Rap protein signal transduction / GRB2:SOS provides linkage to MAPK signaling for Integrins / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / MAP2K and MAPK activation / regulation of cell junction assembly / nerve growth factor signaling pathway / positive regulation of vasculogenesis / negative regulation of synaptic vesicle exocytosis ...Rap protein signal transduction / GRB2:SOS provides linkage to MAPK signaling for Integrins / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / MAP2K and MAPK activation / regulation of cell junction assembly / nerve growth factor signaling pathway / positive regulation of vasculogenesis / negative regulation of synaptic vesicle exocytosis / guanyl-nucleotide exchange factor complex / ARMS-mediated activation / Rap1 signalling / establishment of endothelial barrier / anchoring junction / MET activates RAP1 and RAC1 / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / T cell receptor complex / Frs2-mediated activation / p130Cas linkage to MAPK signaling for integrins / synaptic vesicle exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of cell adhesion / positive regulation of protein kinase activity / specific granule membrane / cellular response to cAMP / sperm midpiece / Integrin signaling / guanyl-nucleotide exchange factor activity / small monomeric GTPase / cellular response to nerve growth factor stimulus / positive regulation of GTPase activity / G protein activity / protein localization to plasma membrane / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / small GTPase binding / positive regulation of neuron projection development / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / GDP binding / Signaling by BRAF and RAF1 fusions / late endosome / presynapse / lamellipodium / cell junction / nervous system development / positive regulation of ERK1 and ERK2 cascade / early endosome / cytoskeleton / endosome membrane / neuron projection / focal adhesion / GTPase activity / glutamatergic synapse / Neutrophil degranulation / protein-containing complex binding / GTP binding / perinuclear region of cytoplasm / signal transduction / extracellular exosome / plasma membrane / cytoplasm / cytosol Similarity search - Function
GRB/APBB1IP / APBB1IP, PH domain / Ras-related protein Rap1 / 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 ...GRB/APBB1IP / APBB1IP, PH domain / Ras-related protein Rap1 / 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. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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 / 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 / Ras-related protein Rap-1A / Amyloid beta A4 precursor protein-binding family B member 1-interacting protein Similarity search - Component
A: Ras-related protein Rap-1A B: Amyloid beta A4 precursor protein-binding family B member 1-interacting protein C: Ras-related protein Rap-1A D: Amyloid beta A4 precursor protein-binding family B member 1-interacting protein hetero molecules
Monochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Resolution: 1.65→1.68 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 137303 / Rsym value: 0.448 / % possible all: 93.8
-
Processing
Software
Name
Version
Classification
HKL-2000
datacollection
PHASER
phasing
REFMAC
5.6.0117
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→47.82 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.035 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2189
6891
5 %
RANDOM
Rwork
0.1971
-
-
-
obs
0.19821
130322
99.3 %
-
all
-
137303
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 29.323 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0.01 Å2
Refinement step
Cycle: LAST / Resolution: 1.65→47.82 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6704
0
74
725
7503
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.005
0.02
7154
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.07
1.976
9705
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.245
5
885
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.178
24.652
359
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.148
15
1380
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
12.495
15
46
X-RAY DIFFRACTION
r_chiral_restr
0.075
0.2
1068
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
5352
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.648→1.69 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.285
441
-
Rwork
0.275
8590
-
obs
-
-
92.65 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°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)
1
1.6106
-0.2656
0.5614
1.0517
0.3739
4.4254
-0.0116
0.1394
0.0298
0.0139
-0.0275
-0.0381
0.1856
-0.0307
0.0391
0.0513
-0.0138
0.0041
0.0764
-0.0222
0.0632
-33.027
-26.558
-2.561
2
1.1043
0.2347
0.2149
0.5585
0.0715
0.6454
-0.0124
-0.0693
0.0046
-0.0144
-0.0145
-0.0111
0.0058
-0.0509
0.0269
0.0509
0.0216
0.0103
0.0524
-0.0119
0.093
-21.489
-14.007
34.972
3
4.7048
-2.0989
-0.5894
5.5723
-3.1552
7.1834
0.3558
0.5668
0.1716
-1.1827
-0.459
-0.2365
0.6331
0.3514
0.1032
0.4143
0.1912
0.1128
0.2021
0.0814
0.0405
-10.456
29.64
-1.195
4
1.3124
-0.0452
-0.2255
0.494
0.0339
0.8188
0.0053
-0.0001
-0.0323
-0.0123
-0.0422
0.0517
-0.0134
-0.035
0.0369
0.0445
0.0243
-0.004
0.0464
-0.0007
0.0884
-19.826
20.918
37.948
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
0 - 167
2
X-RAY DIFFRACTION
2
B
178 - 437
3
X-RAY DIFFRACTION
3
C
1 - 166
4
X-RAY DIFFRACTION
4
D
178 - 437
+
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