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- PDB-1shx: Ephrin A5 ligand structure -

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Basic information

Entry
Database: PDB / ID: 1shx
TitleEphrin A5 ligand structure
ComponentsEphrin-A5Ephrin A5
KeywordsHORMONE/GROWTH FACTOR / ephrin signaling / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


neurotrophin TRKB receptor binding / EPH-Ephrin signaling / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / negative regulation of substrate adhesion-dependent cell spreading / synaptic membrane adhesion / regulation of cell-cell adhesion / collateral sprouting / cellular response to follicle-stimulating hormone stimulus / positive regulation of collateral sprouting ...neurotrophin TRKB receptor binding / EPH-Ephrin signaling / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / negative regulation of substrate adhesion-dependent cell spreading / synaptic membrane adhesion / regulation of cell-cell adhesion / collateral sprouting / cellular response to follicle-stimulating hormone stimulus / positive regulation of collateral sprouting / regulation of insulin secretion involved in cellular response to glucose stimulus / chemorepellent activity / regulation of cell morphogenesis / retinal ganglion cell axon guidance / positive regulation of synapse assembly / regulation of focal adhesion assembly / regulation of GTPase activity / basement membrane / GABA-ergic synapse / ephrin receptor signaling pathway / regulation of microtubule cytoskeleton organization / cellular response to forskolin / ephrin receptor binding / caveola / cell periphery / axon guidance / regulation of actin cytoskeleton organization / adherens junction / positive regulation of peptidyl-tyrosine phosphorylation / external side of plasma membrane / plasma membrane
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. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like ...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. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
triacetyl-beta-chitotriose / Ephrin-A5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHimanen, J.P. / Barton, W.A. / Nikolov, D.B. / Jeffrey, P.D.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Three distinct molecular surfaces in ephrin-A5 are essential for a functional interaction with EphA3.
Authors: Day, B. / To, C. / Himanen, J.P. / Smith, F.M. / Nikolov, D.B. / Boyd, A.W. / Lackmann, M.
#1: Journal: Nat.Neurosci. / Year: 2004
Title: Repelling class discrimination: ephrin-A5 binds to and activates EphB2 receptor signaling.
Authors: Himanen, J.P. / Chumley, M.J. / Lackmann, M. / Li, C. / Barton, W.A. / Jeffrey, P.D. / Vearing, C. / Geleick, D. / Feldheim, D.A. / Boyd, A.W. / Henkemeyer, M. / Nikolov, D.B.
History
DepositionFeb 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
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.auth_asym_id / _atom_site.auth_seq_id ..._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_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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
Revision 2.1Apr 3, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ephrin-A5
B: Ephrin-A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6934
Polymers32,6412
Non-polymers1,0522
Water1,892105
1
A: Ephrin-A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9482
Polymers16,3201
Non-polymers6281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ephrin-A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7452
Polymers16,3201
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.21, 70.08, 58.46
Angle α, β, γ (deg.)90, 95.94, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ephrin-A5 / Ephrin A5 / EPH-related receptor tyrosine kinase ligand 7 / LERK-7 / AL-1


Mass: 16320.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: EFNA5, EPLG7, LERK7, EPL7 / Cell line (production host): HEK293 / Organ (production host): kidney / Production host: Homo sapiens (human) / References: UniProt: O08543
#2: 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.: 1
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
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 3350, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 17042 / Num. obs: 16487 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Net I/σ(I): 16.5
Reflection shellResolution: 2→2.09 Å / Rmerge(I) obs: 0.056 / Num. unique all: 17958 / % possible all: 54.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EprinB2

Resolution: 2.1→8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.278 846 RANDOM
Rwork0.224 --
all-17042 -
obs-16487 -
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2302 0 70 105 2477
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.36
X-RAY DIFFRACTIONc_bond_d0.006

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