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- PDB-3mbw: Crystal structure of the human ephrin A2 LBD and CRD domains in c... -

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Basic information

Entry
Database: PDB / ID: 3mbw
TitleCrystal structure of the human ephrin A2 LBD and CRD domains in complex with ephrin A1
Components
  • Ephrin type-A receptor 2
  • Ephrin-A1
KeywordsTRANSFERASE/SIGNALING PROTEIN / ATP-binding / kinase / nucleotide-binding / receptor / transferase / phosphorylation / transmembrane / tyrosine-protein kinase / glycoprotein / cysteine-rich domain / phosphoprotein / GPI-anchor / lipoprotein / transferase-signaling protein complex / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


endocardial cushion to mesenchymal transition involved in heart valve formation / negative regulation of dendritic spine morphogenesis / negative regulation of proteolysis involved in protein catabolic process / notochord cell development / positive regulation of amyloid precursor protein catabolic process / notochord formation / mitral valve morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis ...endocardial cushion to mesenchymal transition involved in heart valve formation / negative regulation of dendritic spine morphogenesis / negative regulation of proteolysis involved in protein catabolic process / notochord cell development / positive regulation of amyloid precursor protein catabolic process / notochord formation / mitral valve morphogenesis / 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 / negative regulation of thymocyte apoptotic process / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / aortic valve morphogenesis / central nervous system neuron differentiation / RND1 GTPase cycle / RND2 GTPase cycle / tight junction / RND3 GTPase cycle / neural tube development / positive regulation of peptidyl-tyrosine phosphorylation / mammary gland epithelial cell proliferation / regulation of peptidyl-tyrosine phosphorylation / negative regulation of epithelial to mesenchymal transition / regulation of axonogenesis / RHOV GTPase cycle / positive regulation of amyloid-beta formation / growth factor binding / EPHA-mediated growth cone collapse / regulation of cell adhesion mediated by integrin / RHOU GTPase cycle / positive regulation of intracellular signal transduction / 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 / side of membrane / keratinocyte differentiation / ephrin receptor binding / negative regulation of MAPK cascade / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / substrate adhesion-dependent cell spreading / axon guidance / 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 / cell-cell signaling / lamellipodium / virus receptor activity / angiogenesis / receptor complex / cell adhesion / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / protein stabilization / positive regulation of cell migration / cadherin binding / inflammatory response / signaling receptor binding / focal adhesion / cell surface / negative regulation of transcription by RNA polymerase II / extracellular region / ATP binding / plasma membrane
Similarity search - Function
ephrin a2 ectodomain / Ephrin-A ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Ephrin type-A receptor 2, ligand binding domain / Ephrin receptor type-A /type-B ...ephrin a2 ectodomain / Ephrin-A ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / 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 / Cupredoxins - blue copper proteins / Sterile alpha motif/pointed domain superfamily / Fibronectin type III domain / Growth factor receptor cysteine-rich domain superfamily / Cupredoxin / 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 / Jelly Rolls / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ephrin-A1 / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 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)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Architecture of Eph receptor clusters.
Authors: Himanen, J.P. / Yermekbayeva, L. / Janes, P.W. / Walker, J.R. / Xu, K. / Atapattu, L. / Rajashankar, K.R. / Mensinga, A. / Lackmann, M. / Nikolov, D.B. / Dhe-Paganon, S.
History
DepositionMar 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 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 2.2Nov 6, 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-A receptor 2
B: Ephrin-A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7344
Polymers57,9862
Non-polymers7492
Water48627
1
A: Ephrin type-A receptor 2
B: Ephrin-A1
hetero molecules

A: Ephrin type-A receptor 2
B: Ephrin-A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4698
Polymers115,9714
Non-polymers1,4974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area8100 Å2
ΔGint-3 kcal/mol
Surface area40520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.265, 215.787, 107.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Ephrin type-A receptor 2 / Tyrosine-protein kinase receptor ECK / Epithelial cell kinase


Mass: 36587.008 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ECK, EPHA2 / Plasmid: PFHMSP-LIC-N / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: P29317, receptor protein-tyrosine kinase
#2: Protein Ephrin-A1 / EPH-related receptor tyrosine kinase ligand 1 / LERK-1 / Immediate early response protein B61 / ...EPH-related receptor tyrosine kinase ligand 1 / LERK-1 / Immediate early response protein B61 / Tumor necrosis factor alpha-induced protein 4 / TNF alpha-induced protein 4 / Ephrin-A1 / secreted form


Mass: 21398.688 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EFNA1, EPLG1, LERK1, TNFAIP4 / Plasmid: PFHMSP-LIC-N / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P20827
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Rhap]{}}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSTATE THAT THE CORRECT SEQUENCE IS PROVIDED IN GENBANK ENTRY NP_004422

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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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 290.9 K / pH: 8
Details: 10.0% PEG 3350, 0.16M AMMONIUM PHOSPHATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.9K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2008
RadiationMonochromator: DOUBLE-CRYSTAL SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98792 Å / Relative weight: 1
ReflectionResolution: 2.8→39 Å / Num. obs: 16953 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 83.52 Å2 / Rsym value: 0.066 / Net I/σ(I): 23.65
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.17 / Rsym value: 0.668 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3C8X, 1SHW

3c8x

1shw


Resolution: 2.81→34.1 Å / Cor.coef. Fo:Fc: 0.9127 / Cor.coef. Fo:Fc free: 0.8839 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2723 874 5.17 %RANDOM
Rwork0.2261 ---
obs0.2286 16891 --
all-16953 --
Displacement parametersBiso mean: 80.12 Å2
Baniso -1Baniso -2Baniso -3
1-5.0869 Å20 Å20 Å2
2---2.0623 Å20 Å2
3----3.0246 Å2
Refine analyzeLuzzati coordinate error obs: 0.551 Å
Refinement stepCycle: LAST / Resolution: 2.81→34.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3207 0 50 27 3284
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093361HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.154577HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1105SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes84HARMONIC2
X-RAY DIFFRACTIONt_gen_planes487HARMONIC5
X-RAY DIFFRACTIONt_it3361HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 2.81→3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2866 134 4.48 %
Rwork0.2628 2860 -
all0.2639 2994 -
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)
14.3052-0.4682.00763.2317-2.11674.4096-0.53120.38351.07080.1626-0.361-0.8244-0.46830.37720.8922-0.2426-0.0272-0.198-0.08030.16770.2303-13.55337.20822.9196
24.3243-2.89580.023116.10842.81262.9390.09720.0195-1.16110.26550.33160.07390.68060.2163-0.4288-0.0729-0.0294-0.1913-0.25020.00690.2449-9.7932-30.249222.7907
37.36051.67252.06675.95743.70120.0004-0.005-0.00330.0942-0.1979-0.1754-0.00020.17790.27530.18030.66240.1682-0.3364-0.5524-0.1040.554-10.221-56.71819.2561
40.00010.6589-1.966910.3192-2.04424.3982-0.06210.31020.48080.2301-0.1436-0.3974-0.5982-0.89930.2057-0.21240.1457-0.2694-0.0075-0.01950.1874-30.542325.11064.264
50-0.41872.22176.0812-1.49222.95850.00840.24930.0379-0.3444-0.4466-0.13870.2191-0.320.43830.0339-0.22670.05570.12120.1374-0.1325-31.808313.1374-4.113
61.05872.9912-0.81940.2108-1.23012.434200.02320.01960.01730.0267-0.062-0.08340.0025-0.02680.15870.11560.132-0.16120.25330.2813-18.323827.5733-7.8833
72.1334-2.08481.28722.2842-2.23738.2029-0.18270.45910.6267-0.2116-0.7628-1.2030.26520.18310.9456-0.1962-0.0878-0.1558-0.11440.42530.3738-21.018215.92985.3643
81.1955.027-0.28750.0038-1.43520.31590.03740.18520.02330.1194-0.0783-0.2827-0.4805-0.11040.0409-0.1206-0.1765-0.383-0.12940.43140.4927-16.252828.65534.8242
90.3929-4.8628-1.52545.8728-2.98430-0.14420.48730.2734-0.0964-0.0608-0.37840.0457-0.27480.2050.03450.08610.0477-0.00890.231-0.0345-27.047623.1363-5.8738
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|25 - 198}A25 - 198
2X-RAY DIFFRACTION2{A|199 - 263}A199 - 263
3X-RAY DIFFRACTION3{A|264 - 325}A264 - 325
4X-RAY DIFFRACTION4{B|19 - 54}B19 - 54
5X-RAY DIFFRACTION5{B|55 - 71}B55 - 71
6X-RAY DIFFRACTION6{B|72 - 81}B72 - 81
7X-RAY DIFFRACTION7{B|82 - 117}B82 - 117
8X-RAY DIFFRACTION8{B|118 - 129}B118 - 129
9X-RAY DIFFRACTION9{B|130 - 148}B130 - 148

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