[English] 日本語
Yorodumi
- PDB-2x11: Crystal structure of the complete EphA2 ectodomain in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x11
TitleCrystal structure of the complete EphA2 ectodomain in complex with ephrin A5 receptor binding domain
Components
  • EPHRIN TYPE-A RECEPTOR 2
  • EPHRIN-A5
KeywordsRECEPTOR/SIGNALING PROTEIN / RECEPTOR-SIGNALING PROTEIN COMPLEX / DEVELOPMENTAL PROTEIN / SIGNALING PLATFORM / KINASE / TRANSFERASE / NEUROGENESIS / RECEPTOR / CATARACT / APOPTOSIS / ERYTHROPOIETIN-PRODUCING HEPATOCELLULAR CARCINOMA / ANGIOGENESIS / SIGNALING PROTEIN
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 / notochord cell development / synaptic membrane adhesion / 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 / notochord cell development / synaptic membrane adhesion / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / cellular response to follicle-stimulating hormone stimulus / pericyte cell differentiation / collateral sprouting / cAMP metabolic process / positive regulation of bicellular tight junction assembly / positive regulation of collateral sprouting / regulation of blood vessel endothelial cell migration / ephrin receptor activity / regulation of insulin secretion involved in cellular response to glucose stimulus / leading edge membrane / negative regulation of chemokine production / post-anal tail morphogenesis / bone remodeling / chemorepellent activity / neurotrophin TRKA receptor binding / response to growth factor / regulation of cell morphogenesis / tight junction / activation of GTPase activity / positive regulation of synapse assembly / regulation of lamellipodium assembly / 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 / retinal ganglion cell axon guidance / 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 / basement membrane / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / RAC2 GTPase cycle / GABA-ergic synapse / RAC3 GTPase cycle / vasculogenesis / regulation of angiogenesis / regulation of microtubule cytoskeleton organization / keratinocyte differentiation / cellular response to forskolin / RAC1 GTPase cycle / ephrin receptor binding / transmembrane receptor protein tyrosine kinase activity / negative regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / osteoclast differentiation / cell chemotaxis / skeletal system development / molecular function activator activity / caveola / axon guidance / protein localization to plasma membrane / cell motility / 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 / positive regulation of peptidyl-tyrosine phosphorylation / intrinsic apoptotic signaling pathway in response to DNA damage / cell migration / lamellipodium / virus receptor activity / nervous system development / receptor complex / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / inflammatory response / cadherin binding / positive regulation of protein phosphorylation / external side of plasma membrane / focal adhesion / cell surface / ATP binding / 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. / Ephrin type-A receptor 2, ligand binding domain / : / Ephrin receptor type-A /type-B ...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 / 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 / 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 2 / Ephrin-A5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.83 Å
AuthorsSeiradake, E. / Harlos, K. / Sutton, G. / Aricescu, A.R. / Jones, E.Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: An Extracellular Steric Seeding Mechanism for Eph-Ephrin Signalling Platform Assembly
Authors: Seiradake, E. / Harlos, K. / Sutton, G. / Aricescu, A.R. / Jones, E.Y.
History
DepositionDec 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Version format compliance
Revision 1.2Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Dec 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EPHRIN TYPE-A RECEPTOR 2
B: EPHRIN-A5


Theoretical massNumber of molelcules
Total (without water)80,2622
Polymers80,2622
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-11.6 kcal/mol
Surface area33010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.630, 59.630, 112.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

-
Components

#1: Protein EPHRIN TYPE-A RECEPTOR 2 / TYROSINE-PROTEIN KINASE RECEPTOR ECK / EPITHELIAL CELL KINASE / EPHA2


Mass: 59859.215 Da / Num. of mol.: 1 / Fragment: ECTODOMAIN, RESIDUES 27-534
Source method: isolated from a genetically manipulated source
Details: NAG ON ASN407, DI-METHYLATION OF LYSINES / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHLSEC / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Variant (production host): GNTI-DEFICIENT
References: UniProt: P29317, receptor protein-tyrosine kinase
#2: Protein EPHRIN-A5 / EPH-RELATED RECEPTOR TYROSINE KINASE LIGAND 7 / LERK-7 / AL-1 / HUMAN EPHRIN A5


Mass: 20402.324 Da / Num. of mol.: 1 / Fragment: RECEPTOR BINDING DOMAIN, RESIDUES 26-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHLSEC / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Variant (production host): GNTI-DEFICIENT / References: UniProt: P52803
Sequence detailsCONTAINS FOREIGN SIGNAL PEPTIDE AND POLY-HIS TAG

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growDetails: TWO PARTS OF PROTEIN SOLUTION WERE MIXED WITH ONE PART WATER, ONE PART RESERVOIR SOLUTION (8 % POLYETHYLENE GLYCOL 6000, 0.8 M LICL, 0.08 M CITRATE PH 5) AND ONE PART 1 % POLYVINYLPYRROLIDONE K15.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 4.8→173 Å / Num. obs: 6016 / % possible obs: 98.2 % / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Biso Wilson estimate: 166.11 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.95
Reflection shellResolution: 4.8→4.9 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.8 / % possible all: 75.7

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3CZU, 3FL7, 1SHW

3czu

3fl7

1shw


Resolution: 4.83→40.482 Å / σ(F): 0.03 / Phase error: 34 / Stereochemistry target values: ML
Details: DUE TO LOW RESOLUTION, THE REFINEMENT PROTOCOL WAS LIMITED TO THE FOLLOWING THREE STEPS AFTER MOLECULAR REPLACEMENT. 1. RIGID BODY REFINEMENT OF INDIVIDUAL DOMAINS 2. TLS REFINEMENT OF ...Details: DUE TO LOW RESOLUTION, THE REFINEMENT PROTOCOL WAS LIMITED TO THE FOLLOWING THREE STEPS AFTER MOLECULAR REPLACEMENT. 1. RIGID BODY REFINEMENT OF INDIVIDUAL DOMAINS 2. TLS REFINEMENT OF SELECTED PORTIONS 3. STRUCTURE REGULARIZATION TO AVOID MINOR CLASHES. WE PERFORMED NO INDIVIDUAL ATOM REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.3143 260 4.6 %
Rwork0.3123 --
obs0.313 5643 93.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 99 Å2 / ksol: 0.298 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--46.5561 Å2-0 Å20 Å2
2---4.8023 Å20 Å2
3---48.1254 Å2
Refinement stepCycle: LAST / Resolution: 4.83→40.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4870 0 0 0 4870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035039
X-RAY DIFFRACTIONf_angle_d0.6756844
X-RAY DIFFRACTIONf_dihedral_angle_d17.7071778
X-RAY DIFFRACTIONf_chiral_restr0.044729
X-RAY DIFFRACTIONf_plane_restr0.004901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.8261-6.07710.33411170.34012537X-RAY DIFFRACTION90
6.0771-40.4830.30741430.30122846X-RAY DIFFRACTION97

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more