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- PDB-6olu: RIAM RA-PH core structure in the P212121 space group -

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Basic information

Entry
Database: PDB / ID: 6olu
TitleRIAM RA-PH core structure in the P212121 space group
ComponentsAmyloid beta A4 precursor protein-binding family B member 1-interacting protein
KeywordsSIGNALING PROTEIN / RAP1 Effector RA-PH
Function / homology
Function and homology information


GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / MAP2K and MAPK activation / T cell receptor complex / positive regulation of cell adhesion / GABA-ergic synapse / lamellipodium / presynapse ...GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / MAP2K and MAPK activation / T cell receptor complex / positive regulation of cell adhesion / GABA-ergic synapse / lamellipodium / presynapse / cytoskeleton / protein-macromolecule adaptor activity / intracellular signal transduction / focal adhesion / plasma membrane / cytosol
Similarity search - Function
GRB/APBB1IP / APBB1IP, PH domain / RA like domain / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / PH domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PH domain profile. ...GRB/APBB1IP / APBB1IP, PH domain / RA like domain / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / PH domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ubiquitin-like (UB roll) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Amyloid beta A4 precursor protein-binding family B member 1-interacting protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM119560 United States
CitationJournal: Structure / Year: 2021
Title: Phosphorylation of RIAM by src promotes integrin activation by unmasking the PH domain of RIAM.
Authors: Cho, E.A. / Zhang, P. / Kumar, V. / Kavalchuk, M. / Zhang, H. / Huang, Q. / Duncan, J.S. / Wu, J.
History
DepositionApr 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.title / _citation.year
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amyloid beta A4 precursor protein-binding family B member 1-interacting protein


Theoretical massNumber of molelcules
Total (without water)31,0541
Polymers31,0541
Non-polymers00
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.315, 80.624, 82.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Amyloid beta A4 precursor protein-binding family B member 1-interacting protein / APBB1-interacting protein 1 / Proline-rich EVH1 ligand 1 / PREL-1 / Proline-rich protein 48


Mass: 31053.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Apbb1ip, Prel1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8R5A3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 8% v/v Tacsimate pH 6, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9791 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 24074 / % possible obs: 98 % / Redundancy: 3.2 % / Net I/σ(I): 2
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 1111

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→35.7 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.909 / SU B: 3.739 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.18 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2556 1081 5.2 %RANDOM
Rwork0.21241 ---
obs0.21468 19675 84.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.861 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å20 Å2
2--1.62 Å20 Å2
3----0.67 Å2
Refinement stepCycle: 1 / Resolution: 1.9→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 0 293 2314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192071
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2391.9542796
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9775244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21924.151106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51515380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4311513
X-RAY DIFFRACTIONr_chiral_restr0.0850.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021569
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_it0.6892.094976
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2093.1351217
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8852.1751095
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.6118.3753467
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 70 -
Rwork0.257 1404 -
obs--82.62 %

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