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- PDB-4l9m: Autoinhibited state of the Ras-specific exchange factor RasGRP1 -

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Basic information

Entry
Database: PDB / ID: 4l9m
TitleAutoinhibited state of the Ras-specific exchange factor RasGRP1
ComponentsRAS guanyl-releasing protein 1
KeywordsSIGNALING PROTEIN / Ras nucleotide exchange factor
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
Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Son of sevenless (SoS) protein; Chain S, domain 1 / Son of sevenless (SoS) protein Chain: S domain 1 / Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / EF-hand domain / 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. ...Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Son of sevenless (SoS) protein; Chain S, domain 1 / Son of sevenless (SoS) protein Chain: S domain 1 / Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / EF-hand domain / 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 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 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 / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / RAS guanyl-releasing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6285
Polymers64,2131
Non-polymers4154
Water1086
1
A: RAS guanyl-releasing protein 1
hetero molecules

A: RAS guanyl-releasing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,25510
Polymers128,4252
Non-polymers8308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area3670 Å2
ΔGint-29 kcal/mol
Surface area52020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.380, 76.380, 408.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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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: 64212.590 Da / Num. of mol.: 1
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.15 M sodium citrate tribasic, 22% PEG 3350, 1 mM MnCl2, pH 7.5, VAPOR DIFFUSION, HANGING 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: Oct 28, 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: 3→47.44 Å / Num. all: 15299 / Num. obs: 15253 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3-3.24199.8
7.94-47.44197.1

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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
Starting model: PDB ENTRY 2IJE and 1BKD

2ije

1bkd


Resolution: 3→47.435 Å / SU ML: 0.5 / σ(F): 1.92 / Phase error: 26.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2691 774 5.1 %Random
Rwork0.2243 ---
obs0.2266 15253 99.7 %-
all-15299 --
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→47.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4223 0 21 6 4250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074338
X-RAY DIFFRACTIONf_angle_d1.025857
X-RAY DIFFRACTIONf_dihedral_angle_d12.8961621
X-RAY DIFFRACTIONf_chiral_restr0.076647
X-RAY DIFFRACTIONf_plane_restr0.005742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10720.40241540.36482494X-RAY DIFFRACTION99
3.1072-3.23160.33371540.35372516X-RAY DIFFRACTION99
3.2316-3.37870.33471340.31972524X-RAY DIFFRACTION100
3.3787-3.55670.29281280.26592514X-RAY DIFFRACTION100
3.5567-3.77950.26551540.24032527X-RAY DIFFRACTION100
3.7795-4.07120.29961210.21692532X-RAY DIFFRACTION100
4.0712-4.48060.22721360.19122548X-RAY DIFFRACTION100
4.4806-5.12830.24441230.18882541X-RAY DIFFRACTION100
5.1283-6.45850.29021370.23552486X-RAY DIFFRACTION99
6.4585-47.44140.22921120.18412506X-RAY DIFFRACTION98
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)
13.2382-1.0934-2.22147.9743-1.22672.6262-0.74310.5299-0.3923-0.54740.89590.1870.6349-0.1523-0.01850.8779-0.21160.21321.02130.4450.9538-23.644450.8418-44.07
26.8441-0.75841.6820.89240.47233.4011-0.22530.2782-0.0749-0.01230.69761.1279-0.5832-0.824-0.31060.90040.15870.22250.94260.58371.1957-38.7642.6818-28.8377
33.43160.0566-2.22521.54641.16312.37580.1233-1.4708-1.490.8697-0.3446-0.68060.2663-0.16651.27930.99160.18850.13221.09410.76650.9391-19.4382-10.3697-4.8531
48.65052.66432.70346.16553.76025.3173-0.28351.1663-0.0737-0.23240.4904-0.2733-0.55-0.2149-0.04760.78760.16450.11850.89830.57240.9459-27.689-7.8734-26.1466
53.59490.74910.49753.3124-0.86332.4730.3894-0.0472-0.11610.29550.68180.392-0.4212-0.28980.08271.16220.06810.32410.72940.92950.7606-32.858731.7219-10.2258
60.602-1.854-0.09445.2798-2.1172.74570.0354-0.006-0.24490.61860.27420.3920.054-0.3262-0.33330.84430.0110.09120.83990.41560.8637-26.843820.2673-8.6378
78.9938-0.89211.0259.7542-1.83739.5882-1.2782-0.6406-0.76712.0919-0.2012-1.34340.51532.64011.21621.1616-0.0754-0.11550.93830.62851.5701-20.472928.0801-14.0928
85.476.76530.2458.35560.388.6650.3461-0.0807-2.90470.91860.5719-1.10270.3522-1.1992-0.95340.94780.28920.07970.84460.38111.1737-28.3777-13.9954-17.369
98.9985-6.1116-3.74155.02854.39125.38510.0197-1.77360.30561.3910.9904-0.1547-0.1866-0.82320.24121.2452-0.04920.35181.06830.41960.9022-29.335233.61625.7949
109.72971.69794.73720.31270.83522.30590.513-1.44730.87381.447-0.17880.5101-1.086-1.4299-0.4921.25380.07390.54271.06710.20321.1037-41.61687.3572-30.0443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 541:593))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 465:540))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 53:61))
4X-RAY DIFFRACTION4chain 'A' and ((resseq 80:171))
5X-RAY DIFFRACTION5chain 'A' and ((resseq 193:314))
6X-RAY DIFFRACTION6chain 'A' and ((resseq 339:436))
7X-RAY DIFFRACTION7chain 'A' and ((resseq 449:464))
8X-RAY DIFFRACTION8chain 'A' and ((resseq 62:79))
9X-RAY DIFFRACTION9chain 'A' and ((resseq 315:338))
10X-RAY DIFFRACTION10chain 'A' and ((resseq 172:187))

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