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- PDB-9olb: Identification of ligands for E3 ligases using fragment-based methods -

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Basic information

Entry
Database: PDB / ID: 9olb
TitleIdentification of ligands for E3 ligases using fragment-based methods
Components
  • Epidermal growth factor receptor
  • TNF receptor-associated factor 4
KeywordsLIGASE / small molecule / complex crystal structure / CBL-c / TKB (TYROSINE KINASE BINDING) / REGULATOR OF EGFR MEDIATED SIGNAL TRANSDUCTION
Function / homology
Function and homology information


respiratory tube development / respiratory gaseous exchange by respiratory system / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR ...respiratory tube development / respiratory gaseous exchange by respiratory system / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / regulation of peptidyl-tyrosine phosphorylation / epidermal growth factor binding / response to UV-A / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / morphogenesis of an epithelial fold / WW domain binding / PTK6 promotes HIF1A stabilization / ERBB2 Activates PTK6 Signaling / digestive tract morphogenesis / Signaling by EGFR / intracellular vesicle / negative regulation of epidermal growth factor receptor signaling pathway / eyelid development in camera-type eye / cerebral cortex cell migration / protein insertion into membrane / ERBB2 Regulates Cell Motility / positive regulation of protein kinase activity / protein tyrosine kinase activator activity / Respiratory syncytial virus (RSV) attachment and entry / Signaling by ERBB4 / PI3K events in ERBB2 signaling / positive regulation of phosphorylation / positive regulation of peptidyl-serine phosphorylation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / hair follicle development / MAP kinase kinase kinase activity / bicellular tight junction / GAB1 signalosome / positive regulation of G1/S transition of mitotic cell cycle / embryonic placenta development / salivary gland morphogenesis / signaling adaptor activity / Signaling by ERBB2 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / transmembrane receptor protein tyrosine kinase activity / EGFR Transactivation by Gastrin / GRB2 events in ERBB2 signaling / ossification / SHC1 events in ERBB2 signaling / positive regulation of DNA repair / basal plasma membrane / cellular response to epidermal growth factor stimulus / positive regulation of DNA replication / epithelial cell proliferation / positive regulation of epithelial cell proliferation / Signal transduction by L1 / positive regulation of protein localization to plasma membrane / positive regulation of JNK cascade / NOTCH3 Activation and Transmission of Signal to the Nucleus / cellular response to amino acid stimulus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to estradiol stimulus / EGFR downregulation / clathrin-coated endocytic vesicle membrane / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / cell-cell adhesion / receptor protein-tyrosine kinase / Signaling by ERBB2 ECD mutants / RING-type E3 ubiquitin transferase / negative regulation of protein catabolic process / Signaling by ERBB2 KD Mutants / positive regulation of miRNA transcription / kinase binding / ruffle membrane / Downregulation of ERBB2 signaling / epidermal growth factor receptor signaling pathway / fibrillar center / positive regulation of protein phosphorylation / cell morphogenesis / neuron differentiation / positive regulation of fibroblast proliferation / HCMV Early Events / Constitutive Signaling by Aberrant PI3K in Cancer / actin filament binding / cell junction / transmembrane signaling receptor activity / positive regulation of canonical Wnt signaling pathway / Cargo recognition for clathrin-mediated endocytosis / PIP3 activates AKT signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / transferase activity / ATPase binding / virus receptor activity
Similarity search - Function
TNF receptor-associated factor 4, MATH domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology ...TNF receptor-associated factor 4, MATH domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Growth factor receptor cysteine-rich domain superfamily / : / Zinc finger RING-type profile. / Zinc finger, RING-type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Zinc finger, RING/FYVE/PHD-type / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Epidermal growth factor receptor / TNF receptor-associated factor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsPhan, J. / Fesik, S.W.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Rsc Chem Biol / Year: 2025
Title: Identification of ligands for E3 ligases with restricted expression using fragment-based methods.
Authors: Waterson, A.G. / Lehmann, B.D. / Lu, Z. / Sensintaffar, J.L. / Olejniczak, E.T. / Zhao, B. / Rietz, T. / Payne, W.G. / Phan, J. / Fesik, S.W.
History
DepositionMay 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TNF receptor-associated factor 4
B: TNF receptor-associated factor 4
C: TNF receptor-associated factor 4
D: Epidermal growth factor receptor


Theoretical massNumber of molelcules
Total (without water)67,4764
Polymers67,4764
Non-polymers00
Water1,00956
1
A: TNF receptor-associated factor 4
D: Epidermal growth factor receptor


Theoretical massNumber of molelcules
Total (without water)23,2482
Polymers23,2482
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-3 kcal/mol
Surface area9490 Å2
MethodPISA
2
B: TNF receptor-associated factor 4


Theoretical massNumber of molelcules
Total (without water)22,1141
Polymers22,1141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8190 Å2
MethodPISA
3
C: TNF receptor-associated factor 4


Theoretical massNumber of molelcules
Total (without water)22,1141
Polymers22,1141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.550, 84.963, 68.018
Angle α, β, γ (deg.)90.00, 113.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TNF receptor-associated factor 4 / Cysteine-rich domain associated with RING and Traf domains protein 1 / Metastatic lymph node gene ...Cysteine-rich domain associated with RING and Traf domains protein 1 / Metastatic lymph node gene 62 protein / MLN 62 / RING finger protein 83


Mass: 22113.926 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF4, CART1, MLN62, RNF83 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BUZ4, RING-type E3 ubiquitin transferase
#2: Protein/peptide Epidermal growth factor receptor / Proto-oncogene c-ErbB-1 / Receptor tyrosine-protein kinase erbB-1


Mass: 1134.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P00533, receptor protein-tyrosine kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10-15% PEG 3350, 0.1 M Bis-TRIS pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Mar 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 17400 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.049 / Rrim(I) all: 0.129 / Χ2: 0.952 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
2.64-2.696.50.9398610.7890.9390.3941.020.783
2.69-2.736.60.8128700.8020.9440.3380.880.787
2.73-2.796.60.6998590.870.9650.2910.7580.79
2.79-2.846.60.5558700.910.9760.2310.6020.809
2.84-2.916.60.4998560.9190.9790.2080.5410.793
2.91-2.976.60.4218840.9320.9820.1760.4570.822
2.97-3.056.70.3568390.9510.9870.1480.3860.854
3.05-3.136.60.2838890.9750.9940.1180.3070.837
3.13-3.226.70.2388580.9750.9940.0990.2580.886
3.22-3.336.60.2028570.9820.9950.0840.220.963
3.33-3.446.70.1628660.9880.9970.0670.1751.039
3.44-3.586.60.1428730.9860.9970.0590.1541.125
3.58-3.746.60.128710.9930.9980.050.131.127
3.74-3.946.60.0898540.9960.9990.0370.0961.069
3.94-4.196.60.0768820.9970.9990.0310.0821.109
4.19-4.516.60.0628700.9970.9990.0260.0681.075
4.51-4.966.60.0538810.9980.9990.0220.0571.019
4.96-5.686.60.0558790.99810.0230.060.968
5.68-7.146.50.068760.9980.9990.0250.0650.961
7.14-306.30.0459050.99810.0190.0491.225

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→29.25 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2764 802 4.62 %
Rwork0.2017 --
obs0.2052 17373 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.62→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3776 0 0 56 3832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083889
X-RAY DIFFRACTIONf_angle_d1.055304
X-RAY DIFFRACTIONf_dihedral_angle_d7.41539
X-RAY DIFFRACTIONf_chiral_restr0.054562
X-RAY DIFFRACTIONf_plane_restr0.006701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.790.39431440.27412640X-RAY DIFFRACTION96
2.79-30.30541060.23792777X-RAY DIFFRACTION100
3-3.30.31041430.22812781X-RAY DIFFRACTION100
3.3-3.780.32941280.20672782X-RAY DIFFRACTION100
3.78-4.760.25281320.1742774X-RAY DIFFRACTION100
4.76-29.250.21111490.18472817X-RAY DIFFRACTION100

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