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- PDB-2bz8: N-terminal Sh3 domain of CIN85 bound to Cbl-b peptide -

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Basic information

Entry
Database: PDB / ID: 2bz8
TitleN-terminal Sh3 domain of CIN85 bound to Cbl-b peptide
Components
  • SH3-DOMAIN KINASE BINDING PROTEIN 1
  • SIGNAL TRANSDUCTION PROTEIN CBL-B SH3-BINDING PROTEIN CBL-B, RING FINGER PROTEIN 56, CBL-B
KeywordsSH3 DOMAIN / CIN85 ADAPTOR PROTEIN / CBL UBIQUITIN LIGASE / ENDOCYTOSIS
Function / homology
Function and homology information


regulation of platelet-derived growth factor receptor-alpha signaling pathway / Reelin signalling pathway / T cell anergy / positive regulation of T cell anergy / CD4-positive, alpha-beta T cell proliferation / positive regulation of B cell activation / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of T cell receptor signaling pathway / NLS-bearing protein import into nucleus / endocytic vesicle ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / Reelin signalling pathway / T cell anergy / positive regulation of T cell anergy / CD4-positive, alpha-beta T cell proliferation / positive regulation of B cell activation / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of T cell receptor signaling pathway / NLS-bearing protein import into nucleus / endocytic vesicle / cytoskeleton organization / phosphotyrosine residue binding / InlB-mediated entry of Listeria monocytogenes into host cell / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of protein ubiquitination / actin filament organization / EGFR downregulation / protein catabolic process / RING-type E3 ubiquitin transferase / cytoplasmic vesicle membrane / Negative regulation of MET activity / receptor tyrosine kinase binding / SH3 domain binding / endocytosis / positive regulation of protein catabolic process / ubiquitin protein ligase activity / cell-cell junction / Antigen processing: Ubiquitination & Proteasome degradation / cell migration / Cargo recognition for clathrin-mediated endocytosis / cell-cell signaling / Clathrin-mediated endocytosis / T cell receptor signaling pathway / regulation of cell shape / Potential therapeutics for SARS / cytoskeleton / protein ubiquitination / intracellular signal transduction / neuron projection / immune response / membrane raft / focal adhesion / apoptotic process / ubiquitin protein ligase binding / synapse / calcium ion binding / signal transduction / zinc ion binding / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
SH3 domain-containing kinase-binding protein 1, first SH3 domain / SH3 domain-containing kinase-binding protein 1, second SH3 domain / SH3 domain-containing kinase-binding protein 1, 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 ...SH3 domain-containing kinase-binding protein 1, first SH3 domain / SH3 domain-containing kinase-binding protein 1, second SH3 domain / SH3 domain-containing kinase-binding protein 1, 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 / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / SH3 Domains / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / 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 / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase CBL-B / SH3 domain-containing kinase-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCardenes, N. / Moncalian, G. / Bravo, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Cbl Promotes Clustering of Endocytic Adaptor Proteins
Authors: Jozic, D. / Cardenes, N. / Lissanu-Deribe, Y. / Moncalian, G. / Hoeller, D. / Groemping, Y. / Dikic, I. / Rittinger, K. / Bravo, J.
History
DepositionAug 12, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SH3-DOMAIN KINASE BINDING PROTEIN 1
B: SH3-DOMAIN KINASE BINDING PROTEIN 1
C: SIGNAL TRANSDUCTION PROTEIN CBL-B SH3-BINDING PROTEIN CBL-B, RING FINGER PROTEIN 56, CBL-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9245
Polymers14,8783
Non-polymers462
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.158, 51.158, 97.472
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.423197, 0.905071, 0.041843), (0.905856, 0.423586, -0.000489), (-0.018166, 0.037696, -0.999124)
Vector: -3.5481, 2.547, 73.5087)

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Components

#1: Protein SH3-DOMAIN KINASE BINDING PROTEIN 1 / CBL-INTERACTING PROTEIN OF 85KDA / HUMAN SRC-FAMILY KINASE BINDING PROTEIN 1 / HSB-1 / CD2 BINDING ...CBL-INTERACTING PROTEIN OF 85KDA / HUMAN SRC-FAMILY KINASE BINDING PROTEIN 1 / HSB-1 / CD2 BINDING PROTEIN 3 / CD2BP3 / CIN85


Mass: 6772.526 Da / Num. of mol.: 2 / Fragment: N-TERMINAL SH3 DOMAIN RESIDUES 1-58
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Organ: BRAIN, KIDNEY, HEART, PLACENTA, LUNG, LIVER, SKELETAL MUSCLE, PANCREAS
Plasmid: PET29B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA(DE3)PLYS / References: UniProt: Q96B97
#2: Protein/peptide SIGNAL TRANSDUCTION PROTEIN CBL-B SH3-BINDING PROTEIN CBL-B, RING FINGER PROTEIN 56, CBL-B


Mass: 1332.622 Da / Num. of mol.: 1 / Fragment: POLYPROLINE RICH REGION RESIDUES 902-912 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q13191
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.4 Å3/Da / Density % sol: 47.3 %
Description: STARTING MODEL FOR MOLECULAR REPLACEMENT WAS THE ISOLATED CIN85 N-TERMINAL SH3, UNPUBLISHED.
Crystal growpH: 7.5
Details: 0.8 M NA CITRATE, 0.1 M BIS-TRIS PH 7.5, 0.2 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Site: SRS / Beamline: 14.2 / Type: BRUKER / Wavelength: 1.5418
DetectorType: BRUKER / Detector: CCD / Date: Nov 3, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→2 Å / Num. obs: 9738 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 29
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 2.87 / % possible all: 98.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1029899.76 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: A TWINING FRACTION OF 0.305 WAS CONSIDERED DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 746 7.7 %RANDOM
Rwork0.221 ---
obs0.221 9742 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 82.5224 Å2 / ksol: 0.386287 e/Å3
Displacement parametersBiso mean: 34.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-1.26 Å20 Å2
2---0.08 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1025 0 2 82 1109
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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