23021280.19782735X-RAY DIFFRACTION97
2.9525-3.04780.25521550.20122689X-RAY DIFFRACTION96
3.0478-3.15670.25521800.20912720X-RAY DIFFRACTION98
3.1567-3.2830.25021360.20432781X-RAY DIFFRACTION98
3.283-3.43230.2441450.19932758X-RAY DIFFRACTION98
3.4323-3.61310.21661330.18322793X-RAY DIFFRACTION99
3.6131-3.83920.21121440.17442813X-RAY DIFFRACTION99
3.8392-4.13530.22361470.16962782X-RAY DIFFRACTION99
4.1353-4.55080.17661850.15182773X-RAY DIFFRACTION99
4.5508-5.20770.19761310.16312806X-RAY DIFFRACTION99
5.2077-6.55520.2371370.20452814X-RAY DIFFRACTION100
6.5552-36.86210.26331120.24092598X-RAY DIFFRACTION91
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)
12.7429-0.556-1.47572.90820.78390.7269-0.2714-0.6649-0.56430.41060.2740.13650.27710.2715-0.00030.35310.1521-0.01110.42570.07780.3336-27.1649.570817.3208
20.39730.30520.42621.6460.24241.6397-0.0099-0.55150.11980.05270.3664-0.2568-0.040.3271-0.00130.33630.148-0.03360.5821-0.15070.3573-21.364120.613313.3037
31.99370.0137-0.88281.79290.09233.94170.1075-0.02980.2342-0.19730.0897-0.1438-0.0779-0.1133-0.00040.33230.03360.0590.3339-0.10620.3492-18.987224.6681-6.8242
41.05840.04860.142.4756-1.36682.3871-0.1110.1198-0.0058-0.11510.21920.26770.1777-0.2535-0.00060.2093-0.0353-0.06420.18660.00160.2699-28.7954-3.8765-34.1803
50.8747-0.845-0.0051-0.1982-0.02471.47220.00650.11150.57830.09580.3179-0.01-0.77150.35490.0320.3203-0.1548-0.06550.31990.00390.3999-12.77512.4286-32.5589
62.083-0.57151.22041.4827-0.2183.0463-0.2753-0.28480.01840.3570.2222-0.03290.17720.2143-0.00030.3640.1172-0.04280.2982-0.03940.3117-12.3204-10.1085-13.0989
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1560:1658)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 1659:1711)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 1712:1815)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 1560:1687)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 1688:1712)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 1713:1815)

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