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- PDB-3mx0: Crystal Structure of EphA2 ectodomain in complex with ephrin-A5 -

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Basic information

Entry
Database: PDB / ID: 3mx0
TitleCrystal Structure of EphA2 ectodomain in complex with ephrin-A5
Components
  • Ephrin type-A receptor 2
  • Ephrin-A5Ephrin A5
KeywordsTRANSFERASE RECEPTOR/SIGNALLING PROTEIN / ectodomain / receptor-ligand complex / receptor-receptor interaction / TRANSFERASE RECEPTOR-SIGNALLING PROTEIN complex
Function / homology
Function and homology information


neurotrophin TRKC receptor binding / neurotrophin TRKB receptor binding / negative regulation of substrate adhesion-dependent cell spreading / regulation of cell-cell adhesion / synaptic membrane adhesion / notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis ...neurotrophin TRKC receptor binding / neurotrophin TRKB receptor binding / negative regulation of substrate adhesion-dependent cell spreading / regulation of cell-cell adhesion / synaptic membrane adhesion / notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / collateral sprouting / pericyte cell differentiation / cellular response to follicle-stimulating hormone stimulus / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration / positive regulation of collateral sprouting / negative regulation of chemokine production / regulation of insulin secretion involved in cellular response to glucose stimulus / ephrin receptor activity / leading edge membrane / bone remodeling / post-anal tail morphogenesis / neurotrophin TRKA receptor binding / chemorepellent activity / response to growth factor / activation of GTPase activity / regulation of cell morphogenesis / regulation of lamellipodium assembly / retinal ganglion cell axon guidance / positive regulation of synapse assembly / tight junction / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / neural tube development / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / mammary gland epithelial cell proliferation / regulation of focal adhesion assembly / RHOV GTPase cycle / regulation of GTPase activity / EPHA-mediated growth cone collapse / transmembrane receptor protein tyrosine kinase activator activity / growth factor binding / regulation of cell adhesion mediated by integrin / lamellipodium membrane / RHOU GTPase cycle / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / GABA-ergic synapse / ephrin receptor signaling pathway / RAC2 GTPase cycle / RAC3 GTPase cycle / vasculogenesis / regulation of angiogenesis / regulation of microtubule cytoskeleton organization / cellular response to forskolin / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / ephrin receptor binding / cell chemotaxis / negative regulation of angiogenesis / osteoclast differentiation / regulation of ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / skeletal system development / molecular function activator activity / cell motility / caveola / axon guidance / protein localization to plasma membrane / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / adherens junction / receptor protein-tyrosine kinase / neuron differentiation / ruffle membrane / osteoblast differentiation / cell surface receptor protein tyrosine kinase signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / cell migration / positive regulation of peptidyl-tyrosine phosphorylation / virus receptor activity / lamellipodium / nervous system development / receptor complex / cell adhesion / positive regulation of cell migration / defense response to Gram-positive bacterium / cadherin binding / inflammatory response / positive regulation of protein phosphorylation / external side of plasma membrane / phosphorylation / focal adhesion
Similarity search - Function
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 ...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) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Cupredoxins - blue copper proteins / Sterile alpha motif/pointed domain superfamily / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type III domain / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Immunoglobulins / 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
triacetyl-beta-chitotriose / Ephrin type-A receptor 2 / Ephrin-A5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.506 Å
AuthorsHimanen, 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.
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
DepositionMay 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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-A5
C: Ephrin type-A receptor 2
D: Ephrin-A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,3318
Polymers122,6344
Non-polymers1,6984
Water0
1
A: Ephrin type-A receptor 2
B: Ephrin-A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1664
Polymers61,3172
Non-polymers8492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint2 kcal/mol
Surface area28950 Å2
MethodPISA
2
C: Ephrin type-A receptor 2
D: Ephrin-A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1664
Polymers61,3172
Non-polymers8492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint4 kcal/mol
Surface area28430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.859, 89.049, 198.150
Angle α, β, γ (deg.)90.00, 96.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 44996.477 Da / Num. of mol.: 2 / Fragment: Ectodomain (UNP Residues 27-435)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK / Plasmid: pDT101 / Cell line (production host): HEK-293 / Production host: Homo sapiens (human)
References: UniProt: P29317, receptor protein-tyrosine kinase
#2: Protein Ephrin-A5 / Ephrin A5 / EPH-related receptor tyrosine kinase ligand 7 / LERK-7 / AL-1


Mass: 16320.332 Da / Num. of mol.: 2 / Fragment: Ectodomain (UNP Residues 28-165)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EFNA5, EPLG7, LERK7 / Cell line (production host): HEK-293 / Production host: Homo sapiens (human) / References: UniProt: P52803
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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

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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: 4.14 Å3/Da / Density % sol: 70.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 20% PEG 3350, 200 mM Ammonium Citrate, 100 mM Na Citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98792 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 23143 / % possible obs: 91.4 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 8.8
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 6.2 / Rsym value: 0.22 / % possible all: 71.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.506→45.028 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 0.16 / Phase error: 33.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2951 1123 5.02 %
Rwork0.2338 --
obs0.2369 22383 88.12 %
all-23129 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 91.597 Å2 / ksol: 0.301 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--20.6855 Å20 Å22.415 Å2
2--78.283 Å20 Å2
3----57.5975 Å2
Refinement stepCycle: LAST / Resolution: 3.506→45.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8462 0 112 0 8574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018852
X-RAY DIFFRACTIONf_angle_d1.47212024
X-RAY DIFFRACTIONf_dihedral_angle_d20.553202
X-RAY DIFFRACTIONf_chiral_restr0.0931286
X-RAY DIFFRACTIONf_plane_restr0.0061574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.506-3.6650.38191060.28831995X-RAY DIFFRACTION66
3.665-3.85820.31591150.2542248X-RAY DIFFRACTION75
3.8582-4.09980.27761330.2242482X-RAY DIFFRACTION83
4.0998-4.4160.28931440.21092694X-RAY DIFFRACTION90
4.416-4.860.26451510.18482858X-RAY DIFFRACTION95
4.86-5.56210.27281520.19332917X-RAY DIFFRACTION97
5.5621-7.00340.28041590.22212989X-RAY DIFFRACTION99
7.0034-45.0320.30761630.24593077X-RAY DIFFRACTION99

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