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- PDB-2qkq: Structure of the SAM Domain of Human Ephrin Type-B Receptor 4 -

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Basic information

Entry
Database: PDB / ID: 2qkq
TitleStructure of the SAM Domain of Human Ephrin Type-B Receptor 4
ComponentsEphrin type-B receptor 4
KeywordsTRANSFERASE / ATP-binding / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphorylation / Receptor / Transmembrane / Tyrosine-protein kinase / Structural Genomics / Structural Genomics Consortium / SGC
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 / Transcription Factor, Ets-1 / 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-B receptor 4, ligand binding domain / EPH-B4, SAM domain / Transcription Factor, Ets-1 / 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) / 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 / DNA polymerase; domain 1 / 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ephrin type-B receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWalker, J.R. / Cuerrier, D. / Butler-Cole, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: SAM Domain of Human Ephrin Type-B Receptor 4 (EPHB4)
Authors: Walker, J.R. / Cuerrier, D. / Butler-Cole, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionJul 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,1684
Polymers18,0972
Non-polymers712
Water57632
1
A: Ephrin type-B receptor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0842
Polymers9,0481
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ephrin type-B receptor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0842
Polymers9,0481
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.566, 73.566, 25.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

#1: Protein Ephrin type-B receptor 4 / Tyrosine-protein kinase receptor HTK / Tyrosine-protein kinase TYRO11


Mass: 9048.308 Da / Num. of mol.: 2 / Fragment: SAM (Sterile Alpha Motif) Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHB4, HTK, TYRO11 / Plasmid: pET28-MHL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P54760, receptor protein-tyrosine kinase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 1.92 Å3/Da / Density % sol: 35.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 2.3 M NaKPO4, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97918 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 11, 2007 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→37 Å / Num. all: 8210 / Num. obs: 8210 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rsym value: 0.064 / Net I/σ(I): 39
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.87 / Num. unique all: 772 / Rsym value: 0.73 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F0M

1f0m


Resolution: 2.1→36.79 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.953 / SU B: 13.755 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24406 349 4.3 %RANDOM
Rwork0.21952 ---
obs0.22071 7859 98.67 %-
all-7859 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.737 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å20 Å2
2--1.25 Å20 Å2
3----2.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms948 0 2 33 983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021967
X-RAY DIFFRACTIONr_angle_refined_deg1.0061.9381300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0415126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57423.17141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.19615167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.48156
X-RAY DIFFRACTIONr_chiral_restr0.0830.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02726
X-RAY DIFFRACTIONr_nbd_refined0.2090.2400
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2689
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.239
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.210
X-RAY DIFFRACTIONr_mcbond_it0.321.5630
X-RAY DIFFRACTIONr_mcangle_it0.5252962
X-RAY DIFFRACTIONr_scbond_it0.9843386
X-RAY DIFFRACTIONr_scangle_it1.3894.5338
LS refinement shellResolution: 2.102→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 27 -
Rwork0.262 547 -
obs--93.94 %
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)
111.66575.151-9.279653.62318.66964.72160.0785-1.896-1.36261.0737-0.5018-2.98970.61093.24680.4233-0.165-0.1176-0.09030.29490.18510.323123.4138.6999.8531
232.7053.1195-1.54693.15522.06347.2666-0.91950.39830.6303-0.23250.4192-0.3095-1.23230.28720.50040.008-0.12520.011-0.09890.08690.010215.650812.14835.0382
334.68528.6374-5.8414.54559.267848.9946-0.4493-1.22881.9244-0.0666-0.09190.2239-1.1353-0.14980.5412-0.1150.0013-0.0317-0.0322-0.02120.01511.197310.1312.6215
45.2751-3.7764-4.613211.65920.76429.3455-0.6491-1.1047-1.03010.09160.0411-0.66590.64690.96930.608-0.02740.12220.10740.12420.20920.206316.1849-0.084412.3288
520.1835-2.8895-2.236918.3824-0.48867.5616-0.3907-1.0795-1.2240.06540.45490.50440.2802-0.9457-0.0642-0.108-0.04340.01180.09050.1104-0.0095.91332.51696.4426
635.8803-21.74750.523119.65348.337111.5798-0.52282.0282-1.4526-1.7121-0.58940.8422-1.97380.32221.11220.13320.1131-0.01670.1080.0238-0.15467.9087.0748-1.8322
724.259313.71759.583927.85113.958935.7654-0.05110.7965-1.7152-1.29090.4542-3.19110.95741.935-0.4032-0.00390.00630.27380.1562-0.03360.245617.66752.3120.0203
829.160321.50341.145717.877810.298944.2767-0.85120.1798-2.2754-0.73630.3021-0.98492.3640.6370.54910.2602-0.12420.139-0.17-0.01190.338528.170813.3680.8251
94.33612.88326.124418.7569-3.345111.91750.217-0.75750.0983-0.0413-0.37050.37950.325-1.46860.1535-0.0771-0.14920.09950.06760.04370.029124.494820.20495.9953
102.6954-5.0894-0.297111.3553-6.651629.83420.377-0.0751-0.1322-1.2326-0.29410.8294-0.2149-1.3028-0.0829-0.0234-0.0484-0.0217-0.0294-0.0347-0.047926.172726.0133-1.4494
1119.9525-7.99257.13683.9504-2.642619.0439-0.59440.2059-1.6151-0.9494-0.3086-1.45940.86110.83860.9030.14580.08130.2325-0.05670.10780.225236.196120.3214-1.5316
1227.8334-18.6894-4.860526.6574-3.4758.70951.136-0.27570.8603-0.9275-0.5467-1.4601-0.21691.4382-0.58930.0079-0.0860.11540.00140.08670.144738.934727.60234.2754
139.1597-2.70591.737325.11990.81215.0256-0.3409-0.61560.25930.4837-0.0383-0.3946-0.3952-0.60080.3792-0.074-0.01060.0048-0.08210.0146-0.126130.95729.0318.5249
1410.84784.19264.464875.97651.16361.84190.4131-1.7633-2.58312.28950.7063-4.07423.61122.9355-1.11930.3416-0.0399-0.16430.68930.20640.463236.402217.081910.983
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA908 - 91414 - 20
2X-RAY DIFFRACTION2AA915 - 92421 - 30
3X-RAY DIFFRACTION3AA925 - 92931 - 35
4X-RAY DIFFRACTION4AA930 - 94136 - 47
5X-RAY DIFFRACTION5AA942 - 95348 - 59
6X-RAY DIFFRACTION6AA954 - 95960 - 65
7X-RAY DIFFRACTION7AA960 - 96866 - 74
8X-RAY DIFFRACTION8BB908 - 91414 - 20
9X-RAY DIFFRACTION9BB915 - 92321 - 29
10X-RAY DIFFRACTION10BB924 - 93030 - 36
11X-RAY DIFFRACTION11BB931 - 94037 - 46
12X-RAY DIFFRACTION12BB941 - 94647 - 52
13X-RAY DIFFRACTION13BB947 - 96253 - 68
14X-RAY DIFFRACTION14BB963 - 96869 - 74

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