[English] 日本語
Yorodumi
- PDB-2wo1: Crystal Structure of the EphA4 Ligand Binding Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wo1
TitleCrystal Structure of the EphA4 Ligand Binding Domain
ComponentsEPHRIN TYPE-A RECEPTOR
KeywordsTRANSFERASE / GLYCOPROTEIN / AXON GUIDANCE / VASCULAR DEVELOPMENT / CELL SURFACE RECEPTOR / CELL SIGNALING
Function / homology
Function and homology information


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 / fasciculation of sensory neuron axon / fasciculation of motor neuron axon ...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 / fasciculation of sensory neuron axon / fasciculation of motor neuron axon / regulation of synapse pruning / synapse pruning / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / negative regulation of cellular response to hypoxia / negative regulation of axon regeneration / glial cell migration / transmembrane-ephrin receptor activity / PH domain binding / GPI-linked ephrin receptor activity / regulation of modification of synaptic structure / regulation of dendritic spine morphogenesis / negative regulation of cell adhesion / negative regulation of epithelial to mesenchymal transition / motor neuron axon guidance / adult walking behavior / adherens junction organization / positive regulation of dendrite morphogenesis / EPH-Ephrin signaling / Somitogenesis / positive regulation of amyloid-beta formation / regulation of axonogenesis / cochlea development / regulation of GTPase activity / EPHA-mediated growth cone collapse / positive regulation of protein tyrosine kinase activity / positive regulation of cell adhesion / negative regulation of long-term synaptic potentiation / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / axonal growth cone / axon terminus / ephrin receptor binding / protein tyrosine kinase binding / negative regulation of cell migration / filopodium / dendritic shaft / axon guidance / adherens junction / postsynaptic density membrane / neuromuscular junction / Schaffer collateral - CA1 synapse / receptor protein-tyrosine kinase / negative regulation of ERK1 and ERK2 cascade / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / negative regulation of neuron projection development / kinase activity / presynaptic membrane / amyloid-beta binding / early endosome membrane / perikaryon / protein tyrosine kinase activity / mitochondrial outer membrane / protein autophosphorylation / dendritic spine / protein stabilization / negative regulation of translation / cell adhesion / protein kinase activity / positive regulation of cell migration / axon / glutamatergic synapse / dendrite / 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 / 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 4, SAM domain / Ephrin type-A receptor 4, ligand binding domain / 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) / Galactose-binding domain-like / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Fibronectin type III domain / 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 / Jelly Rolls / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
N-PROPANOL / Ephrin type-A receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBowden, T.A. / Aricescu, A.R. / Nettleship, J.E. / Siebold, C. / Rahman-Huq, N. / Owens, R.J. / Stuart, D.I. / Jones, E.Y.
CitationJournal: Structure / Year: 2009
Title: Structural Plasticity of Eph-Receptor A4 Facilitates Cross-Class Ephrin Signalling
Authors: Bowden, T.A. / Aricescu, A.R. / Nettleship, J.E. / Siebold, C. / Rahman-Huq, N. / Owens, R.J. / Stuart, D.I. / Jones, E.Y.
History
DepositionJul 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 23, 2011Group: Database references
Revision 1.3Feb 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_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EPHRIN TYPE-A RECEPTOR
B: EPHRIN TYPE-A RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2357
Polymers42,9342
Non-polymers3005
Water5,350297
1
A: EPHRIN TYPE-A RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6474
Polymers21,4671
Non-polymers1803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EPHRIN TYPE-A RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5873
Polymers21,4671
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.736, 73.228, 54.420
Angle α, β, γ (deg.)90.00, 98.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A29 - 38
2114B29 - 38
1124A46 - 56
2124B46 - 56
1134A67 - 103
2134B67 - 103
1144A120 - 133
2144B120 - 133
1154A141 - 155
2154B141 - 155
1164A167 - 203
2164B167 - 203

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein EPHRIN TYPE-A RECEPTOR / TYROSINE-PROTEIN KINASE RECEPTOR SEK / RECEPTOR PROTEIN-TYROSINE KINASE HEK8 / TYROSINE-PROTEIN KINASE TYRO1


Mass: 21467.191 Da / Num. of mol.: 2 / Fragment: EPHRIN LIGAND BINDING DOMAIN, RESIDUES 30-202
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: Chemical
ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 45.1 % / Description: NONE
Crystal growpH: 8.5
Details: 30% PEG 4000, 8% PROPAN-1-OL, AND 100 MM TRIS PH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.977
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 4, 2005 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.85→25 Å / Num. obs: 31875 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.5
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NUK

1nuk


Resolution: 1.85→23.75 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.851 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23379 1595 5 %RANDOM
Rwork0.18682 ---
obs0.18921 30277 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.744 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å20.3 Å2
2---1.17 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.85→23.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2890 0 20 297 3207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223018
X-RAY DIFFRACTIONr_bond_other_d0.0010.022073
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9464083
X-RAY DIFFRACTIONr_angle_other_deg0.77135032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6595366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89724.194155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0315534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1841524
X-RAY DIFFRACTIONr_chiral_restr0.0740.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02633
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7861.51801
X-RAY DIFFRACTIONr_mcbond_other0.1771.5734
X-RAY DIFFRACTIONr_mcangle_it1.42422929
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.77631217
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9234.51151
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A114medium positional0.60.5
12B114medium positional0.60.5
21A134medium positional0.370.5
22B134medium positional0.370.5
31A512medium positional0.530.5
32B512medium positional0.530.5
41A210medium positional0.310.5
42B210medium positional0.310.5
51A193medium positional0.240.5
52B193medium positional0.240.5
61A493medium positional0.430.5
62B493medium positional0.430.5
11A114medium thermal0.862
12B114medium thermal0.862
21A134medium thermal0.622
22B134medium thermal0.622
31A512medium thermal0.792
32B512medium thermal0.792
41A210medium thermal0.532
42B210medium thermal0.532
51A193medium thermal0.812
52B193medium thermal0.812
61A493medium thermal0.592
62B493medium thermal0.592
LS refinement shellResolution: 1.848→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 116 -
Rwork0.224 2151 -
obs--96.02 %
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)
13.28820.1127-0.05591.10740.03290.6438-0.070.01650.077-0.06080.01820.04780.07510.01760.05180.0235-0.00020.01360.03010.01630.028817.67527.04147.335
20.87830.43110.05432.02541.01352.6505-0.02230.0860.0854-0.3585-0.03140.0208-0.1255-0.1310.05370.10370.01120.02870.04120.0110.045536.83147.02333.076
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 209
2X-RAY DIFFRACTION2B29 - 203

+
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