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- PDB-7k7j: EphB6 receptor ectodomain -

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Basic information

Entry
Database: PDB / ID: 7k7j
TitleEphB6 receptor ectodomain
ComponentsEphrin type-B receptor 6
KeywordsTRANSFERASE / receptor tyrosine kinase
Function / homology
Function and homology information


positive regulation of T cell costimulation / type IV hypersensitivity / ephrin receptor activity / activated T cell proliferation / cell surface / ATP binding / plasma membrane
Similarity search - Function
ephrin a2 ectodomain / 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 a2 ectodomain / 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 / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Jelly Rolls / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.004 Å
AuthorsGoldgur, Y. / Himanen, J.
CitationJournal: Plos One / Year: 2021
Title: Structure of the EphB6 receptor ectodomain.
Authors: Mason, E.O. / Goldgur, Y. / Robev, D. / Freywald, A. / Nikolov, D.B. / Himanen, J.P.
History
DepositionSep 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ephrin type-B receptor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8662
Polymers58,4421
Non-polymers4241
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.310, 105.310, 188.724
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ephrin type-B receptor 6


Mass: 58441.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHB6 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: F8WCM8
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
Has ligand of interestN
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: 4.48 Å3/Da / Density % sol: 72.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.5 M sodium nitrate, 0.1 M sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 21919 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 20.1
Reflection shellResolution: 3→3.05 Å / Num. unique obs: 1066 / CC1/2: 0.608

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FL7

3fl7


Resolution: 3.004→48.055 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2883 1046 4.79 %
Rwork0.2346 --
obs0.2371 21858 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.004→48.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 0 28 0 3256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113341
X-RAY DIFFRACTIONf_angle_d1.4234551
X-RAY DIFFRACTIONf_dihedral_angle_d9.7961986
X-RAY DIFFRACTIONf_chiral_restr0.066487
X-RAY DIFFRACTIONf_plane_restr0.01615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.004-3.16240.43721390.35272887X-RAY DIFFRACTION99
3.1624-3.36050.36091610.29142898X-RAY DIFFRACTION100
3.3605-3.61990.2891530.26162929X-RAY DIFFRACTION100
3.6199-3.9840.28651460.22632935X-RAY DIFFRACTION100
3.984-4.56010.2481460.20192974X-RAY DIFFRACTION100
4.5601-5.74370.2641430.20313013X-RAY DIFFRACTION100
5.7437-48.050.28751580.23963176X-RAY DIFFRACTION100
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)
12.6337-0.9744-1.67076.07771.26834.4021-0.1754-0.32020.0278-0.07210.2013-0.3118-0.0193-0.11580.02030.4982-0.0529-0.08450.47660.03870.4247.6667-11.058-16.9529
25.0423-3.21170.37443.23760.31940.1435-0.2052-0.29080.2020.52790.20450.0125-0.4348-0.4208-0.0030.75750.19690.09190.6640.05410.4388-10.88472.7107-12.598
32.9776-1.0318-1.1971.90360.71443.45870.1501-0.05480.0905-0.1223-0.05720.235-0.3041-0.5854-0.05350.47650.0420.01720.5582-0.01590.5525-73.52742.2984-9.88
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 113 )
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 285 )
3X-RAY DIFFRACTION3chain 'A' and (resid 286 through 460 )

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