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- PDB-3zfx: Crystal structure of EphB1 -

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Basic information

Entry
Database: PDB / ID: 3zfx
TitleCrystal structure of EphB1
ComponentsEPHRIN TYPE-B RECEPTOR 1
KeywordsTRANSFERASE
Function / homology
Function and homology information


skeletal muscle satellite cell activation / negative regulation of skeletal muscle satellite cell proliferation / hindbrain tangential cell migration / optic nerve morphogenesis / negative regulation of satellite cell differentiation / axon guidance receptor activity / central nervous system projection neuron axonogenesis / transmembrane-ephrin receptor activity / immunological synapse formation / filopodium tip ...skeletal muscle satellite cell activation / negative regulation of skeletal muscle satellite cell proliferation / hindbrain tangential cell migration / optic nerve morphogenesis / negative regulation of satellite cell differentiation / axon guidance receptor activity / central nervous system projection neuron axonogenesis / transmembrane-ephrin receptor activity / immunological synapse formation / filopodium tip / dendritic spine development / camera-type eye morphogenesis / dendritic spine morphogenesis / positive regulation of synapse assembly / neural precursor cell proliferation / EPH-Ephrin signaling / Ephrin signaling / retinal ganglion cell axon guidance / establishment of cell polarity / cell-substrate adhesion / detection of temperature stimulus involved in sensory perception of pain / regulation of JNK cascade / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / EPHB-mediated forward signaling / regulation of ERK1 and ERK2 cascade / cell chemotaxis / neurogenesis / axon guidance / modulation of chemical synaptic transmission / receptor protein-tyrosine kinase / early endosome membrane / angiogenesis / protein autophosphorylation / membrane raft / axon / glutamatergic synapse / dendrite / protein-containing complex binding / endoplasmic reticulum / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol
Similarity search - Function
Ephrin type-B receptor 1, ligand binding domain / EphB1 , SAM domain / 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. ...Ephrin type-B receptor 1, ligand binding domain / EphB1 , SAM domain / 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) / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ephrin type-B receptor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDebreczeni, J.E. / Overman, R. / Truman, C. / McAlister, M. / Attwood, T.K.
CitationJournal: Protein Sci. / Year: 2014
Title: Completing the Structural Family Portrait of the Human Ephb Tyrosine Kinase Domains
Authors: Overman, R.C. / Debreczeni, J.E. / Truman, C.M. / Mcalister, M.S. / Attwood, T.K.
History
DepositionDec 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Apr 9, 2014Group: Database references
Revision 1.3May 7, 2014Group: Database references
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 1
B: EPHRIN TYPE-B RECEPTOR 1
C: EPHRIN TYPE-B RECEPTOR 1
D: EPHRIN TYPE-B RECEPTOR 1
E: EPHRIN TYPE-B RECEPTOR 1
F: EPHRIN TYPE-B RECEPTOR 1
G: EPHRIN TYPE-B RECEPTOR 1
H: EPHRIN TYPE-B RECEPTOR 1
I: EPHRIN TYPE-B RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,32010
Polymers303,2249
Non-polymers961
Water2,414134
1
A: EPHRIN TYPE-B RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7882
Polymers33,6921
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EPHRIN TYPE-B RECEPTOR 1


Theoretical massNumber of molelcules
Total (without water)33,6921
Polymers33,6921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: EPHRIN TYPE-B RECEPTOR 1


Theoretical massNumber of molelcules
Total (without water)33,6921
Polymers33,6921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: EPHRIN TYPE-B RECEPTOR 1


Theoretical massNumber of molelcules
Total (without water)33,6921
Polymers33,6921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: EPHRIN TYPE-B RECEPTOR 1


Theoretical massNumber of molelcules
Total (without water)33,6921
Polymers33,6921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: EPHRIN TYPE-B RECEPTOR 1


Theoretical massNumber of molelcules
Total (without water)33,6921
Polymers33,6921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: EPHRIN TYPE-B RECEPTOR 1


Theoretical massNumber of molelcules
Total (without water)33,6921
Polymers33,6921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: EPHRIN TYPE-B RECEPTOR 1


Theoretical massNumber of molelcules
Total (without water)33,6921
Polymers33,6921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: EPHRIN TYPE-B RECEPTOR 1


Theoretical massNumber of molelcules
Total (without water)33,6921
Polymers33,6921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)195.980, 195.980, 60.242
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A607 - 889
2116B607 - 889
3116C607 - 889
4116D607 - 889
5116E607 - 889
6116F607 - 889
7116G607 - 889
8116H607 - 889
9116I607 - 889

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.825817, -0.563821, 0.011482), (0.562908, -0.825368, -0.043602), (0.034061, -0.029544, 0.998983)92.07188, -121.92316, 25.87333
3given(-0.060741, 0.998128, -0.007188), (-0.998134, -0.060692, 0.006774), (0.006326, 0.007586, 0.999951)156.25623, -29.03192, 9.48438
4given(0.504265, 0.863546, -0.002377), (0.863543, -0.50427, -0.002414), (-0.003284, -0.000835, -0.999994)97.89926, -56.70824, -1.18663
5given(0.806658, -0.590749, -0.017839), (-0.589686, -0.806498, 0.042785), (-0.039662, -0.023993, -0.998925)43.53585, -18.71254, 9.802
6given(0.880726, -0.473612, -0.003682), (0.47362, 0.880647, 0.01205), (-0.002464, -0.012357, 0.999921)43.86538, -21.8531, -11.62737
7given(-0.898757, -0.438185, -0.015153), (-0.438445, 0.898103, 0.034309), (-0.001425, 0.037479, -0.999296)156.99539, -26.93791, 27.38687
8given(-0.999204, -0.039883, 3.7E-5), (-0.039883, 0.999193, -0.004732), (0.000152, -0.004729, -0.999989)93.39616, 56.5048, 38.37903
9given(0.060475, 0.998167, 0.002127), (0.998122, -0.060451, -0.009954), (-0.009807, 0.002725, -0.999948)95.12352, -121.96201, 48.60216

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Components

#1: Protein
EPHRIN TYPE-B RECEPTOR 1 / 2.7.10.1 / ELK / EPH TYROSINE KINASE 2 / EPH-LIKE KINASE 6 / EK6 / HEK6 / NEURONALLY-EXPRESSED EPH- ...2.7.10.1 / ELK / EPH TYROSINE KINASE 2 / EPH-LIKE KINASE 6 / EK6 / HEK6 / NEURONALLY-EXPRESSED EPH-RELATED TYROSINE KINASE / NET / TYROSINE-PROTEIN KINASE RECEPTOR EPH-2 / EPHB1


Mass: 33691.535 Da / Num. of mol.: 9 / Fragment: KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: P54762, receptor protein-tyrosine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1.88 Å3/Da / Density % sol: 38 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14 / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: May 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.031
11-K, -H, -L20.03
11-h,-k,l30.432
11K, H, -L40.507
ReflectionResolution: 2.5→49.11 Å / Num. obs: 89433 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.911 / SU B: 25.424 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21669 4536 5.1 %RANDOM
Rwork0.18835 ---
obs0.18982 84523 99.83 %-
Solvent computationVDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.319 Å2
Baniso -1Baniso -2Baniso -3
1-14.85 Å20 Å20 Å2
2--14.85 Å20 Å2
3----29.71 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18019 0 5 134 18158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01918369
X-RAY DIFFRACTIONr_bond_other_d0.0050.0212246
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.95324882
X-RAY DIFFRACTIONr_angle_other_deg1.146329808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46252290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2724.055794
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.081153058
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.70915114
X-RAY DIFFRACTIONr_chiral_restr0.0680.22815
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02120337
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023753
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3027 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.160.1
2Bloose positional0.180.1
3Cloose positional0.110.1
4Dloose positional0.130.1
5Eloose positional0.20.1
6Floose positional0.110.1
7Gloose positional0.230.1
8Hloose positional0.20.1
9Iloose positional0.160.1
1Aloose thermal0.5510
2Bloose thermal0.4110
3Cloose thermal0.2710
4Dloose thermal0.410
5Eloose thermal0.4410
6Floose thermal0.3710
7Gloose thermal0.3610
8Hloose thermal0.3110
9Iloose thermal0.2310
LS refinement shellResolution: 2.499→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 296 -
Rwork0.231 5988 -
obs--98.11 %
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)
11.74620.3885-0.43661.2977-0.64272.505-0.03970.0107-0.09270.1742-0.0151-0.0098-0.01930.06180.05490.07420.0719-0.03940.1871-0.05910.318681.124-50.220415.2577
21.16530.1835-0.56041.0480.25192.25280.0071-0.0521-0.01380.03320.0313-0.0190.0947-0.0883-0.03840.2883-0.0146-0.05570.3417-0.00930.363249.3267-52.7533-14.6013
30.95720.00930.31550.82360.18031.63210.0072-0.0178-0.03140.0612-0.00430.0889-0.1125-0.0532-0.0030.5426-0.0639-0.0490.29880.0010.425425.413-73.53355.0869
41.49220.37950.4931.2898-0.24352.840.0590.0687-0.0351-0.0503-0.07050.06940.16440.02090.01150.2108-0.01220.03080.0118-0.01640.2259-2.7484-17.7429-16.3708
51.2518-0.1074-0.41621.4977-0.20691.861-0.0190.0961-0.0148-0.00390.0268-0.08690.14860.0711-0.00780.2272-0.0434-0.01770.4729-0.01960.317448.58663.029-6.9742
61.1860.1121-0.08290.9576-0.23771.41070.0588-0.0434-0.00960.2007-0.01280.0310.09710.1583-0.04610.47110.1132-0.01370.35010.01570.424819.3773-42.693525.6027
71.4591-0.1162-0.14451.10420.4862.52410.010.0757-0.0444-0.07130.0107-0.01950.1168-0.1766-0.02070.3635-0.12710.01470.26240.01190.304378.233612.174113.0998
81.4535-0.3867-0.31231.07720.5772.7344-0.01550.0007-0.0603-0.14420.0119-0.0062-0.14480.13970.00360.0568-0.0811-0.01090.18330.02710.243216.3241-106.106623.7139
90.97290.18730.01790.9926-0.22991.23020.04860.1107-0.0405-0.0119-0.0341-0.0157-0.12620.0207-0.01440.5419-0.0289-0.0280.3037-0.02980.497470.9698-18.413832.7254
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A607 - 889
2X-RAY DIFFRACTION2B607 - 888
3X-RAY DIFFRACTION3C610 - 888
4X-RAY DIFFRACTION4D607 - 889
5X-RAY DIFFRACTION5E607 - 889
6X-RAY DIFFRACTION6F608 - 889
7X-RAY DIFFRACTION7G607 - 888
8X-RAY DIFFRACTION8H607 - 888
9X-RAY DIFFRACTION9I607 - 887

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