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- PDB-4kvg: Crystal structure of RIAM RA-PH domains in complex with GTP bound Rap1 -

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Basic information

Entry
Database: PDB / ID: 4kvg
TitleCrystal structure of RIAM RA-PH domains in complex with GTP bound Rap1
Components
  • Amyloid beta A4 precursor protein-binding family B member 1-interacting protein
  • Ras-related protein Rap-1A
KeywordsSIGNALING PROTEIN / Ras-related protein / ubiquitin fold / GTPase / actin polymerization / integrin activation / cell adhesion / RIAM / RAPL / Mst1 / PDK / Rap1 / Ena/VASP / Profilin / membrane
Function / homology
Function and homology information


Rap protein signal transduction / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / 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 / guanyl-nucleotide exchange factor complex ...Rap protein signal transduction / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / 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 / guanyl-nucleotide exchange factor complex / negative regulation of synaptic vesicle exocytosis / ARMS-mediated activation / Rap1 signalling / anchoring junction / establishment of endothelial barrier / 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 / cellular response to nerve growth factor stimulus / small monomeric GTPase / G protein activity / protein localization to plasma membrane / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of neuron projection development / small GTPase binding / positive regulation of GTPase activity / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / 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 / Signaling by BRAF and RAF1 fusions / late endosome / presynapse / lamellipodium / cell junction / nervous system development / positive regulation of ERK1 and ERK2 cascade / cytoskeleton / early endosome / 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 / cytosol / cytoplasm
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
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsZhang, H. / Chang, Y.E. / Brennan, M.L. / Wu, J.
CitationJournal: J Mol Cell Biol / Year: 2014
Title: The structure of Rap1 in complex with RIAM reveals specificity determinants and recruitment mechanism.
Authors: Zhang, H. / Chang, Y.C. / Brennan, M.L. / Wu, J.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: 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


Theoretical massNumber of molelcules
Total (without water)101,49810
Polymers100,2794
Non-polymers1,2196
Water13,061725
1
A: Ras-related protein Rap-1A
B: Amyloid beta A4 precursor protein-binding family B member 1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7495
Polymers50,1392
Non-polymers6103
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ras-related protein Rap-1A
D: Amyloid beta A4 precursor protein-binding family B member 1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7495
Polymers50,1392
Non-polymers6103
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.467, 85.848, 160.852
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Ras-related protein Rap-1A / C21KG / G-22K / GTP-binding protein smg p21A / Ras-related protein Krev-1


Mass: 19236.854 Da / Num. of mol.: 2 / Fragment: UNP residues 1-167 / Mutation: G12V, Q63E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KREV1, RAP1A / Plasmid: pET281 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62834
#2: 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: 30902.496 Da / Num. of mol.: 2 / Fragment: RA-PH domains (UNP residues 179-437)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Apbb1ip, Prel1 / Plasmid: pET281 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8R5A3

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Non-polymers , 4 types, 731 molecules

#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 725 / 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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M ammonium sulfate, 0.1M Tris, 15% PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2012
RadiationMonochromator: 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
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 137303 / Num. obs: 130322 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 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

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 6891 5 %RANDOM
Rwork0.1971 ---
obs0.19821 130322 99.3 %-
all-137303 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.323 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.65→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6704 0 74 725 7503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.027154
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.071.9769705
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2455885
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17824.652359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.148151380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4951546
X-RAY DIFFRACTIONr_chiral_restr0.0750.21068
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025352
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: 1.648→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 441 -
Rwork0.275 8590 -
obs--92.65 %
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)
11.6106-0.26560.56141.05170.37394.4254-0.01160.13940.02980.0139-0.0275-0.03810.1856-0.03070.03910.0513-0.01380.00410.0764-0.02220.0632-33.027-26.558-2.561
21.10430.23470.21490.55850.07150.6454-0.0124-0.06930.0046-0.0144-0.0145-0.01110.0058-0.05090.02690.05090.02160.01030.0524-0.01190.093-21.489-14.00734.972
34.7048-2.0989-0.58945.5723-3.15527.18340.35580.56680.1716-1.1827-0.459-0.23650.63310.35140.10320.41430.19120.11280.20210.08140.0405-10.45629.64-1.195
41.3124-0.0452-0.22550.4940.03390.81880.0053-0.0001-0.0323-0.0123-0.04220.0517-0.0134-0.0350.03690.04450.0243-0.0040.0464-0.00070.0884-19.82620.91837.948
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 167
2X-RAY DIFFRACTION2B178 - 437
3X-RAY DIFFRACTION3C1 - 166
4X-RAY DIFFRACTION4D178 - 437

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