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- PDB-5hkw: Crystal Structure of Apo c-Cbl TKBD Refined to 2.25 A Resolution -

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Basic information

Entry
Database: PDB / ID: 5hkw
TitleCrystal Structure of Apo c-Cbl TKBD Refined to 2.25 A Resolution
ComponentsE3 ubiquitin-protein ligase CBL
KeywordsLIGASE / SPRY2 / Cbl / Protein-protein interaction / anticancer target
Function / homology
Function and homology information


regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / entry of bacterium into host cell / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation / Interleukin-6 signaling ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / entry of bacterium into host cell / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation / Interleukin-6 signaling / response to testosterone / negative regulation of epidermal growth factor receptor signaling pathway / cellular response to platelet-derived growth factor stimulus / response to starvation / protein monoubiquitination / TGF-beta receptor signaling activates SMADs / protein autoubiquitination / FLT3 signaling by CBL mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / phosphotyrosine residue binding / ephrin receptor binding / InlB-mediated entry of Listeria monocytogenes into host cell / cellular response to nerve growth factor stimulus / response to activity / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / response to gamma radiation / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / EGFR downregulation / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / Constitutive Signaling by EGFRvIII / RING-type E3 ubiquitin transferase / cilium / Negative regulation of MET activity / receptor tyrosine kinase binding / SH3 domain binding / protein polyubiquitination / cytokine-mediated signaling pathway / positive regulation of receptor-mediated endocytosis / ubiquitin-protein transferase activity / male gonad development / Signaling by CSF1 (M-CSF) in myeloid cells / ubiquitin protein ligase activity / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / growth cone / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / response to ethanol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / cadherin binding / membrane raft / focal adhesion / DNA damage response / calcium ion binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / plasma membrane / cytosol
Similarity search - Function
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 / 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 / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / SH2 domain / SHC Adaptor Protein / 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
E3 ubiquitin-protein ligase CBL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 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 Apo c-Cbl TKBD Refined to 2.25 A Resolution
Authors: Zhang, N. / Ferris, D. / Lovell, S. / Smalter-Hall, A. / Battaile, K.P. / Anbanandam, A. / Gao, P. / Hanzlik, R. / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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: E3 ubiquitin-protein ligase CBL
C: E3 ubiquitin-protein ligase CBL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,1766
Polymers107,1073
Non-polymers693
Water4,432246
1
A: E3 ubiquitin-protein ligase CBL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7252
Polymers35,7021
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 ubiquitin-protein ligase CBL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7252
Polymers35,7021
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: E3 ubiquitin-protein ligase CBL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7252
Polymers35,7021
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)159.116, 106.523, 84.984
Angle α, β, γ (deg.)90.000, 92.130, 90.000
Int Tables number5
Space group name H-MC121

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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.: 3
Fragment: Tyrosine kinase binding domain (TKBD), residues 47-351
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) / Strain (production host): BL21 (DE3) pLyseS-RARE
References: UniProt: P22681, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 3.36 Å3/Da / Density % sol: 63.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 3350, 0.2M sodium citrate dibasic trihyrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→45.12 Å / Num. obs: 67019 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 40.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.5 / Num. measured all: 227494 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 % / Rejects: 0

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2% possible all
2.25-2.30.6421507144950.78199.8
10.55-45.120.02149.922096540.99995.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.3.6data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BUM

3bum


Resolution: 2.25→42.463 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 25.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 3346 4.99 %
Rwork0.1798 63663 -
obs0.1825 67009 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.91 Å2 / Biso mean: 52.2536 Å2 / Biso min: 24.74 Å2
Refinement stepCycle: final / Resolution: 2.25→42.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7262 0 3 246 7511
Biso mean--37.39 45.82 -
Num. residues----906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137478
X-RAY DIFFRACTIONf_angle_d0.97510099
X-RAY DIFFRACTIONf_chiral_restr0.0451098
X-RAY DIFFRACTIONf_plane_restr0.0071280
X-RAY DIFFRACTIONf_dihedral_angle_d14.5982728
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.28220.31131540.269626562810100
2.2822-2.31620.29951400.27126052745100
2.3162-2.35240.33651460.251226632809100
2.3524-2.3910.31251370.249526442781100
2.391-2.43220.2581390.240226572796100
2.4322-2.47640.31291260.236326442770100
2.4764-2.5240.30211610.230326392800100
2.524-2.57560.29461610.232826162777100
2.5756-2.63160.30351120.217726522764100
2.6316-2.69280.26781300.223526482778100
2.6928-2.76010.30391330.215926822815100
2.7601-2.83470.27711420.214226612803100
2.8347-2.91810.25281500.213926242774100
2.9181-3.01230.26981290.213226672796100
3.0123-3.11990.24681230.194226582781100
3.1199-3.24480.22361330.192626762809100
3.2448-3.39240.21151280.18372660278899
3.3924-3.57110.26231410.184526392780100
3.5711-3.79480.22611530.16742627278099
3.7948-4.08750.19751560.149726422798100
4.0875-4.49850.19871540.13622644279899
4.4985-5.14840.2051440.13852634277899
5.1484-6.48280.20081390.16312692283199
6.4828-42.47020.18621150.1442733284899

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