[English] 日本語
Yorodumi
- PDB-6nkp: EphA2 LBD in complex with bA-WLA-YSKbio peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nkp
TitleEphA2 LBD in complex with bA-WLA-YSKbio peptide
Components
  • Ephrin type-A receptor 2
  • bA-WLA-YSKbio peptide
KeywordsTRANSFERASE / protein-peptide interaction / kinase / ephrin / eph receptor / drug development / SIGNALING PROTEIN
Function / homology
Function and homology information


notochord cell development / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / ephrin receptor activity ...notochord cell development / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / ephrin receptor activity / leading edge membrane / negative regulation of chemokine production / response to growth factor / post-anal tail morphogenesis / activation of GTPase activity / bone remodeling / positive regulation of bicellular tight junction assembly / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / central nervous system neuron differentiation / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / tight junction / neural tube development / mammary gland epithelial cell proliferation / RHOV GTPase cycle / growth factor binding / EPHA-mediated growth cone collapse / regulation of cell adhesion mediated by integrin / RHOU GTPase cycle / lamellipodium membrane / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of angiogenesis / ephrin receptor signaling pathway / regulation of ERK1 and ERK2 cascade / vasculogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / osteoclast differentiation / molecular function activator activity / negative regulation of angiogenesis / cell chemotaxis / skeletal system development / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / cell motility / receptor protein-tyrosine kinase / ruffle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / osteoblast differentiation / cell migration / lamellipodium / virus receptor activity / angiogenesis / receptor complex / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / cadherin binding / inflammatory response / focal adhesion / cell surface / ATP binding / plasma membrane
Similarity search - Function
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. ...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) / Galactose-binding domain-like / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Fibronectin type III domain / Growth factor receptor cysteine-rich domain superfamily / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Jelly Rolls / 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
BIOTIN / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.033 Å
AuthorsLechtenberg, B.C. / Pasquale, E.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS087070 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA030199 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Engineering nanomolar peptide ligands that differentially modulate EphA2 receptor signaling.
Authors: Gomez-Soler, M. / Petersen Gehring, M. / Lechtenberg, B.C. / Zapata-Mercado, E. / Hristova, K. / Pasquale, E.B.
History
DepositionJan 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ephrin type-A receptor 2
B: Ephrin type-A receptor 2
C: bA-WLA-YSKbio peptide
D: bA-WLA-YSKbio peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9185
Polymers45,6744
Non-polymers2441
Water4,972276
1
A: Ephrin type-A receptor 2
C: bA-WLA-YSKbio peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0813
Polymers22,8372
Non-polymers2441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-13 kcal/mol
Surface area9760 Å2
MethodPISA
2
B: Ephrin type-A receptor 2
C: bA-WLA-YSKbio peptide
D: bA-WLA-YSKbio peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5794
Polymers24,3343
Non-polymers2441
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-14 kcal/mol
Surface area9980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.916, 67.094, 93.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Ephrin type-A receptor 2 / Epithelial cell kinase / Tyrosine-protein kinase receptor ECK


Mass: 21339.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK / Production host: Escherichia coli (E. coli)
References: UniProt: P29317, receptor protein-tyrosine kinase
#2: Protein/peptide bA-WLA-YSKbio peptide


Mass: 1497.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Biotin linked to Lys 13 side-chain / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.09 M BIS-TRIS pH 5.5, 22.5% w/v PEG 3,350, 3% w/v 6-aminohexanoic acid

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→29.39 Å / Num. obs: 24912 / % possible obs: 98.9 % / Redundancy: 7 % / Biso Wilson estimate: 21.95 Å2 / CC1/2: 0.997 / Χ2: 1 / Net I/σ(I): 13.2
Reflection shellResolution: 2.03→2.09 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1673 / CC1/2: 0.714 / Χ2: 0.95 / % possible all: 92.3

-
Processing

Software
NameVersionClassification
PHENIX(1.14rc2_3191: ???)refinement
XDSJan 26, 2018data reduction
Aimless0.7.2data scaling
PDB_EXTRACT3.24data extraction
PHASER2.8.2phasing
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HEI

3hei


Resolution: 2.033→28.949 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.5
RfactorNum. reflection% reflection
Rfree0.2132 1204 4.84 %
Rwork0.1675 --
obs0.1697 24868 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.033→28.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 15 276 3323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123174
X-RAY DIFFRACTIONf_angle_d1.1714312
X-RAY DIFFRACTIONf_dihedral_angle_d11.5371859
X-RAY DIFFRACTIONf_chiral_restr0.067450
X-RAY DIFFRACTIONf_plane_restr0.008551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.033-2.11440.31561250.23842442X-RAY DIFFRACTION93
2.1144-2.21060.22611280.20062596X-RAY DIFFRACTION99
2.2106-2.32710.20621390.18052594X-RAY DIFFRACTION99
2.3271-2.47280.22871340.18452584X-RAY DIFFRACTION99
2.4728-2.66360.24671410.18092627X-RAY DIFFRACTION99
2.6636-2.93150.23581300.18292635X-RAY DIFFRACTION100
2.9315-3.35510.20911410.15882665X-RAY DIFFRACTION100
3.3551-4.2250.19141340.13382692X-RAY DIFFRACTION100
4.225-28.95150.18181320.15682829X-RAY DIFFRACTION100
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)
15.10063.8895-3.98023.4982-2.74433.26580.0362-0.20080.0143-0.0672-0.1919-0.0160.09820.25320.1810.10950.0261-0.00020.17270.00690.1427-23.4699-12.192937.1397
23.08912.59470.63694.30232.04931.52230.13890.03220.31310.1312-0.03540.1275-0.6346-0.03640.03690.30230.0186-0.02520.159-0.00390.1707-24.59476.445436.0288
38.7777-0.0296-2.77186.78942.09652.2616-0.1516-0.8632-0.3280.60030.3261-0.12090.80220.3794-0.04970.31080.0527-0.00510.3310.06310.279-7.0489-29.957313.8701
45.58510.25040.84315.7226-0.54787.15320.09010.50530.1331-0.80830.06170.44740.4439-0.5092-0.18580.21770.0004-0.05390.2251-0.00450.2163-41.2498-15.82331.6328
54.8662-0.09691.08127.06310.17933.2418-0.09260.1819-0.06150.51650.2332-0.5522-0.12020.46320.03670.13840.0092-0.02430.2644-0.07690.1674-4.5061-9.627717.4631
64.42330.11371.0064.3134-0.13144.4893-0.03660.0392-0.50850.20550.04950.07830.520.0444-0.00690.2037-0.02090.02870.14510.00770.1707-12.7202-23.986613.023
71.5586-0.9666-0.54351.4898-0.42352.21520.10110.0415-0.0391-0.3707-0.0659-0.0495-0.2793-0.11160.00520.1308-0.01960.00010.150.00710.1716-11.5988-13.79455.7815
82.50190.71410.19917.82241.47560.29010.14310.43370.0559-0.283-0.27870.7431-0.5915-0.75320.03460.22590.06660.0190.3790.0170.2004-23.9147-6.688518.4879
95.0735-5.46930.51837.73190.02112.0015-0.0971-0.08970.0251-0.12320.1504-0.20550.01560.136-0.00110.1461-0.06380.02440.1244-0.00230.165-7.2007-21.28412.6665
101.8679-0.3414-0.5254.3651-0.17481.64920.0203-0.01980.1635-0.21210.0916-0.2135-0.2478-0.0402-0.10120.1912-0.02190.01140.15830.00270.1112-10.0026-8.14478.3625
116.6876-0.80930.38733.6634-3.26963.2334-0.11720.11120.115-0.40470.23870.7024-0.2535-0.44120.01330.20650.0403-0.05160.21780.08130.1401-27.9756-0.089728.5819
125.87390.94860.47313.628-0.02716.1588-0.06030.30680.0285-0.33780.09570.3330.0155-0.43760.04110.2047-0.057-0.03260.1708-0.00330.1509-35.278-13.490129.2921
132.45811.3144-0.97861.7268-0.52621.783-0.0377-0.0593-0.02470.0056-0.01380.0843-0.0180.03470.05210.10420.026-0.01310.1466-0.00240.1327-26.0467-11.207439.4268
141.33412.5281-1.01168.5528-1.17563.29480.055-0.9835-0.03040.3826-0.3135-0.62710.25910.01980.26590.16180.0672-0.03890.4138-0.01510.2244-12.4332-12.080826.8021
155.51943.4552-0.33494.7455-2.43861.94470.0330.1785-0.44380.0263-0.1569-0.3930.21420.62210.15740.1310.0637-0.03420.2853-0.0180.1524-17.619-11.363941.2117
166.24763.0872-1.70362.3696-0.95371.45030.1914-0.13940.20010.1056-0.10450.2184-0.07520.0159-0.05540.16540.0464-0.00620.1338-0.01990.2325-33.5351-6.173942.6643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 177 through 188 )
2X-RAY DIFFRACTION2chain 'B' and (resid 189 through 204 )
3X-RAY DIFFRACTION3chain 'C' and (resid 2 through 12 )
4X-RAY DIFFRACTION4chain 'D' and (resid 2 through 12 )
5X-RAY DIFFRACTION5chain 'A' and (resid 26 through 43 )
6X-RAY DIFFRACTION6chain 'A' and (resid 44 through 82 )
7X-RAY DIFFRACTION7chain 'A' and (resid 83 through 126 )
8X-RAY DIFFRACTION8chain 'A' and (resid 127 through 135 )
9X-RAY DIFFRACTION9chain 'A' and (resid 136 through 163 )
10X-RAY DIFFRACTION10chain 'A' and (resid 164 through 200 )
11X-RAY DIFFRACTION11chain 'B' and (resid 26 through 43 )
12X-RAY DIFFRACTION12chain 'B' and (resid 44 through 69 )
13X-RAY DIFFRACTION13chain 'B' and (resid 70 through 126 )
14X-RAY DIFFRACTION14chain 'B' and (resid 127 through 135 )
15X-RAY DIFFRACTION15chain 'B' and (resid 136 through 146 )
16X-RAY DIFFRACTION16chain 'B' and (resid 147 through 176 )

+
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