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- PDB-2ak5: beta PIX-SH3 complexed with a Cbl-b peptide -

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Basic information

Entry
Database: PDB / ID: 2ak5
Titlebeta PIX-SH3 complexed with a Cbl-b peptide
Components
  • 8-residue peptide from a signal transduction protein CBL-B
  • Rho guanine nucleotide exchange factor 7
KeywordsENDOCYTOSIS/EXOCYTOSIS / adaptor proteins / Cin85 / PIX/COOL / Cbl / protein-protein interaction / endocytosis / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


presynaptic actin cytoskeleton organization / negative regulation of microtubule nucleation / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / NRAGE signals death through JNK / EGFR downregulation / G alpha (12/13) signalling events / RHOQ GTPase cycle / RAC1 GTPase cycle ...presynaptic actin cytoskeleton organization / negative regulation of microtubule nucleation / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / NRAGE signals death through JNK / EGFR downregulation / G alpha (12/13) signalling events / RHOQ GTPase cycle / RAC1 GTPase cycle / RHOA GTPase cycle / regulation of platelet-derived growth factor receptor-alpha signaling pathway / T cell anergy / positive regulation of T cell anergy / storage vacuole / astrocyte cell migration / positive regulation of growth hormone secretion / postsynaptic actin cytoskeleton organization / CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / gamma-tubulin binding / lamellipodium assembly / negative regulation of T cell receptor signaling pathway / NLS-bearing protein import into nucleus / small GTPase-mediated signal transduction / mitotic spindle pole / Golgi organization / Rho protein signal transduction / GABA-ergic synapse / hematopoietic progenitor cell differentiation / ruffle / phosphotyrosine residue binding / guanyl-nucleotide exchange factor activity / positive regulation of protein ubiquitination / RING-type E3 ubiquitin transferase / protein catabolic process / receptor tyrosine kinase binding / SH3 domain binding / positive regulation of protein catabolic process / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / lamellipodium / T cell receptor signaling pathway / cell cortex / growth cone / postsynapse / protein ubiquitination / intracellular signal transduction / neuron projection / immune response / membrane raft / positive regulation of apoptotic process / focal adhesion / centrosome / neuronal cell body / calcium ion binding / protein kinase binding / signal transduction / protein-containing complex / zinc ion binding / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rho guanine nucleotide exchange factor 6/7, coiled-coil domain / betaPIX coiled coil / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / Unstructured region two on RhoGEF 6 and 7 / E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain ...Rho guanine nucleotide exchange factor 6/7, coiled-coil domain / betaPIX coiled coil / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / Unstructured region two on RhoGEF 6 and 7 / E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / CBL proto-oncogene N-terminal domain 1 / CBL proto-oncogene N-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. / Adaptor protein Cbl, N-terminal domain superfamily / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Ubiquitin associated domain / Variant SH3 domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / SH3 Domains / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / PH domain / Ring finger / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Zinc finger RING-type profile. / Zinc finger, RING-type / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain pair / PH-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 7 / E3 ubiquitin-protein ligase CBL-B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsJozic, D. / Cardenes, N. / Deribe, Y.L. / Moncalian, G. / Hoeller, D. / Groemping, Y. / Dikic, I. / Rittinger, K. / Bravo, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Cbl promotes clustering of endocytic adaptor proteins.
Authors: Jozic, D. / Cardenes, N. / Deribe, Y.L. / Moncalian, G. / Hoeller, D. / Groemping, Y. / Dikic, I. / Rittinger, K. / Bravo, J.
History
DepositionAug 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Aug 23, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 7
B: Rho guanine nucleotide exchange factor 7
D: 8-residue peptide from a signal transduction protein CBL-B


Theoretical massNumber of molelcules
Total (without water)15,5893
Polymers15,5893
Non-polymers00
Water2,954164
1
A: Rho guanine nucleotide exchange factor 7
B: Rho guanine nucleotide exchange factor 7
D: 8-residue peptide from a signal transduction protein CBL-B

A: Rho guanine nucleotide exchange factor 7
B: Rho guanine nucleotide exchange factor 7
D: 8-residue peptide from a signal transduction protein CBL-B


Theoretical massNumber of molelcules
Total (without water)31,1786
Polymers31,1786
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_565x-y,-y+1,-z+1/31
Unit cell
Length a, b, c (Å)69.338, 69.338, 58.113
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Rho guanine nucleotide exchange factor 7 / PAK-interacting exchange factor beta / Beta-Pix


Mass: 7290.925 Da / Num. of mol.: 2 / Fragment: beta-pix SH3A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: O55043
#2: Protein/peptide 8-residue peptide from a signal transduction protein CBL-B


Mass: 1007.236 Da / Num. of mol.: 1 / Fragment: residues 904-911 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide can be naturally found in Homo sapiens (Human)Cbl-b
References: UniProt: Q13191
#3: Water ChemComp-HOH / water / SH3-binding protein CBL-B / RING finger protein 56 / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 291 K / pH: 6.5
Details: PEG 3000, SODIUM CITRATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 1.5418
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→26.17 Å / Num. obs: 14106 / % possible obs: 99.5 % / Redundancy: 2.94 % / Rsym value: 0.086 / Net I/σ(I): 31.8
Reflection shellResolution: 1.85→1.93 Å / % possible all: 98.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1SEM

1sem


Resolution: 1.85→26.17 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.9263 / SU B: 9.0032 / SU ML: 0.1122 / Cross valid method: THROUGHOUT / ESU R: 0.3046 / ESU R Free: 0.1528
RfactorNum. reflection% reflectionSelection details
Rfree0.269 -4.9993 %RANDOM
Rwork0.227 ---
obs0.2202 13340 99.5181 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å2-
2--0.04 Å2-
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.85→26.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 0 164 1216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d00.0211083
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.041.8921465
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.053129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.315189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.070.2145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg00.02853
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined0.230.3496
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other0.180.5209
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.260.363
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.050.51
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

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