[English] 日本語
Yorodumi
- PDB-4w4z: Structure of the EphA4 LBD in complex with peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4w4z
TitleStructure of the EphA4 LBD in complex with peptide
Components
  • APY-bAla8.am peptide
  • Ephrin type-A receptor 4
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Protein-Inhibitor Complex / Ligand Binding Domain / Signal Transduction / Receptor-Tyrosine Kinase / Cyclic Peptide / EphA4 / Phage Display / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / regulation of synapse pruning / fasciculation of sensory 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 / 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 / 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 / Somitogenesis / regulation of axonogenesis / positive regulation of amyloid-beta formation / cochlea development / regulation of GTPase activity / EPHA-mediated growth cone collapse / negative regulation of long-term synaptic potentiation / positive regulation of cell adhesion / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / positive regulation of protein tyrosine kinase activity / axon terminus / axonal growth cone / protein tyrosine kinase binding / 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 / presynaptic membrane / amyloid-beta binding / kinase activity / perikaryon / early endosome membrane / protein tyrosine kinase activity / mitochondrial outer membrane / dendritic spine / protein autophosphorylation / negative regulation of translation / protein stabilization / 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 2 transmembrane 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
HEXANE-1,6-DIOL / Ephrin type-A receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 2.41 Å
AuthorsLechtenberg, B.C. / Mace, P.D. / Riedl, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01CA138390 United States
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Development and Structural Analysis of a Nanomolar Cyclic Peptide Antagonist for the EphA4 Receptor.
Authors: Lamberto, I. / Lechtenberg, B.C. / Olson, E.J. / Mace, P.D. / Dawson, P.E. / Riedl, S.J. / Pasquale, E.B.
History
DepositionAug 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_symm_contact / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _struct_keywords.text
Revision 1.3Sep 27, 2017Group: Data collection / Refinement description / Category: diffrn_detector / software / Item: _diffrn_detector.detector
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ephrin type-A receptor 4
B: Ephrin type-A receptor 4
C: Ephrin type-A receptor 4
D: Ephrin type-A receptor 4
E: APY-bAla8.am peptide
F: APY-bAla8.am peptide
G: APY-bAla8.am peptide
H: APY-bAla8.am peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,69229
Polymers87,5758
Non-polymers2,11721
Water2,702150
1
A: Ephrin type-A receptor 4
E: APY-bAla8.am peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4067
Polymers21,8942
Non-polymers5135
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-7 kcal/mol
Surface area10650 Å2
MethodPISA
2
B: Ephrin type-A receptor 4
F: APY-bAla8.am peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4988
Polymers21,8942
Non-polymers6056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-9 kcal/mol
Surface area9790 Å2
MethodPISA
3
C: Ephrin type-A receptor 4
G: APY-bAla8.am peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2626
Polymers21,8942
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-3 kcal/mol
Surface area9970 Å2
MethodPISA
4
D: Ephrin type-A receptor 4
H: APY-bAla8.am peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5258
Polymers21,8942
Non-polymers6316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-1 kcal/mol
Surface area9980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.220, 127.190, 84.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Ephrin type-A receptor 4 / EPH-like kinase 8 / hEK8 / Tyrosine-protein kinase TYRO1 / Tyrosine-protein kinase receptor SEK


Mass: 20489.143 Da / Num. of mol.: 4 / Fragment: UNP residues 29-204 / Mutation: C204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA4, HEK8, SEK, TYRO1 / Plasmid: NKI His-3C-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2
References: UniProt: P54764, receptor protein-tyrosine kinase
#2: Protein/peptide
APY-bAla8.am peptide


Mass: 1404.617 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MgCl2, 0.1M Tris pH8.5, 25% PEG3350, 3% 1,6-hexanediol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jun 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.631
11-h,-k,l20.369
ReflectionResolution: 2.41→50.83 Å / Num. obs: 27979 / % possible obs: 92.3 % / Redundancy: 3.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.041 / Net I/σ(I): 13.1 / Num. measured all: 99518 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.41-2.513.30.2264.8918127660.9350.13880.6
8.69-50.833.70.04220.624566650.9970.02598.1

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
MOSFLMdata reduction
Aimless0.2.1data scaling
REFMAC5.8.0073refinement
Coot0.7.2model building
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.41→40.14 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.876 / WRfactor Rfree: 0.2329 / WRfactor Rwork: 0.17 / FOM work R set: 0.766 / SU B: 17.428 / SU ML: 0.212 / SU R Cruickshank DPI: 0.222 / SU Rfree: 0.0629 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2406 1439 5.1 %RANDOM
Rwork0.1733 26512 --
obs0.1767 27951 91.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.71 Å2 / Biso mean: 22.933 Å2 / Biso min: 5.6 Å2
Baniso -1Baniso -2Baniso -3
1--20.34 Å20 Å210.53 Å2
2--19.36 Å20 Å2
3---0.97 Å2
Refinement stepCycle: final / Resolution: 2.41→40.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6040 0 140 150 6330
Biso mean--33.08 20.54 -
Num. residues----755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.026319
X-RAY DIFFRACTIONr_bond_other_d0.0020.025945
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.9578503
X-RAY DIFFRACTIONr_angle_other_deg0.743313652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7715733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40724.019311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.804151069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4861548
X-RAY DIFFRACTIONr_chiral_restr0.0830.2915
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021485
X-RAY DIFFRACTIONr_mcbond_it0.951.182992
X-RAY DIFFRACTIONr_mcbond_other0.9511.182990
X-RAY DIFFRACTIONr_mcangle_it1.7091.7643733
LS refinement shellResolution: 2.41→2.472 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 102 -
Rwork0.199 1676 -
all-1778 -
obs--78.43 %
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)
10.4168-0.0773-0.31410.59070.13491.445-0.0163-0.0154-0.02850.00370.00380.02210.08310.08140.01260.15980.0164-0.13810.0055-0.010.1264-7.0095-18.18-5.0874
20.3953-0.0514-0.0130.7374-0.16861.550.0182-0.0297-0.01910.00160.02240.0101-0.1021-0.0582-0.04060.1360.0227-0.11860.0079-0.0160.1149-7.39121.182137.2257
30.45380.0918-0.29181.20680.18391.2733-0.00340.0151-0.0261-0.06420.00960.0070.0395-0.0338-0.00620.14480.009-0.12740.002-0.00990.11594.5324-27.175439.4348
40.6665-0.0457-0.26481.1562-0.38931.49390.04980.05230.03250.0039-0.04020.0424-0.0446-0.0907-0.00960.14070.0051-0.12590.0108-0.00010.1242-18.730610.2592-2.5454
52.73024.47020.16537.9915-1.38744.4467-0.05280.00660.0117-0.1317-0.05870.0545-0.05610.03830.11150.10830.0362-0.10770.0933-0.06540.1195-9.6744-23.4333-21.7976
65.2582.18851.03827.3083.60241.91490.07470.320.1339-0.3472-0.11150.1923-0.15560.11190.03680.1590.0042-0.09550.2417-0.03970.0784-4.64436.445820.7104
70.98871.26-1.00118.80020.71081.97420.01470.1092-0.1093-0.2048-0.26670.1642-0.1027-0.06590.2520.1165-0.0038-0.07380.0953-0.00290.06534.9586-33.747322.8357
85.63954.35761.88813.88131.23120.7352-0.04320.25110.0493-0.26740.0170.04220.0710.15950.02620.26710.0553-0.10570.15130.04010.0974-20.142317.1541-18.8043
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 204
2X-RAY DIFFRACTION2B28 - 204
3X-RAY DIFFRACTION3C28 - 204
4X-RAY DIFFRACTION4D28 - 204
5X-RAY DIFFRACTION5E1 - 13
6X-RAY DIFFRACTION6F1 - 13
7X-RAY DIFFRACTION7G1 - 13
8X-RAY DIFFRACTION8H1 - 13

+
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://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