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- PDB-4bkf: crystal structure of the human EphA4 ectodomain in complex with h... -

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Basic information

Entry
Database: PDB / ID: 4bkf
Titlecrystal structure of the human EphA4 ectodomain in complex with human ephrinB3
Components
  • EPHRIN TYPE-A RECEPTOR 4
  • EPHRIN-B3
KeywordsTRANSFERASE / CELL ADHESION / CELL REPULSION / RECEPTOR CLUSTERING / RECEPTOR CIS INTERACTION / ERYTHROPOETIN-PRODUCING HEPATOCELLULAR RECEPTOR / LBD / SUSHI / EGF / FN
Function / homology
Function and homology information


axon choice point recognition / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / DH domain binding / : / neuron projection fasciculation / positive regulation of Rho guanyl-nucleotide exchange factor activity / corticospinal tract morphogenesis / regulation of astrocyte differentiation / negative regulation of proteolysis involved in protein catabolic process / : ...axon choice point recognition / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / DH domain binding / : / neuron projection fasciculation / positive regulation of Rho guanyl-nucleotide exchange factor activity / corticospinal tract morphogenesis / regulation of astrocyte differentiation / negative regulation of proteolysis involved in protein catabolic process / : / neuron projection guidance / nephric duct morphogenesis / regulation of synapse pruning / fasciculation of sensory neuron axon / fasciculation of motor neuron axon / synapse pruning / negative regulation of cellular response to hypoxia / negative regulation of axon regeneration / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / glial cell migration / negative regulation of axonogenesis / transmembrane-ephrin receptor activity / PH domain binding / GPI-linked ephrin receptor activity / regulation of modification of synaptic structure / negative regulation of epithelial to mesenchymal transition / regulation of dendritic spine morphogenesis / negative regulation of cell adhesion / motor neuron axon guidance / adult walking behavior / adherens junction organization / positive regulation of dendrite morphogenesis / EPH-Ephrin signaling / Ephrin signaling / Somitogenesis / regulation of axonogenesis / positive regulation of amyloid-beta formation / cochlea development / regulation of GTPase activity / EPHA-mediated growth cone collapse / plasma membrane => GO:0005886 / negative regulation of long-term synaptic potentiation / EPH-ephrin mediated repulsion of cells / positive regulation of cell adhesion / ephrin receptor signaling pathway / positive regulation of protein tyrosine kinase activity / axon terminus / axonal growth cone / EPHB-mediated forward signaling / protein tyrosine kinase binding / T cell costimulation / hippocampal mossy fiber to CA3 synapse / ephrin receptor binding / negative regulation of cell migration / dendritic shaft / filopodium / axon guidance / postsynaptic density membrane / adherens junction / Schaffer collateral - CA1 synapse / neuromuscular junction / negative regulation of ERK1 and ERK2 cascade / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / negative regulation of neuron projection development / virus receptor activity / cell-cell signaling / presynaptic membrane / nervous system development / amyloid-beta binding / kinase activity / perikaryon / early endosome membrane / protein tyrosine kinase activity / mitochondrial outer membrane / negative regulation of translation / dendritic spine / protein autophosphorylation / protein stabilization / cell adhesion / protein kinase activity / positive regulation of cell migration / axon / dendrite / glutamatergic synapse / positive regulation of cell population proliferation / cell surface / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Ephrin type-A receptor 4, SAM domain / Ephrin type-A receptor 4, ligand binding domain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like ...Ephrin type-A receptor 4, SAM domain / Ephrin type-A receptor 4, ligand binding domain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / 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 / 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 / Serine/Threonine protein kinases, 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
Similarity search - Domain/homology
Ephrin type-A receptor 4 / Ephrin-B3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.65 Å
AuthorsSeiradake, E. / Schaupp, A. / del Toro Ruiz, D. / Kaufmann, R. / Mitakidis, N. / Harlos, K. / Aricescu, A.R. / Klein, R. / Jones, E.Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structurally Encoded Intraclass Differences in Epha Clusters Drive Distinct Cell Responses
Authors: Seiradake, E. / Schaupp, A. / Del Toro Ruiz, D. / Kaufmann, R. / Mitakidis, N. / Harlos, K. / Aricescu, A.R. / Klein, R. / Jones, E.Y.
History
DepositionApr 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Aug 21, 2013Group: Database references
Revision 1.3Nov 11, 2015Group: Data collection
Revision 1.4Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EPHRIN TYPE-A RECEPTOR 4
B: EPHRIN TYPE-A RECEPTOR 4
C: EPHRIN-B3
D: EPHRIN-B3


Theoretical massNumber of molelcules
Total (without water)166,1674
Polymers166,1674
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-28.5 kcal/mol
Surface area68320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)300.530, 300.530, 300.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein EPHRIN TYPE-A RECEPTOR 4 / EPH-LIKE KINASE 8 / EK8 / HEK8 / TYROSINE-PROTEIN KINASE TYRO1 / TYROSINE-PROTEIN KINASE RECEPTOR SEK


Mass: 62679.359 Da / Num. of mol.: 2 / Fragment: HEPHA4 ECTODOMAIN, RESIDUES 20-547
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human)
References: UniProt: P54764, receptor protein-tyrosine kinase
#2: Protein EPHRIN-B3 / EPH-RELATED RECEPTOR TRANSMEMBRANE LIGAND ELK-L3 / EPH-RELATED RECEPTOR TYROSINE KINASE LIGAND 8 / LERK-8


Mass: 20404.375 Da / Num. of mol.: 2
Fragment: HEPHRINA5 RECEPTOR BINDING DOMAIN, RESIDUES 27-169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q15768
Sequence detailsSEQUENCE CORRESPONDS TO HEPHA4 RESIDUES 20-547 FUSED TO AN N-TERMINAL SECRETION SIGNAL SEQUENCE AND ...SEQUENCE CORRESPONDS TO HEPHA4 RESIDUES 20-547 FUSED TO AN N-TERMINAL SECRETION SIGNAL SEQUENCE AND A POLY-HISTIDINE TAG CONTAINS AN N-TERMINAL ARTIFICIAL SECRETION SIGNAL AND A C- TERMINAL POLY-HISTIDINE TAG

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity % sol: 83.3 %
Description: WE USED THE CC CRITERIA TO SELECT THE HIGH RESOLUTION CUT-OFF. THE CC-HALF VALUE IN THE HIGHERST RESOLUTION SHELL IS 16.1.
Crystal growDetails: PROTEIN SAMPLE WAS MIXED 1:1:1 (V/V/V) WITH (0.08 M MAGNESIUM ACETATE TETRAHYDRATE. 0.05 M CACODYLATE PH 6.5, 15% POLYETHYLENE GLYCOL 400) AND 0.1 M SPERMIDINE (HAMPTON).

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONDiamond I2410.9173
SYNCHROTRONDiamond I0420.9173
Detector
TypeIDDetector
ADSC CCD1CCD
ADSC CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 4.65→106 Å / Num. obs: 25557 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Biso Wilson estimate: 220.26 Å2 / Rmerge(I) obs: 0.26 / Net I/σ(I): 7.7
Reflection shellResolution: 4.65→4.7 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 0.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4BK4, 3D12

4bk4

3d12


Resolution: 4.65→106.25 Å / Cor.coef. Fo:Fc: 0.8642 / Cor.coef. Fo:Fc free: 0.9053 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 1.014
Details: ONLY RIGID BODY AND TLS REFIN MOLECULAR REPLACEMENT, DUE TO THE LOW RESOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.3508 1298 5.09 %RANDOM
Rwork0.3274 ---
obs0.3286 25492 99.83 %-
Displacement parametersBiso mean: 209.75 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 1.895 Å
Refinement stepCycle: LAST / Resolution: 4.65→106.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10126 0 0 0 10126
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110309HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9914005HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3541SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes282HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1483HARMONIC5
X-RAY DIFFRACTIONt_it10309HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.51
X-RAY DIFFRACTIONt_other_torsion18.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1347SEMIHARMONIC5
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_contact11538SEMIHARMONIC0
LS refinement shellResolution: 4.65→4.84 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2232 142 5.07 %
Rwork0.2138 2660 -
all0.2143 2802 -
obs--99.83 %

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