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- PDB-5hl0: Crystal Structure of c-Cbl TKBD in complex with SPRY2 peptide (54... -

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Basic information

Entry
Database: PDB / ID: 5hl0
TitleCrystal Structure of c-Cbl TKBD in complex with SPRY2 peptide (54-60, pY55) Refined to 2.2A Resolution
Components
  • E3 ubiquitin-protein ligase CBL
  • Sprouty 2 (SPRY2)
KeywordsLIGASE / SPRY2 / Cbl / Protein-protein interaction / anticancer target
Function / homology
Function and homology information


microtubule end / negative regulation of cell projection organization / negative regulation of lens fiber cell differentiation / lung growth / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / animal organ development / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of vascular endothelial growth factor signaling pathway ...microtubule end / negative regulation of cell projection organization / negative regulation of lens fiber cell differentiation / lung growth / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / animal organ development / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of vascular endothelial growth factor signaling pathway / regulation of Rap protein signal transduction / ubiquitin-protein transferase inhibitor activity / bud elongation involved in lung branching / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / negative regulation of Ras protein signal transduction / protein serine/threonine kinase inhibitor activity / positive regulation of epidermal growth factor receptor signaling pathway / Interleukin-6 signaling / negative regulation of epithelial to mesenchymal transition / inner ear morphogenesis / Regulation of KIT signaling / mast cell degranulation / response to starvation / negative regulation of epidermal growth factor receptor signaling pathway / response to testosterone / TGF-beta receptor signaling activates SMADs / establishment of mitotic spindle orientation / cellular response to vascular endothelial growth factor stimulus / cell fate commitment / protein monoubiquitination / fibroblast growth factor receptor signaling pathway / protein autoubiquitination / positive regulation of peptidyl-serine phosphorylation / cellular response to platelet-derived growth factor stimulus / ephrin receptor binding / phosphotyrosine residue binding / FLT3 signaling by CBL mutants / negative regulation of protein ubiquitination / Negative regulation of FLT3 / ERK1 and ERK2 cascade / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / cellular response to leukemia inhibitory factor / negative regulation of angiogenesis / protein serine/threonine kinase activator activity / InlB-mediated entry of Listeria monocytogenes into host cell / response to activity / response to gamma radiation / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / sensory perception of sound / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / negative regulation of transforming growth factor beta receptor signaling pathway / Negative regulation of FGFR1 signaling / EGFR downregulation / cellular response to nerve growth factor stimulus / Spry regulation of FGF signaling / Constitutive Signaling by EGFRvIII / cytokine-mediated signaling pathway / negative regulation of ERK1 and ERK2 cascade / Negative regulation of MET activity / RING-type E3 ubiquitin transferase / receptor tyrosine kinase binding / SH3 domain binding / positive regulation of receptor-mediated endocytosis / ruffle membrane / male gonad development / protein polyubiquitination / Signaling by CSF1 (M-CSF) in myeloid cells / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Cargo recognition for clathrin-mediated endocytosis / actin cytoskeleton / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / microtubule cytoskeleton / growth cone / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / response to ethanol / cytoskeleton / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / protein ubiquitination / cilium / positive regulation of cell migration / cadherin binding / membrane raft / symbiont entry into host cell / negative regulation of cell population proliferation / focal adhesion / calcium ion binding / DNA damage response / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction
Similarity search - Function
: / Sprouty / Sprouty protein (Spry) / Sprouty (SPR) domain profile. / Adaptor protein Cbl, N-terminal domain / 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 ...: / Sprouty / Sprouty protein (Spry) / Sprouty (SPR) domain profile. / Adaptor protein Cbl, N-terminal domain / 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 / Transcription Elongation Factor S-II; Chain A / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / SH2 domain / SHC Adaptor Protein / UBA-like superfamily / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Recoverin; domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / EF-hand domain pair / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Protein sprouty homolog 2 / E3 ubiquitin-protein ligase CBL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsLovell, S. / Battaile, K.P. / Mehzabeen, N. / Zhang, N. / Cooper, A. / Gao, P. / Perez, R.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5P20RR017708-10 / 8P20GM103420-10 United States
CitationJournal: To Be Published
Title: Crystal Structure of c-Cbl TKBD in complex with SPRY2 peptide (54-60, pY55) Refined to 2.2A Resolution
Authors: Zhang, N. / Ferris, D. / Lovell, S. / Smalter-Hall, A. / Battaile, K.P. / Anbanandam, A. / Gao, P. / Perez, R.P.
History
DepositionJan 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase CBL
B: Sprouty 2 (SPRY2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6273
Polymers36,6042
Non-polymers231
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-25 kcal/mol
Surface area14290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.180, 123.180, 56.786
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

#1: Protein E3 ubiquitin-protein ligase CBL / Casitas B-lineage lymphoma proto-oncogene / Proto-oncogene c-Cbl / RING finger protein 55 / Signal ...Casitas B-lineage lymphoma proto-oncogene / Proto-oncogene c-Cbl / RING finger protein 55 / Signal transduction protein CBL


Mass: 35702.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBL, CBL2, RNF55 / Plasmid: pTBSG / Production host: Escherichia coli (E. coli)
References: UniProt: P22681, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Sprouty 2 (SPRY2)


Mass: 901.808 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthesized by New England Peptide with an acetylated N-terminus
Source: (synth.) Homo sapiens (human) / References: UniProt: O43597*PLUS
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.4 Å3/Da / Density % sol: 63.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 16% (w/v) PEG 8000, 0.04M Potassium phosphate (monobasic), 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→41.75 Å / Num. obs: 25191 / % possible obs: 100 % / Redundancy: 10.2 % / Biso Wilson estimate: 36.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.042 / Net I/σ(I): 12.1 / Num. measured all: 257967 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.2-2.2710.41.23622261121750.8970.403100
9.07-41.759.80.04743.438503910.9990.01699

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BUM

3bum


Resolution: 2.2→40.32 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 31.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2366 1187 4.72 %
Rwork0.1902 23960 -
obs0.1923 25147 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.43 Å2 / Biso mean: 45.8552 Å2 / Biso min: 21.44 Å2
Refinement stepCycle: final / Resolution: 2.2→40.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 1 85 2537
Biso mean--46.62 42.25 -
Num. residues----310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122526
X-RAY DIFFRACTIONf_angle_d1.093432
X-RAY DIFFRACTIONf_chiral_restr0.049376
X-RAY DIFFRACTIONf_plane_restr0.008434
X-RAY DIFFRACTIONf_dihedral_angle_d15.158910
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.30010.41461540.303229563110
2.3001-2.42140.30981360.257129733109
2.4214-2.57310.29181590.229429733132
2.5731-2.77170.26631400.213429663106
2.7717-3.05050.26961700.202429703140
3.0505-3.49180.24191630.194329933156
3.4918-4.39840.19911330.160730353168
4.3984-40.32690.1871320.164530943226

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