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- PDB-4l9u: Structure of C-terminal coiled coil of RasGRP1 -

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Basic information

Entry
Database: PDB / ID: 4l9u
TitleStructure of C-terminal coiled coil of RasGRP1
ComponentsRAS guanyl-releasing protein 1
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


positive regulation of natural killer cell differentiation / diacylglycerol binding / positive regulation of T cell differentiation in thymus / secretory granule localization / Effects of PIP2 hydrolysis / vesicle transport along microtubule / positive regulation of natural killer cell mediated cytotoxicity / phosphatidylcholine binding / natural killer cell activation / Rap1 signalling ...positive regulation of natural killer cell differentiation / diacylglycerol binding / positive regulation of T cell differentiation in thymus / secretory granule localization / Effects of PIP2 hydrolysis / vesicle transport along microtubule / positive regulation of natural killer cell mediated cytotoxicity / phosphatidylcholine binding / natural killer cell activation / Rap1 signalling / inflammatory response to antigenic stimulus / positive regulation of Ras protein signal transduction / activation of GTPase activity / positive regulation of granulocyte macrophage colony-stimulating factor production / mast cell degranulation / B cell activation / B cell proliferation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Activation of RAS in B cells / T cell proliferation / T cell activation / Integrin signaling / regulation of ERK1 and ERK2 cascade / guanyl-nucleotide exchange factor activity / positive regulation of GTPase activity / positive regulation of JNK cascade / positive regulation of MAP kinase activity / FCERI mediated NF-kB activation / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / RAF/MAP kinase cascade / Ras protein signal transduction / positive regulation of ERK1 and ERK2 cascade / cell differentiation / positive regulation of protein phosphorylation / Golgi membrane / lipid binding / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus / signal transduction / zinc ion binding / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2730 / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2730 / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / EF-hand, calcium binding motif / Special / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
RAS guanyl-releasing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6014 Å
AuthorsIwig, J.S. / Vercoulen, Y. / Das, R. / Barros, T. / Limnander, A. / Che, Y. / Pelton, J.G. / Wemmer, D.E. / Roose, J.P. / Kuriyan, J.
CitationJournal: Elife / Year: 2013
Title: Structural analysis of autoinhibition in the Ras-specific exchange factor RasGRP1.
Authors: Iwig, J.S. / Vercoulen, Y. / Das, R. / Barros, T. / Limnander, A. / Che, Y. / Pelton, J.G. / Wemmer, D.E. / Roose, J.P. / Kuriyan, J.
History
DepositionJun 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: RAS guanyl-releasing protein 1
B: RAS guanyl-releasing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6316
Polymers13,2592
Non-polymers3724
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-33 kcal/mol
Surface area7290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.878, 165.047, 28.319
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein RAS guanyl-releasing protein 1 / Calcium and DAG-regulated guanine nucleotide exchange factor II / CalDAG-GEFII / Ras guanyl-releasing protein


Mass: 6629.548 Da / Num. of mol.: 2 / Fragment: UNP Residues 739-793
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RASGRP1, RASGRP / Production host: Escherichia coli (E. coli) / References: UniProt: O95267
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 3.6
Details: 20 mM sodium acetate, 22% PEG 3350, 100 mM lithium sulfate, 0.4% formamide, pH 3.6, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 27, 2011
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→27.911 Å / Num. all: 16277 / Num. obs: 16098 / % possible obs: 98.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.6-1.63197.4
8.47-27.91189.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6014→27.911 Å / SU ML: 0.2 / σ(F): 0.83 / Phase error: 22.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2351 1352 4.97 %
Rwork0.2007 --
obs0.2024 27209 91.6 %
all-16277 -
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6014→27.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms748 0 23 74 845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01819
X-RAY DIFFRACTIONf_angle_d1.1461109
X-RAY DIFFRACTIONf_dihedral_angle_d15.116341
X-RAY DIFFRACTIONf_chiral_restr0.067127
X-RAY DIFFRACTIONf_plane_restr0.004142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6014-1.65860.29451450.29412558X-RAY DIFFRACTION89
1.6586-1.7250.33191590.28582528X-RAY DIFFRACTION91
1.725-1.80350.34621500.27822529X-RAY DIFFRACTION90
1.8035-1.89860.321270.24742595X-RAY DIFFRACTION91
1.8986-2.01750.25021030.20422556X-RAY DIFFRACTION91
2.0175-2.17320.20981270.18352543X-RAY DIFFRACTION90
2.1732-2.39180.21891270.17722627X-RAY DIFFRACTION93
2.3918-2.73760.2171580.1722631X-RAY DIFFRACTION94
2.7376-3.44810.20581470.18392633X-RAY DIFFRACTION94
3.4481-27.91560.2211090.19892657X-RAY DIFFRACTION93
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)
13.89790.273-0.1295.63450.2982.38620.0926-0.001-0.56280.33290.1217-0.53160.29060.04530.21380.1125-0.0021-0.03250.160.02640.1145-9.236730.5929-3.7696
22.2027-0.5310.11991.71511.72862.34350.14970.12620.1628-0.05990.0248-0.0437-0.05650.18110.0180.3853-0.0014-0.00650.29660.02210.1798-8.209951.961-21.6716
32.93230.3784-0.11567.9917-1.09451.8632-0.01580.2111-0.6022-0.13110.22720.24910.2949-0.0583-0.02820.15320.0041-0.02910.1689-0.01770.1473-13.328627.9121-9.457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B'
2X-RAY DIFFRACTION2chain 'A' and ((resseq 784:793))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 745:783))

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