[English] 日本語
Yorodumi
- PDB-5zrz: Crystal Structure of EphA5/SAMD5 Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zrz
TitleCrystal Structure of EphA5/SAMD5 Complex
Components
  • Ephrin type-A receptor 5
  • Sterile alpha motif domain-containing protein 5
KeywordsPROTEIN BINDING / SAM DOMAIN / HETERODIMER / SIGNALING PROTEIN / CELL SIGNALING / RECEPTOR / TRANSMEMBRANE / TYROSINE-PROTEIN KINASE / CELL ADHESION
Function / homology
Function and homology information


EPH-Ephrin signaling / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / positive regulation of CREB transcription factor activity / ephrin receptor activity / multicellular organism development / GPI-linked ephrin receptor activity / cellular response to follicle-stimulating hormone stimulus / regulation of insulin secretion involved in cellular response to glucose stimulus / transmembrane-ephrin receptor activity ...EPH-Ephrin signaling / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / positive regulation of CREB transcription factor activity / ephrin receptor activity / multicellular organism development / GPI-linked ephrin receptor activity / cellular response to follicle-stimulating hormone stimulus / regulation of insulin secretion involved in cellular response to glucose stimulus / transmembrane-ephrin receptor activity / negative regulation of cell adhesion / dendritic spine morphogenesis / positive regulation of kinase activity / regulation of GTPase activity / plasma membrane => GO:0005886 / ephrin receptor signaling pathway / rough endoplasmic reticulum / cellular response to forskolin / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / cAMP-mediated signaling / cell periphery / hippocampus development / regulation of actin cytoskeleton organization / adherens junction / axon guidance / receptor protein-tyrosine kinase / receptor complex / neuron projection / external side of plasma membrane / axon / neuronal cell body / dendrite / perinuclear region of cytoplasm / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Transcription Factor, Ets-1 / 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 ...Transcription Factor, Ets-1 / 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 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / EGF-like domain signature 2. / 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 / DNA polymerase; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Sterile alpha motif domain-containing protein 5 / Sterile alpha motif domain-containing protein 5 / Ephrin type-A receptor 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsWang, Y. / Shang, Y. / Li, J. / Chen, W. / Li, G. / Wan, J. / Liu, W. / Zhang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Key R&D Program of China2016YFA0501903 China
CitationJournal: Elife / Year: 2018
Title: Specific Eph receptor-cytoplasmic effector signaling mediated by SAM-SAM domain interactions.
Authors: Wang, Y. / Shang, Y. / Li, J. / Chen, W. / Li, G. / Wan, J. / Liu, W. / Zhang, M.
History
DepositionApr 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ephrin type-A receptor 5
B: Sterile alpha motif domain-containing protein 5


Theoretical massNumber of molelcules
Total (without water)16,6942
Polymers16,6942
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-2 kcal/mol
Surface area8180 Å2
Unit cell
Length a, b, c (Å)98.195, 29.651, 54.170
Angle α, β, γ (deg.)90.000, 109.950, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-111-

HOH

-
Components

#1: Protein Ephrin type-A receptor 5 / Brain-specific kinase / CEK-7 / EPH homology kinase 1 / EHK-1


Mass: 8774.180 Da / Num. of mol.: 1 / Fragment: SAM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Epha5, Bsk, Ehk1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q60629, receptor protein-tyrosine kinase
#2: Protein Sterile alpha motif domain-containing protein 5 / SAM domain-containing protein 5


Mass: 7919.916 Da / Num. of mol.: 1 / Fragment: SAM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Samd5, E130306M17Rik, mCG_52174 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0R4J186, UniProt: Q3V1H9*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.5
Details: 0.2M ammonium acetate, 0.1M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97961 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2015
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97961 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 11829 / % possible obs: 99.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.035 / Rrim(I) all: 0.064 / Χ2: 1.598 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.933.20.7715750.7630.5160.9311.595100
1.93-1.973.20.5235930.7880.350.6321.552100
1.97-2.013.20.355980.860.2320.4211.578100
2.01-2.053.20.2735720.8410.1840.3311.563100
2.05-2.093.20.2175890.8980.1450.2621.713100
2.09-2.143.20.1716130.9520.1130.2051.634100
2.14-2.193.20.1635690.9530.1090.1971.582100
2.19-2.253.20.1746010.960.1150.211.848100
2.25-2.323.10.1465840.9730.0970.1761.728100
2.32-2.393.20.1475990.9780.0980.1771.877100
2.39-2.483.20.1246170.9820.0820.1491.79100
2.48-2.583.20.0925730.9890.0610.1111.63199.7
2.58-2.73.10.0775980.9890.0510.0931.62299.5
2.7-2.8430.0655750.9930.0440.0791.54599.5
2.84-3.0230.0516090.9950.0350.0621.53199
3.02-3.253.30.0435890.9970.0280.0511.52899.7
3.25-3.583.30.0335990.9980.0220.041.51799.8
3.58-4.093.30.0276050.9980.0180.0321.38199.3
4.09-5.163.20.0266120.9980.0170.0311.4298.7
5.16-5030.0265590.9980.0180.0321.28687.1

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KKA

3kka


Resolution: 1.89→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.956 / SU ML: 0.114 / SU R Cruickshank DPI: 0.1562 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.145
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.234 566 4.8 %RANDOM
Rwork0.1938 ---
obs0.1957 11257 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 71.2 Å2 / Biso mean: 33.438 Å2 / Biso min: 18.73 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å2-0.36 Å2
2---0.55 Å20 Å2
3---1.68 Å2
Refinement stepCycle: final / Resolution: 1.89→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1058 0 0 96 1154
Biso mean---42.1 -
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191074
X-RAY DIFFRACTIONr_bond_other_d0.0020.021018
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9641446
X-RAY DIFFRACTIONr_angle_other_deg1.132352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3075131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.11624.03852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.87515199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.092159
X-RAY DIFFRACTIONr_chiral_restr0.1230.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021185
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02216
LS refinement shellResolution: 1.893→1.942 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 45 -
Rwork0.279 763 -
all-808 -
obs--92.98 %
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)
11.63080.3633-0.0050.4622-0.13091.4117-0.00270.20490.1407-0.02950.14530.11420.02540.0635-0.14260.0114-0.0114-0.00730.06120.03090.03972.3086-13.575813.4536
21.32450.4809-0.61970.2215-0.40871.72920.0002-0.1224-0.0511-0.028-0.0447-0.03650.0453-0.01190.04450.02290.00520.0160.0391-0.00260.01943.0446-26.855632.9685
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A804 - 872
2X-RAY DIFFRACTION2B1 - 64

+
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://pdbjlvh1.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