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- PDB-3fl7: Crystal structure of the human ephrin A2 ectodomain -

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Basic information

Entry
Database: PDB / ID: 3fl7
TitleCrystal structure of the human ephrin A2 ectodomain
ComponentsEphrin receptor
KeywordsTRANSFERASE / SIGNALING PROTEIN / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / RECEPTOR / PHOSPHORYLATION / TRANSMEMBRANE / TYROSINE-PROTEIN KINASE / GLYCOPROTEIN / LIGAND BINDING DOMAIN / CYSTEINE-RICH DOMAIN / SUSHI DOMAIN / EGF-LIKE MOTIF / FIBRONECTIN DOMAIN / STRUCTURAL GENOMICS CONSORTIUM / SGC / Membrane / Phosphoprotein
Function / homology
Function and homology information


notochord cell development / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / ephrin receptor activity ...notochord cell development / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / ephrin receptor activity / leading edge membrane / negative regulation of chemokine production / response to growth factor / post-anal tail morphogenesis / activation of GTPase activity / bone remodeling / positive regulation of bicellular tight junction assembly / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / central nervous system neuron differentiation / RND1 GTPase cycle / RND2 GTPase cycle / tight junction / RND3 GTPase cycle / neural tube development / mammary gland epithelial cell proliferation / RHOV GTPase cycle / growth factor binding / EPHA-mediated growth cone collapse / regulation of cell adhesion mediated by integrin / RHOU GTPase cycle / lamellipodium membrane / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of angiogenesis / ephrin receptor signaling pathway / regulation of ERK1 and ERK2 cascade / vasculogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / osteoclast differentiation / molecular function activator activity / negative regulation of angiogenesis / skeletal system development / protein localization to plasma membrane / cell chemotaxis / positive regulation of protein localization to plasma membrane / cell motility / receptor protein-tyrosine kinase / ruffle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / osteoblast differentiation / cell migration / lamellipodium / virus receptor activity / angiogenesis / receptor complex / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / cadherin binding / inflammatory response / focal adhesion / cell surface / ATP binding / plasma membrane
Similarity search - Function
ephrin a2 ectodomain / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Ephrin type-A receptor 2, ligand binding 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 a2 ectodomain / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Ephrin type-A receptor 2, ligand binding 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) / Galactose-binding domain-like / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Fibronectin type III domain / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Ribbon / 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 / Jelly Rolls / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / 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
Ephrin type-A receptor 2 / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWalker, J.R. / Yermekbayeva, L. / Seitova, A. / Butler-Cole, C. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
Citation
#1: Journal: J.Cell Biol. / Year: 2004
Title: Recruitment of Eph receptors into signaling clusters does not require ephrin contact.
Authors: Wimmer-Kleikamp, S.H. / Janes, P.W. / Squire, A. / Bastiaens, P.I. / Lackmann, M.
#2: Journal: J.Biol.Chem. / Year: 1998
Title: Distinct subdomains of the EphA3 receptor mediate ligand binding and receptor dimerization.
Authors: Lackmann, M. / Oates, A.C. / Dottori, M. / Smith, F.M. / Do, C. / Power, M. / Kravets, L. / Boyd, A.W.
#3: Journal: Nature / Year: 2001
Title: Crystal structure of an Eph receptor-ephrin complex.
Authors: Himanen, J.P. / Rajashankar, K.R. / Lackmann, M. / Cowan, C.A. / Henkemeyer, M. / Nikolov, D.B.
History
DepositionDec 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ephrin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5696
Polymers59,2191
Non-polymers3515
Water82946
1
A: Ephrin receptor
hetero molecules

A: Ephrin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,13912
Polymers118,4382
Non-polymers70110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.358, 89.992, 136.476
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ephrin receptor


Mass: 59218.930 Da / Num. of mol.: 1 / Fragment: Ectodomain, UNP residues 23-531
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ECK, EPHA2, hCG_24712, RP11-276H7.1-001 / Plasmid: pFHMSP-LIC-N / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: Q8N3Z2, UniProt: P29317*PLUS, receptor protein-tyrosine kinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
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: 3.08 Å3/Da / Density % sol: 60.03 %
Crystal growTemperature: 290.9 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 3.0% PEG 4000, 0.1M Sodium acetate, 0.1 M Cacodylate pH 5.5, 0.5 M NDSB 256, VAPOR DIFFUSION, HANGING DROP, temperature 290.9K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97948 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 20, 2008 / Details: Mirrors
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.5→41 Å / Num. obs: 25966 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rsym value: 0.07 / Net I/σ(I): 22.43
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.94 / Num. unique all: 2510 / Rsym value: 0.375 / % possible all: 98.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0063refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3C8X, 2E7H

3c8x

2e7h


Resolution: 2.5→40.59 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.895 / SU B: 25.979 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.398 / ESU R Free: 0.3 / 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
Rfree0.29943 1311 5.1 %RANDOM
Rwork0.246 ---
obs0.24873 24331 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.468 Å2
Baniso -1Baniso -2Baniso -3
1--5.42 Å20 Å20 Å2
2--9.4 Å20 Å2
3----3.97 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 18 46 3722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223798
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9585185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6395477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70523.913161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.37415554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0031521
X-RAY DIFFRACTIONr_chiral_restr0.0820.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212924
X-RAY DIFFRACTIONr_mcbond_it0.72522414
X-RAY DIFFRACTIONr_mcangle_it1.25933890
X-RAY DIFFRACTIONr_scbond_it0.70921384
X-RAY DIFFRACTIONr_scangle_it1.12631295
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 80 -
Rwork0.338 1757 -
obs--96.63 %
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)
14.3020.01930.77891.96520.33373.345-0.00040.2142-0.2213-0.18620.011-0.00850.23740.385-0.01060.24050.0217-0.01330.0487-0.00350.263714.418440.22581.1483
24.06580.52251.03191.5933-0.35291.67190.0804-0.1750.0009-0.163-0.0253-0.1335-0.06510.5282-0.05510.2488-0.0402-0.01510.2755-0.01950.226916.356346.4455.4322
36.729-1.65268.79067.4921-1.59211.5301-0.17810.1680.0683-0.25610.1213-0.1107-0.25230.23270.05690.63950.0250.31070.01030.01870.478415.697646.3725-0.053
40.3888-0.13681.0360.2772-0.90485.39510.0707-0.12870.01550.1519-0.0095-0.0109-0.26940.2588-0.06130.3605-0.0254-0.00580.24370.01270.313618.612137.469237.8725
50.6008-0.46321.47330.3828-1.18253.7025-0.0234-0.03170.0065-0.09110.06140.00310.1327-0.1896-0.0380.5330.0334-0.05970.54680.09910.41121.901421.740373.9865
62.7402-0.29520.36781.90210.06744.5672-0.0046-0.20660.35820.2176-0.02870.0368-0.274-0.20510.03320.3906-0.00320.00950.19580.01820.416535.564921.5071102.2759
74.9198-1.23920.66182.09820.34513.43360.06370.8681-0.4193-0.1352-0.0446-0.0070.23460.1484-0.0190.48410.0252-0.01290.2061-0.1210.450864.277129.5405118.9362
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 122
2X-RAY DIFFRACTION2A123 - 179
3X-RAY DIFFRACTION3A180 - 184
4X-RAY DIFFRACTION4A185 - 283
5X-RAY DIFFRACTION5A284 - 334
6X-RAY DIFFRACTION6A335 - 437
7X-RAY DIFFRACTION7A438 - 528

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