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- PDB-2j6f: N-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG) BOUND TO CBL-B... -

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Basic information

Entry
Database: PDB / ID: 2j6f
TitleN-TERMINAL SH3 DOMAIN OF CMS (CD2AP HUMAN HOMOLOG) BOUND TO CBL-B PEPTIDE
Components
  • CD2-ASSOCIATED PROTEIN
  • E3 UBIQUITIN-PROTEIN LIGASE CBL-B
KeywordsPROTEIN BINDING / METAL-BINDING / IMMUNE RESPONSE / SH3 / LIGASE / SH2 DOMAIN / SH3 DOMAIN / ZINC-FINGER / SH3- BINDING / UBL CONJUGATION PATHWAY / CYTOSKELETAL REARRANGEMENTS / PHOSPHORYLATION / ADAPTOR PROTEIN / EGFR DOWNREGULATION / CD2 ASSOCIATED PROTEIN
Function / homology
Function and homology information


response to glial cell derived neurotrophic factor / transforming growth factor beta1 production / negative regulation of small GTPase mediated signal transduction / localization of cell / Rab protein signal transduction / regulation of platelet-derived growth factor receptor-alpha signaling pathway / negative regulation of transforming growth factor beta1 production / slit diaphragm / response to transforming growth factor beta / podocyte differentiation ...response to glial cell derived neurotrophic factor / transforming growth factor beta1 production / negative regulation of small GTPase mediated signal transduction / localization of cell / Rab protein signal transduction / regulation of platelet-derived growth factor receptor-alpha signaling pathway / negative regulation of transforming growth factor beta1 production / slit diaphragm / response to transforming growth factor beta / podocyte differentiation / T cell anergy / immunological synapse formation / endothelium development / nerve growth factor signaling pathway / positive regulation of T cell anergy / protein heterooligomerization / collateral sprouting / renal albumin absorption / CD4-positive, alpha-beta T cell proliferation / regulation protein catabolic process at postsynapse / substrate-dependent cell migration, cell extension / phosphatidylinositol 3-kinase regulatory subunit binding / cell-cell adhesion mediated by cadherin / filopodium assembly / negative regulation of CD4-positive, alpha-beta T cell proliferation / membrane organization / cell-cell junction organization / NLS-bearing protein import into nucleus / Nephrin family interactions / podosome / clathrin binding / negative regulation of T cell receptor signaling pathway / maintenance of blood-brain barrier / regulation of postsynaptic neurotransmitter receptor internalization / nuclear envelope lumen / D-glucose import / cell leading edge / negative regulation of epidermal growth factor receptor signaling pathway / filamentous actin / neurotrophin TRK receptor signaling pathway / protein secretion / adipose tissue development / lymph node development / stress-activated MAPK cascade / ruffle / actin filament polymerization / phosphotyrosine residue binding / ERK1 and ERK2 cascade / liver development / actin filament organization / trans-Golgi network membrane / positive regulation of protein ubiquitination / positive regulation of protein secretion / regulation of actin cytoskeleton organization / phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to insulin / synapse organization / protein catabolic process / neuromuscular junction / RING-type E3 ubiquitin transferase / regulation of synaptic plasticity / response to virus / receptor tyrosine kinase binding / SH3 domain binding / structural constituent of cytoskeleton / positive regulation of protein localization to nucleus / lipid metabolic process / response to wounding / centriolar satellite / fibrillar center / male gonad development / positive regulation of protein catabolic process / actin filament binding / ubiquitin protein ligase activity / late endosome / Antigen processing: Ubiquitination & Proteasome degradation / cell migration / actin cytoskeleton / T cell receptor signaling pathway / growth cone / protein-containing complex assembly / vesicle / negative regulation of neuron apoptotic process / response to oxidative stress / cell population proliferation / postsynapse / intracellular signal transduction / protein ubiquitination / immune response / cadherin binding / inflammatory response / membrane raft / axon / cell division / apoptotic process / dendrite / calcium ion binding / glutamatergic synapse / signal transduction / extracellular exosome
Similarity search - Function
CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 domain / 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 ...CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 domain / 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 / Variant SH3 domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / SH3 Domains / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / SH3 domain / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain pair / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase CBL-B / CD2-associated protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMoncalian, G. / Cardenes, N. / Deribe, Y.L. / Spinola-Amilibia, M. / Dikic, I. / Bravo, J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Atypical Polyproline Recognition by the Cms N- Terminal SH3 Domain.
Authors: Moncalian, G. / Cardenes, N. / Deribe, Y.L. / Spinola-Amilibia, M. / Dikic, I. / Bravo, J.
History
DepositionSep 28, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 5, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / diffrn_source ...atom_site / diffrn_source / pdbx_distant_solvent_atoms / pdbx_struct_sheet_hbond / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.occupancy / _diffrn_source.type / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id
Revision 2.1Oct 24, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 2.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD2-ASSOCIATED PROTEIN
C: E3 UBIQUITIN-PROTEIN LIGASE CBL-B


Theoretical massNumber of molelcules
Total (without water)8,7452
Polymers8,7452
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.510, 66.510, 67.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-148-

HOH

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Components

#1: Protein CD2-ASSOCIATED PROTEIN / CAS LIGAND WITH MULTIPLE SH3 DOMAINS / ADAPTER PROTEIN CMS


Mass: 7412.285 Da / Num. of mol.: 1 / Fragment: SH3, RESIDUES 1-62
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL SH3 DOMAIN (SH3A) OF CD2- ASSOCIATED PROTEIN (CD2AP)OR CAS LIGAND WITH MULTIPLE SRC HOMOLOGY 3 DOMAINS (CMS)
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA (DE3) PLYS / References: UniProt: Q9Y5K6
#2: Protein/peptide E3 UBIQUITIN-PROTEIN LIGASE CBL-B / CAS-BR-M MURINE ECTROPIC RETROVIRAL TRANSFORMING SEQUENCE B / CBL-B / SIGNAL TRANSDUCTION PROTEIN ...CAS-BR-M MURINE ECTROPIC RETROVIRAL TRANSFORMING SEQUENCE B / CBL-B / SIGNAL TRANSDUCTION PROTEIN CBL-B / SH3-BINDING PROTEIN CBL-B / CASITAS B-LINEAGE LYMPHOMA PROTO-ONCOGENE B / RING FINGER PROTEIN 56


Mass: 1332.622 Da / Num. of mol.: 1 / Fragment: PEPTIDE, RESIDUES 902-912 / Source method: obtained synthetically
Details: A.A. 902 TO 912 FROM CAS-BR-M (MURINE) ECTROPIC RETROVIRAL TRANSFORMING SEQUENCE B (CBL-B)
Source: (synth.) HOMO SAPIENS (human)
References: UniProt: Q13191, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal growpH: 5.5 / Details: 20% PEG3000, 0.1M ACETATE PH 5.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54179
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 2, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 8678 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 12.33 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 20.9
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 6.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.32 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.084 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.REFINENEMENT WAS INITIATED WITH CNS V1.1 AND PURSUED WITH REFMAC 5 DISORDERED ATOMS IN SIDE CHAIN S WHERE GIVEN AN OCCUPANCY CG LYS A 31, CD ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.REFINENEMENT WAS INITIATED WITH CNS V1.1 AND PURSUED WITH REFMAC 5 DISORDERED ATOMS IN SIDE CHAIN S WHERE GIVEN AN OCCUPANCY CG LYS A 31, CD LYS A 31, CE LYS A 31, NZ LYS A 31, CD GLU A 39, OE1 GLU A 39, OE2 GLU A 39, CE BMET A 48
RfactorNum. reflection% reflectionSelection details
Rfree0.218 465 5.44 %RANDOM
Rwork0.19 ---
obs0.192 8557 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 31.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.374 Å20 Å20 Å2
2---0.374 Å20 Å2
3---0.749 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms548 0 0 60 608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022598
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.989814
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.691574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.5032435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21715116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.562157
X-RAY DIFFRACTIONr_chiral_restr0.1020.284
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02473
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.2242
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.2380
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.241
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6293355
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3574566
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5794275
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7316242
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 7.09→19.32 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.248 11
Rwork0.309 126
Refinement TLS params.Method: refined / Origin x: 49.98 Å / Origin y: 33.365 Å / Origin z: 21.799 Å
111213212223313233
T-0.122 Å20.0118 Å20.0026 Å2--0.0626 Å20.0149 Å2---0.051 Å2
L2.2475 °21.6542 °2-0.8367 °2-4.8468 °20.7249 °2--5.3382 °2
S-0.0551 Å °0.2886 Å °-0.114 Å °0.0125 Å °-0.011 Å °-0.3258 Å °-0.0053 Å °-0.2867 Å °0.066 Å °

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