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- PDB-5kho: Rasip1 RA domain in complex with Rap1B -

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Basic information

Entry
Database: PDB / ID: 5kho
TitleRasip1 RA domain in complex with Rap1B
Components
  • Ras-interacting protein 1
  • Ras-related protein Rap-1b
KeywordsSIGNALING PROTEIN / Rasip1 / Ras-Association domain / Rap1B / complex
Function / homology
Function and homology information


negative regulation of membrane permeability / negative regulation of Rho-dependent protein serine/threonine kinase activity / Rap protein signal transduction / modification of postsynaptic structure / regulation of cell junction assembly / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / negative regulation of synaptic vesicle exocytosis / Golgi stack / calcium-ion regulated exocytosis ...negative regulation of membrane permeability / negative regulation of Rho-dependent protein serine/threonine kinase activity / Rap protein signal transduction / modification of postsynaptic structure / regulation of cell junction assembly / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / negative regulation of synaptic vesicle exocytosis / Golgi stack / calcium-ion regulated exocytosis / Rap1 signalling / establishment of endothelial barrier / regulation of establishment of cell polarity / MET activates RAP1 and RAC1 / negative regulation of Rho protein signal transduction / azurophil granule membrane / branching morphogenesis of an epithelial tube / regulation of GTPase activity / p130Cas linkage to MAPK signaling for integrins / GRB2:SOS provides linkage to MAPK signaling for Integrins / vasculogenesis / cellular response to cAMP / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / Integrin signaling / negative regulation of autophagy / small monomeric GTPase / G protein activity / establishment of localization in cell / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / GDP binding / 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 / cell-cell junction / Signaling by BRAF and RAF1 fusions / GTPase binding / angiogenesis / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / GTPase activity / glutamatergic synapse / Neutrophil degranulation / protein-containing complex binding / GTP binding / perinuclear region of cytoplasm / signal transduction / protein homodimerization activity / protein-containing complex / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Rasip1/Radil, cargo-binding domain / Ras-related protein Rap1 / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain ...Rasip1/Radil, cargo-binding domain / Ras-related protein Rap1 / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / SMAD/FHA domain superfamily / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / 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 / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rap-1b / Ras-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.78 Å
AuthorsGingras, A.R.
Funding support United States, 2items
OrganizationGrant numberCountry
American Heart Association12SDG11610043 United States
American Heart Association16GRNT29650005 United States
CitationJournal: Structure / Year: 2016
Title: Structural Basis of Dimeric Rasip1 RA Domain Recognition of the Ras Subfamily of GTP-Binding Proteins.
Authors: Gingras, A.R. / Puzon-McLaughlin, W. / Bobkov, A.A. / Ginsberg, M.H.
History
DepositionJun 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Oct 4, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-interacting protein 1
B: Ras-interacting protein 1
C: Ras-related protein Rap-1b
D: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9179
Polymers70,7324
Non-polymers1,1855
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.540, 154.760, 38.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Ras-interacting protein 1 / Rain


Mass: 16345.307 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RASIP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5U651
#2: Protein Ras-related protein Rap-1b / GTP-binding protein smg p21B


Mass: 19020.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAP1B, OK/SW-cl.11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61224

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Non-polymers , 4 types, 19 molecules

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


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.16 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 16% PEG 8K, 200mM Calcium Acetate, and 100mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2016 / Details: Mirror: Rh coated
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 16034 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 89.763 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.31
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.78-38.31.4391.45198.5
3-3.20.6383.63199.9
3.2-3.40.3496.44199.8
3.4-3.70.16812.45199.9
3.7-4.20.07924.6199.9
4.2-4.80.04538.38199.7
4.8-5.90.04240.66199.9
5.9-8.20.03645.03199.4
8.2-500.02755.04198.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0151refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HDQ chain B

4hdq


Resolution: 2.78→48.24 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.914 / SU B: 20.821 / SU ML: 0.392 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.422 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2857 802 5 %RANDOM
Rwork0.2048 ---
obs0.2088 15232 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 176.76 Å2 / Biso mean: 91.413 Å2 / Biso min: 53.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---3.62 Å20 Å2
3---3.95 Å2
Refinement stepCycle: final / Resolution: 2.78→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4046 0 72 14 4132
Biso mean--89.34 79.76 -
Num. residues----541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194176
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.985670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1635532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.57922.905179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.62515643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0061541
X-RAY DIFFRACTIONr_chiral_restr0.0840.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023134
X-RAY DIFFRACTIONr_mcbond_it4.9989.5972154
X-RAY DIFFRACTIONr_mcangle_it8.08714.3732678
X-RAY DIFFRACTIONr_scbond_it5.2029.6692019
LS refinement shellResolution: 2.78→2.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 54 -
Rwork0.426 1030 -
all-1084 -
obs--95.93 %

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