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- PDB-3hil: SAM Domain of Human Ephrin Type-A Receptor 1 (EphA1) -

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Basic information

Entry
Database: PDB / ID: 3hil
TitleSAM Domain of Human Ephrin Type-A Receptor 1 (EphA1)
ComponentsEphrin type-A receptor 1
KeywordsTRANSFERASE / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / RECEPTOR / TYROSINE-PROTEIN KINASE / STERILE ALPHA MOTIF / STRUCTURAL GENOMICS CONSORTIUM / SGC / Glycoprotein / Membrane / Phosphoprotein / Polymorphism / Transmembrane
Function / homology
Function and homology information


POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / transmembrane-ephrin receptor activity / activation of GTPase activity / EPH-Ephrin signaling / positive regulation of cell-matrix adhesion / regulation of GTPase activity / EPHA-mediated growth cone collapse / fibronectin binding / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway ...POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / transmembrane-ephrin receptor activity / activation of GTPase activity / EPH-Ephrin signaling / positive regulation of cell-matrix adhesion / regulation of GTPase activity / EPHA-mediated growth cone collapse / fibronectin binding / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / positive regulation of stress fiber assembly / transmembrane receptor protein tyrosine kinase activity / substrate adhesion-dependent cell spreading / negative regulation of cell migration / negative regulation of protein kinase activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / positive regulation of angiogenesis / angiogenesis / protein autophosphorylation / cell surface receptor signaling pathway / receptor complex / protein kinase activity / positive regulation of cell migration / positive regulation of cell population proliferation / protein kinase binding / ATP binding / plasma membrane
Similarity search - Function
Ephrin type-A receptor 1, ligand binding 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 ...Ephrin type-A receptor 1, ligand binding 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
NITRATE ION / Ephrin type-A receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWalker, J.R. / Yermekbayeva, L. / Butler-Cole, C. / Weigelt, J. / Bountra, C. / 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-A Receptor 1 (EphA1).
Authors: Walker, J.R. / Yermekbayeva, L. / Butler-Cole, C. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionMay 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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-A receptor 1
B: Ephrin type-A receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2174
Polymers19,1202
Non-polymers972
Water64936
1
A: Ephrin type-A receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6573
Polymers9,5601
Non-polymers972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ephrin type-A receptor 1


Theoretical massNumber of molelcules
Total (without water)9,5601
Polymers9,5601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.286, 52.286, 81.307
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Ephrin type-A receptor 1 / Tyrosine-protein kinase receptor EPH


Mass: 9559.910 Da / Num. of mol.: 2 / Fragment: SAM domain, UNP residues 911-974
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPH, EPHA1, EPHT, EPHT1, MGC163163 / Plasmid: PET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P21709, receptor protein-tyrosine kinase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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

Crystal growTemperature: 293.1 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 22% PEG 3350, 0.3 M MG(NO4)2. PRIOR TO SETTING UP CRYSTALLIZATION PLATES, CHYMOTRYPSIN WAS ADDED TO THE PROTEIN SAMPLE AT A FINAL CONCENTRATION OF 0.57 MICROMOLAR., pH 8.0, VAPOR DIFFUSION, ...Details: 22% PEG 3350, 0.3 M MG(NO4)2. PRIOR TO SETTING UP CRYSTALLIZATION PLATES, CHYMOTRYPSIN WAS ADDED TO THE PROTEIN SAMPLE AT A FINAL CONCENTRATION OF 0.57 MICROMOLAR., pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.1K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917 / Wavelength: 0.917 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 3, 2009
RadiationMonochromator: Horizontal bent Si(111), asymmetrically cut with water cooled Cu Block
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 9138 / Num. obs: 9138 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Rsym value: 0.081 / Net I/σ(I): 43
Reflection shellResolution: 2→2.03 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 3.64 / Num. unique all: 447 / Rsym value: 0.84 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QKQ

2qkq


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.912 / SU B: 10.648 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.199 / 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
Rfree0.27942 437 4.8 %RANDOM
Rwork0.20829 ---
all0.21163 ---
obs0.21163 8696 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.149 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1026 0 5 38 1069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211054
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.9651429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2815131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98822.79143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21515191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.019157
X-RAY DIFFRACTIONr_chiral_restr0.1020.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021785
X-RAY DIFFRACTIONr_mcbond_it0.6941.5647
X-RAY DIFFRACTIONr_mcangle_it1.26421047
X-RAY DIFFRACTIONr_scbond_it2.2713407
X-RAY DIFFRACTIONr_scangle_it3.4774.5382
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 37 -
Rwork0.271 620 -
obs--100 %
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)
11.0242-1.3026-0.061910.04433.0719.2382-0.09640.22960.3417-0.67760.3496-0.1936-0.65290.4857-0.25320.2304-0.03880.01230.1450.09250.1765-12.95444.9099-1.9297
26.50383.75230.88139.57911.56419.0960.08260.4150.4863-0.43710.01950.1116-0.3108-0.0661-0.10210.18440.03630.00690.11760.01360.1599-18.10483.2680.5654
35.46880.0809-0.73716.17046.74029.61530.13750.05240.3277-0.2099-0.18710.3029-0.2558-0.60340.04960.16930.05770.0230.11610.03710.1366-22.67691.064.6947
47.10991.30842.45681.39961.77322.36240.3303-0.25060.5558-0.3201-0.2354-0.1039-0.3473-0.2689-0.0950.33230.05120.12470.1024-0.05830.3259-18.74976.623110.9442
59.9491.8558-4.20829.1692-3.03752.3580.4894-0.34731.6124-0.03670.10760.0529-0.19870.0939-0.5970.4573-0.00430.03690.1568-0.11470.4123-12.584811.229710.0817
69.128-1.86662.19789.106-0.21676.1530.18880.28110.7043-0.18560.0142-0.3637-0.75310.7717-0.2030.1807-0.09230.03510.1435-0.00470.2727-6.54065.18344.494
73.7882-1.5109-4.66114.12251.25829.79650.4608-0.73050.30560.4125-0.1673-0.2197-0.73850.8123-0.29340.2754-0.1059-0.04940.3062-0.11880.1994-11.28220.447115.7318
87.0454.3809-1.81467.7715-2.25745.27010.0402-0.45860.11430.1471-0.2148-0.03040.122-0.11530.17460.1210.0480.05510.1511-0.02910.1206-19.5815-4.050114.5827
91.5225-1.43981.04531.50950.14069.4188-0.0241-0.1441-0.09330.05390.12120.09390.1664-0.1598-0.0970.15270.01140.01840.1291-0.00850.1327-15.661-5.57948.8
103.4418-3.4266-2.21544.9268-0.41066.1620.1771-0.10030.3363-0.06840.0767-0.3023-0.31480.3168-0.25380.1667-0.02120.01190.1935-0.00620.1326-9.6427-3.98121.5876
117.31291.2185-3.8445.93653.92278.635-0.02890.7640.6585-0.4275-0.78771.4007-0.1949-0.81470.81650.06880.0769-0.11120.2602-0.11440.3865-26.4161-6.9659-4.8031
129.5268-0.92021.38298.91882.56054.5952-0.23780.32860.6272-0.35490.2370.3688-0.3906-0.61580.00080.16710.0507-0.0570.2010.02860.1813-21.5421-5.9205-7.4634
130.97930.5493-2.42165.13752.92659.79350.05870.05730.1438-0.3858-0.0320.4392-0.4844-0.2109-0.02670.20870.0299-0.03180.17150.02210.1768-17.1846-3.9584-8.7948
141.62280.84533.87636.07833.03569.8093-0.39140.27540.2186-0.7246-0.13430.1992-0.98420.21480.52580.3071-0.0507-0.1250.49560.05830.1598-16.8978-10.7287-15.5239
157.79414.11052.24327.65651.10447.0129-0.05690.45190.3076-0.13990.04180.5133-0.1421-0.41050.0150.13690.0038-0.05180.1774-0.00340.164-23.1721-17.3572-13.2058
1610.127-2.70861.61296.3650.88697.3647-0.0059-0.18420.04550.2221-0.07350.535-0.0641-0.4990.07940.1345-0.02440.00920.1963-0.03360.2212-25.2796-16.4415-3.6606
178.8705-2.1807-3.85448.37894.843110.1888-0.22530.0127-0.30750.18480.040.12020.2079-0.12930.18530.1428-0.0152-0.03610.13030.02020.137-13.6677-21.74-4.7721
189.59546.86627.42386.69187.33518.045-0.07720.0872-0.70290.07340.3565-0.2770.08090.3919-0.27930.1590.0079-0.00030.1815-0.02030.1662-12.3397-21.6177-10.9445
199.00725.64563.26736.55593.32943.9882-0.40060.3821-0.1322-0.55010.4731-0.1615-0.36690.3015-0.07250.1565-0.01130.00970.1448-0.01040.0686-8.9988-14.6118-11.6833
207.45970.8606-2.64322.06872.07788.4969-0.10620.31610.1503-0.27220.21770.0311-0.13530.0693-0.11150.12680.0021-0.01920.11550.00340.0805-10.8131-10.7241-4.8353
217.93912.1156-2.18974.85120.239310.59940.062-0.1642-0.080.2195-0.05240.12580.284-0.0495-0.00960.08150.0189-0.0050.09220.01180.1133-17.8724-11.43171.7002
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A902 - 909
2X-RAY DIFFRACTION2A910 - 914
3X-RAY DIFFRACTION3A915 - 919
4X-RAY DIFFRACTION4A920 - 924
5X-RAY DIFFRACTION5A925 - 930
6X-RAY DIFFRACTION6A931 - 937
7X-RAY DIFFRACTION7A938 - 947
8X-RAY DIFFRACTION8A948 - 953
9X-RAY DIFFRACTION9A954 - 958
10X-RAY DIFFRACTION10A959 - 964
11X-RAY DIFFRACTION11B903 - 909
12X-RAY DIFFRACTION12B910 - 913
13X-RAY DIFFRACTION13B914 - 918
14X-RAY DIFFRACTION14B919 - 923
15X-RAY DIFFRACTION15B924 - 930
16X-RAY DIFFRACTION16B931 - 936
17X-RAY DIFFRACTION17B937 - 941
18X-RAY DIFFRACTION18B942 - 945
19X-RAY DIFFRACTION19B946 - 952
20X-RAY DIFFRACTION20B953 - 959
21X-RAY DIFFRACTION21B960 - 964

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