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- PDB-1nf1: THE GAP RELATED DOMAIN OF NEUROFIBROMIN -

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Basic information

Entry
Database: PDB / ID: 1nf1
TitleTHE GAP RELATED DOMAIN OF NEUROFIBROMIN
ComponentsPROTEIN (NEUROFIBROMIN)
KeywordsSIGNALING PROTEIN / NEUROFIBROMIN / TYPE I NEUROFIBROMATOSIS / NF1 / RAS / GAP / SIGNAL TRANSDUCTION / CANCER / GROWTH REGULATION / GTP HYDROLYSIS / PATIENT MUTATION / ARGININE FINGER
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
GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / 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 ...GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / 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 / PH-like domain superfamily / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsScheffzek, K. / Ahmadian, M.R. / Wiesmueller, L. / Kabsch, W. / Stege, P. / Schmitz, F. / Wittinghofer, A.
Citation
Journal: EMBO J. / Year: 1998
Title: Structural analysis of the GAP-related domain from neurofibromin and its implications.
Authors: Scheffzek, K. / Ahmadian, M.R. / Wiesmuller, L. / Kabsch, W. / Stege, P. / Schmitz, F. / Wittinghofer, A.
#1: Journal: Science / Year: 1997
Title: The Ras-Rasgap Complex: Structural Basis for Gtpase Activation and its Loss in Oncogenic Ras Mutants
Authors: Scheffzek, K. / Ahmadian, M.R. / Kabsch, W. / Wiesmueller, L. / Lautwein, A. / Schmitz, F. / Wittinghofer, A.
#2: Journal: Nat.Struct.Biol. / Year: 1997
Title: Confirmation of the Arginine-Finger Hypothesis for the Gap-Stimulated GTP- Hydrolysis Reaction of Ras
Authors: Ahmadian, M.R. / Stege, P. / Scheffzek, K. / Wittinghofer, A.
#3: Journal: J.Biol.Chem. / Year: 1996
Title: Structural Differences in the Minimal Catalytic Domains of the Gtpasse- Activating Proteins P120Gap and Neurofibromin
Authors: Ahmadian, M.R. / Wiesmueller, L. / Lautwein, A. / Bischoff, F.R. / Wittinghofer, A.
#4: Journal: Nature / Year: 1996
Title: 3-Dimensional Structure of the Gtpase Activating Domain of Human P120Gap and Implications for the Interaction with Ras
Authors: Scheffzek, K. / Lautwein, A. / Kabsch, W. / Ahmadian, M.R. / Wittinghofer, A.
#5: Journal: Science / Year: 1996
Title: Formation of a Transition-State Analog of the Ras Gtpase Reaction by Ras:Gdp, Tetrafluoroaluminate and Gtpase-Activating Proteins
Authors: Mittal, R. / Ahmadian, M.R. / Goody, R.S. / Wittinghofer, A.
#6: Journal: Neuron / Year: 1993
Title: The Neurofibromatosis Type I Gene and its Protein Product
Authors: Gutmann, D.H. / Collins, F.S.
#7: Journal: Cell(Cambridge,Mass.) / Year: 1990
Title: The NF1 Locus Encodes a Protein Functionally Related to Mammalian Gap and Yeast Ira Proteins
Authors: Ballester, R. / Marchuk, D. / Boguski, M. / Saulino, A. / Letcher, R. / Wigler, M. / Collins, F.
#8: Journal: Cell(Cambridge,Mass.) / Year: 1990
Title: The Gap-Related Domain of the Neurofibromatosis Type I Gene Product Interacts with Ras P21
Authors: Martin, G.A. / Viskochil, D. / Bollag, G. / Mccabe, P.C. / Crosier, W.J. / Hausbruck, H. / Conroy, L. / Clark, R. / O'Connell, P. / Cawthon, R.M. / Innis, M.A. / Mccormick, F.
#9: Journal: Cell(Cambridge,Mass.) / Year: 1990
Title: The Catalytic Domain of the Neurofibromatosis Type I Gene Product Stimulates Ras Gtpase and Complements Ira Mutants of S. Cerevisiae
Authors: Xu, G. / Lin, B. / Tanaka, K. / Dunn, D. / Wod, D. / Gesteland, R. / White, R. / Weiss, R. / Tamanoi, F.
#10: Journal: Embo J. / Year: 1990
Title: Refined Crystal Structure of the Triphosphate Conformation of H-Ras P21 at 1.35 A Resolution: Implications for the Mechanism of GTP Hydrolysis
Authors: Pai, E.F. / Krengel, U. / Petsko, G.A. / Goody, R.S. / Kabsch, W. / Wittinghofer, A.
History
DepositionJul 8, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (NEUROFIBROMIN)


Theoretical massNumber of molelcules
Total (without water)37,9831
Polymers37,9831
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.250, 58.300, 74.800
Angle α, β, γ (deg.)90.00, 118.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (NEUROFIBROMIN) / NF1-333


Mass: 37982.672 Da / Num. of mol.: 1 / Fragment: GAP RELATED DOMAIN
Source method: isolated from a genetically manipulated source
Details: SEE REF.5 FOR DETAILS / Source: (gene. exp.) Homo sapiens (human) / Description: S. REF. 4 / Cellular location: CYTOSOL / Plasmid: PETNF1-333 / Production host: Escherichia coli (E. coli) / Strain (production host): DG103 / References: UniProt: P21359

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growpH: 8 / Details: S. REF. DESCRIBING THE STRUCTURE, pH 8
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118-22 %PEG33501reservoir
2100 mMTris-HCl1reservoir
3200 mM1reservoirMgCl2
430 mMTris-Cl1drop
55 mM1dropMgCl2
63 mMDTE1drop
720 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 26, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 50172 / % possible obs: 99 % / Redundancy: 4.3 % / Biso Wilson estimate: 52.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.6
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.6 / % possible all: 99.8
Reflection
*PLUS
Num. obs: 11665 / % possible obs: 99.8 % / Num. measured all: 50172 / Rmerge(I) obs: 0.073

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Processing

Software
NameVersionClassification
X-PLOR3.8refinement
XDS(W.KABSCH)data reduction
XSCALE(KABSCH)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.5→30 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED IN FINAL STAGES
RfactorNum. reflection% reflectionSelection details
Rfree0.369 1152 10 %RANDOM
Rwork0.266 ---
obs0.266 10926 93.1 %-
Displacement parametersBiso mean: 47.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.41 Å
Luzzati d res low-30 Å
Luzzati sigma a0.54 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 0 0 1948
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.02
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.071.5
X-RAY DIFFRACTIONx_mcangle_it5.022
X-RAY DIFFRACTIONx_scbond_it4.612
X-RAY DIFFRACTIONx_scangle_it6.592.5
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.436 143 11.9 %
Rwork0.4 1058 -
obs--82.7 %
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.02
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Rfactor Rfree: 0.436 / % reflection Rfree: 11.9 % / Rfactor Rwork: 0.4

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