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- PDB-4k81: Crystal structure of the Grb14 RA and PH domains in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4k81
TitleCrystal structure of the Grb14 RA and PH domains in complex with GTP-loaded H-Ras
Components
  • GTPase HRasHRAS
  • Growth factor receptor-bound protein 14
KeywordsSIGNALING PROTEIN / ADAPTOR PROTEIN
Function / homology
Function and homology information


GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / T-helper 1 type immune response / positive regulation of wound healing / positive regulation of miRNA metabolic process / defense response to protozoan / Signaling by RAS GAP mutants ...GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / T-helper 1 type immune response / positive regulation of wound healing / positive regulation of miRNA metabolic process / defense response to protozoan / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / positive regulation of protein targeting to membrane / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / adipose tissue development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / : / Schwann cell development / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / p38MAPK events / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / myelination / Signaling by FGFR1 in disease / Ras activation upon Ca2+ influx through NMDA receptor / GRB2 events in ERBB2 signaling / negative regulation of insulin receptor signaling pathway / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / animal organ morphogenesis / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / regulation of long-term neuronal synaptic plasticity / RAF activation / positive regulation of MAP kinase activity / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cellular response to gamma radiation / receptor tyrosine kinase binding / positive regulation of GTPase activity / endocytosis / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / Signaling by RAF1 mutants / GDP binding / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / chemotaxis / MAPK cascade / positive regulation of type II interferon production / cellular senescence / positive regulation of fibroblast proliferation / Signaling by BRAF and RAF1 fusions
Similarity search - Function
Grb14, SH2 domain / BPS (Between PH and SH2) domain / BPS (Between PH and SH2) / GRB/APBB1IP / APBB1IP, PH domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) ...Grb14, SH2 domain / BPS (Between PH and SH2) domain / BPS (Between PH and SH2) / GRB/APBB1IP / APBB1IP, PH domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Small GTPase, Ras-type / small GTPase Ras family profile. / PH domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / PH-like domain superfamily / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / GTPase HRas / Growth factor receptor-bound protein 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsQamra, R. / Hubbard, S.R.
CitationJournal: Plos One / Year: 2013
Title: Structural basis for the interaction of the adaptor protein grb14 with activated ras.
Authors: Qamra, R. / Hubbard, S.R.
History
DepositionApr 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

Downloads & links

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Assembly

Deposited unit
A: Growth factor receptor-bound protein 14
B: GTPase HRas
C: Growth factor receptor-bound protein 14
D: GTPase HRas
E: Growth factor receptor-bound protein 14
F: GTPase HRas
G: Growth factor receptor-bound protein 14
H: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,28625
Polymers197,2678
Non-polymers3,01917
Water3,261181
1
A: Growth factor receptor-bound protein 14
B: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3259
Polymers49,3172
Non-polymers1,0087
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Growth factor receptor-bound protein 14
D: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0496
Polymers49,3172
Non-polymers7324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Growth factor receptor-bound protein 14
F: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0496
Polymers49,3172
Non-polymers7324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Growth factor receptor-bound protein 14
H: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8644
Polymers49,3172
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.727, 115.593, 103.107
Angle α, β, γ (deg.)90.00, 96.75, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a heterodimer between chains A and B (also between chains C and D, between chains E and F, and between chains G and H).

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Growth factor receptor-bound protein 14 / GRB14 adapter protein


Mass: 29996.145 Da / Num. of mol.: 4 / Fragment: RA-PH domains, UNP residues 106-356 / Mutation: K272A,E273A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRB14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14449
#2: Protein
GTPase HRas / HRAS / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras / GTPase HRas / N-terminally processed


Mass: 19320.727 Da / Num. of mol.: 4 / Fragment: GTPase domain, UNP residues 1-166 / Mutation: G12V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112

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Non-polymers , 4 types, 198 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 315 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 14% (w/v) PEG 3350, 100 mM MES, pH 5.9, 200 mM MgCl2, 2% glycerol, and 3% glucose, VAPOR DIFFUSION, HANGING DROP, temperature 315K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 71989 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 23.8

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3HK0 (CHAINS A,C,E,G) AND 1LFD (CHAINS B,D,F,H)

3hk0

1lfd


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.905 / SU B: 20.488 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.556 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2769 3628 5 %RANDOM
Rwork0.21853 ---
obs0.22149 68338 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.457 Å2
Baniso -1Baniso -2Baniso -3
1-1.97 Å20 Å20.8 Å2
2--0.69 Å20 Å2
3----2.48 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13500 0 186 181 13867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213997
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.96118893
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04651648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70223.873692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15152448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7311584
X-RAY DIFFRACTIONr_chiral_restr0.0830.22001
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110572
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.404→2.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 253 -
Rwork0.306 4800 -
obs--96.99 %
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)
10.118-0.12770.12490.3062-0.2170.9534-0.0448-0.04590.0650.00030.03530.01640.13650.01160.00950.17060.0110.00380.1523-0.01540.1077-7.82234.26596.9062
21.84370.2288-0.40450.1075-0.11470.173-0.02130.22220.2698-0.03140.0231-0.06090.0843-0.0927-0.00170.1534-0.03410.02280.1320.060.16072.260323.1577-28.7433
30.18030.2134-0.39910.533-0.08561.52360.0576-0.0053-0.0199-0.0109-0.0459-0.0386-0.17620.0326-0.01170.17280.03820.00430.21570.00840.0291-0.85911.4064-49.319
40.6520.02170.64480.5367-0.49681.2401-0.0258-0.0982-0.0714-0.11910.0658-0.05970.0188-0.1116-0.040.16520.02630.02140.11920.02440.10331.4313-16.5707-11.547
50.2867-0.04450.16610.6486-0.37850.51160.00650.09770.03490.0698-0.00540.0056-0.0359-0.0864-0.00110.09880.0253-0.00520.18190.04070.1358-35.890229.756-25.2785
61.63070.7741-0.23390.438-0.23350.4674-0.0528-0.0221-0.36440.0655-0.0544-0.194-0.1004-0.12810.10720.1255-0.06710.03360.1579-0.02260.1884-42.9923-6.2839-5.8791
70.4423-0.3224-0.59741.25010.4030.8081-0.09340.3241-0.34140.4921-0.41880.02080.1728-0.43050.51220.194-0.1880.01780.2879-0.19930.3147-33.0029-27.0494-24.8633
82.4679-2.88950.62633.4086-0.72490.16350.66240.730.2735-0.6535-0.8296-0.29860.14230.15010.16720.20710.20490.06020.4875-0.00140.0559-38.42958.6172-45.8975
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A106 - 356
2X-RAY DIFFRACTION1A401 - 404
3X-RAY DIFFRACTION1B201
4X-RAY DIFFRACTION2B-4 - 166
5X-RAY DIFFRACTION2B202 - 203
6X-RAY DIFFRACTION3C106 - 356
7X-RAY DIFFRACTION3C400 - 401
8X-RAY DIFFRACTION4D-4 - 166
9X-RAY DIFFRACTION4D200 - 201
10X-RAY DIFFRACTION5E106 - 356
11X-RAY DIFFRACTION5E400 - 401
12X-RAY DIFFRACTION6F-4 - 166
13X-RAY DIFFRACTION6F200 - 201
14X-RAY DIFFRACTION7G106 - 356
15X-RAY DIFFRACTION8H-4 - 166
16X-RAY DIFFRACTION8H200 - 201

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