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- PDB-2bba: Crystal Structure and Thermodynamic Characterization of the EphB4... -

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Basic information

Entry
Database: PDB / ID: 2bba
TitleCrystal Structure and Thermodynamic Characterization of the EphB4 Receptor in Complex with an ephrin-B2 Antagonist Peptide Reveals the Determinants for Receptor Specificity.
Components
  • Agonist peptide
  • Ephrin type-B receptor 4
KeywordsSIGNALING PROTEIN / EphB4 / tumorigenesis / angiogenesis / peptide mimetics / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D
Function / homology
Function and homology information


ephrin receptor activity / cell migration involved in sprouting angiogenesis / EPH-Ephrin signaling / Ephrin signaling / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / heart morphogenesis / EPHB-mediated forward signaling / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase ...ephrin receptor activity / cell migration involved in sprouting angiogenesis / EPH-Ephrin signaling / Ephrin signaling / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / heart morphogenesis / EPHB-mediated forward signaling / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / angiogenesis / protein autophosphorylation / receptor complex / cell adhesion / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol
Similarity search - Function
Ephrin type-B receptor 4, ligand binding domain / EPH-B4, SAM domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain ...Ephrin type-B receptor 4, ligand binding domain / EPH-B4, SAM domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. / Ephrin receptor ligand binding domain / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / Galactose-binding domain-like / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Jelly Rolls / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ephrin type-B receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsChrencik, J.E. / Kuhn, P. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D)
CitationJournal: Structure / Year: 2006
Title: Structure and thermodynamic characterization of the EphB4/Ephrin-B2 antagonist peptide complex reveals the determinants for receptor specificity.
Authors: Chrencik, J.E. / Brooun, A. / Recht, M.I. / Kraus, M.L. / Koolpe, M. / Kolatkar, A.R. / Bruce, R.H. / Martiny-Baron, G. / Widmer, H. / Pasquale, E.B. / Kuhn, P.
History
DepositionOct 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ephrin type-B receptor 4
P: Agonist peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9884
Polymers22,7962
Non-polymers1922
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-36 kcal/mol
Surface area9990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.972, 60.972, 151.681
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Ephrin type-B receptor 4 / Tyrosine-protein kinase receptor HTK


Mass: 21087.953 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHB4, HTK / Plasmid: pBac6 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HIi-5 / References: UniProt: P54760, EC: 2.7.1.112
#2: Protein/peptide Agonist peptide


Mass: 1707.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 3.09 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 2.2 M Ammonium Sulfate, 200 mM NaCl, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 25, 2005
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. obs: 32786 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rsym value: 0.039 / Net I/σ(I): 42.7
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 7.2 / Rsym value: 0.208

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NUK

1nuk


Resolution: 1.65→40 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.352 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.081 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19135 3533 10 %RANDOM
Rwork0.17436 ---
all0.19 ---
obs0.1761 31786 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.498 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1558 0 10 223 1791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211628
X-RAY DIFFRACTIONr_bond_other_d0.0020.021422
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9382229
X-RAY DIFFRACTIONr_angle_other_deg0.88833288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4755201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30322.95871
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.13115240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.174159
X-RAY DIFFRACTIONr_chiral_restr0.1170.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021819
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02348
X-RAY DIFFRACTIONr_nbd_refined0.2720.2240
X-RAY DIFFRACTIONr_nbd_other0.2020.21331
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2741
X-RAY DIFFRACTIONr_nbtor_other0.0870.2893
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2146
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0010.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3420.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5130.213
X-RAY DIFFRACTIONr_mcbond_it1.2761.51076
X-RAY DIFFRACTIONr_mcbond_other0.351.5407
X-RAY DIFFRACTIONr_mcangle_it1.7321606
X-RAY DIFFRACTIONr_scbond_it2.793710
X-RAY DIFFRACTIONr_scangle_it3.9684.5622
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 243 -
Rwork0.159 2286 -
obs--98.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2085-0.1014-0.34990.26220.07870.473100.0222-0.0298-0.00730.0028-0.0081-0.0146-0.0283-0.0028-0.0478-0.00090.0027-0.0117-0.0023-0.031824.607511.827851.1996
23.88750.95162.75441.6018-0.34256.1088-0.19780.1246-0.225-0.13920.1081-0.14180.20430.15350.0897-0.03820.0060.0478-0.0203-0.049-0.025431.41280.927339.8155
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 1961 - 185
2X-RAY DIFFRACTION2PB251 - 2642 - 15

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