[English] 日本語
Yorodumi
- PDB-3h8m: SAM domain of human ephrin type-a receptor 7 (EPHA7) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h8m
TitleSAM domain of human ephrin type-a receptor 7 (EPHA7)
ComponentsEphrin type-A receptor 7
KeywordsTRANSFERASE / SAM DOMAIN / KINASE / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / Alternative splicing / ATP-binding / Glycoprotein / Membrane / Nucleotide-binding / Phosphoprotein / Polymorphism / Receptor / Transmembrane / Tyrosine-protein kinase
Function / homology
Function and homology information


regulation of protein autophosphorylation / regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of synapse assembly / nephric duct morphogenesis / negative regulation of collateral sprouting / axon guidance receptor activity / branching morphogenesis of a nerve / regulation of cell-cell adhesion / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity ...regulation of protein autophosphorylation / regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of synapse assembly / nephric duct morphogenesis / negative regulation of collateral sprouting / axon guidance receptor activity / branching morphogenesis of a nerve / regulation of cell-cell adhesion / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / chemorepellent activity / retinal ganglion cell axon guidance / EPH-Ephrin signaling / regulation of postsynapse organization / negative chemotaxis / EPHA-mediated growth cone collapse / growth factor binding / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / regulation of peptidyl-tyrosine phosphorylation / regulation of ERK1 and ERK2 cascade / axon guidance / brain development / modulation of chemical synaptic transmission / receptor protein-tyrosine kinase / positive regulation of neuron apoptotic process / protein tyrosine kinase activity / neuron apoptotic process / positive regulation of protein phosphorylation / phosphorylation / glutamatergic synapse / dendrite / ATP binding / plasma membrane
Similarity search - Function
Ephrin type-A receptor 7, ligand binding domain / Transcription Factor, Ets-1 / 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 7, ligand binding domain / Transcription Factor, Ets-1 / 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) / 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 / 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
Ephrin type-A receptor 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWalker, J.R. / Yermekbayeva, L. / Butler-Cole, C. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: SAM Domain of Human Ephrin Type-A Receptor 7 (Epha7)
Authors: Walker, J.R. / Yermekbayeva, L. / Butler-Cole, C. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionApr 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ephrin type-A receptor 7
B: Ephrin type-A receptor 7


Theoretical massNumber of molelcules
Total (without water)20,7382
Polymers20,7382
Non-polymers00
Water95553
1
A: Ephrin type-A receptor 7


Theoretical massNumber of molelcules
Total (without water)10,3691
Polymers10,3691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ephrin type-A receptor 7


Theoretical massNumber of molelcules
Total (without water)10,3691
Polymers10,3691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.071, 54.089, 40.455
Angle α, β, γ (deg.)90.00, 104.84, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ephrin type-A receptor 7 / Tyrosine-protein kinase receptor EHK-3 / EPH homology kinase 3 / Receptor protein-tyrosine kinase HEK11


Mass: 10368.828 Da / Num. of mol.: 2 / Fragment: SAM DOMAIN, RESIDUES 919-990
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHK3, EPHA7, HEK11 / Plasmid: PET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)V2R
References: UniProt: Q15375, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.043553 Å3/Da / Density % sol: 39.810699 %
Crystal growTemperature: 293.1 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: WELL SOLUTION: 20% PEG 4000, 0.2 M SODIUM ACETATE, 0.1 M TRIS HCL PH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.1K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 3, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→22.24 Å / Num. all: 9717 / Num. obs: 9717 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rsym value: 0.05 / Net I/σ(I): 25.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.59 / Rsym value: 0.315 / % possible all: 81.1

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHASERphasing
REFMAC5.5.0063refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B4F

1b4f


Resolution: 2.1→22.24 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 13.109 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.22767 458 4.8 %RANDOM
Rwork0.19708 ---
obs0.19867 9162 97.73 %-
all-9717 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.025 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-1.49 Å2
2---1.82 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.1→22.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1174 0 0 55 1229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221193
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.9441604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6325148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89924.08249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.27815223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.234156
X-RAY DIFFRACTIONr_chiral_restr0.0740.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02861
X-RAY DIFFRACTIONr_mcbond_it0.4921.5741
X-RAY DIFFRACTIONr_mcangle_it0.98921193
X-RAY DIFFRACTIONr_scbond_it1.9463452
X-RAY DIFFRACTIONr_scangle_it3.1374.5411
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 18 -
Rwork0.295 555 -
obs--80.7 %
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)
14.63061.86762.44426.29191.29977.1513-0.2248-0.4499-0.59460.6820.1213-0.11290.3229-0.17070.10350.22730.04490.03210.22210.01190.28914.342311.986944.5416
24.32443.11040.68655.45470.99718.79250.121-0.11760.08980.155-0.0082-0.5692-0.04210.4289-0.11280.1617-0.0379-0.0110.213-0.01660.220716.069110.941432.9668
38.2892-3.64053.083711.7361-0.88065.4023-0.0709-0.0881-0.17430.0590.0513-0.44040.14950.46670.01960.1681-0.0068-0.00380.2083-0.00670.18115.24283.389534.5953
40.61892.22350.78528.22831.82177.29460.02910.0164-0.26390.0870.03-0.86280.34730.324-0.05910.20730.01380.01390.22250.00390.344513.0868-1.52829.3564
52.00980.16921.37694.5935-2.33187.87210.00330.29340.0514-0.3009-0.0052-0.267-0.12620.22760.00190.1857-0.015-0.0010.1926-0.01280.17789.03395.494623.8872
67.6681-0.8973-2.61268.05611.0077.9253-0.04750.09640.7153-0.3380.1091-0.0639-0.31120.4162-0.06160.2240.0081-0.01390.21880.010.23287.482612.966729.6941
79.98184.9816-3.2414.55151.35225.33180.00690.17610.4584-0.21270.03540.3066-0.3441-0.0996-0.04230.19410.0104-0.00730.2058-0.00930.20482.030810.381833.5785
89.1047-5.0946-3.7567.8412-3.38817.5902-0.07250.2052-0.3820.05610.13570.41780.016-0.3812-0.06320.2134-0.0356-0.01190.2745-0.00810.247-1.88011.775631.4268
91.089-2.11140.70347.8088-6.7168.28960.03740.0445-0.1156-0.056-0.05940.0391-0.0566-0.0340.02210.2198-0.0129-0.02120.22260.00330.28813.3995-3.722629.3757
100.1742-1.00520.84428.1147-1.49849.1536-0.0389-0.0126-0.01810.33160.08580.15990.12810.1219-0.04690.1859-0.0159-0.03450.25810.02160.24366.4049-2.876636.4376
113.18051.3116-0.97548.7130.11432.51340.0867-0.46080.17030.3811-0.04610.174-0.0923-0.181-0.04060.2169-0.0105-0.00330.24050.00530.22635.66555.330140.827
129.61810.42842.76196.3171-0.48655.3019-0.10860.1594-0.018-0.37650.01580.0380.051-0.13760.09280.2112-0.00560.01730.2332-0.01590.24735.681213.37541.5459
134.69273.36492.78662.46891.51555.90030.1201-0.03590.03650.0532-0.01610.05860.19930.0098-0.1040.37970.0226-0.00870.3535-0.00050.3445-3.6219-0.995622.7928
145.2674-1.44220.77177.1413-0.6143.368-0.00550.51750.4667-0.5155-0.01680.0787-0.294-0.16380.02230.2799-0.0110.01940.26660.01470.2956-8.1332-3.550333.003
151.48112.52461.22454.35391.67664.8492-0.01640.0218-0.166-0.0780.0448-0.26150.30210.1562-0.02830.19210.0372-0.00350.2062-0.02310.2654-3.3282-5.820743.0269
164.92730.65430.37496.9387-1.36183.9230.12880.11820.04580.041-0.1153-0.4573-0.06280.2282-0.01350.1797-0.01260.01140.20230.00860.1898-3.79943.041542.7731
178.0651-0.41223.36221.0929-0.37199.086-0.2065-0.15780.3559-0.07880.2541-0.39190.13980.1274-0.04760.2521-0.03950.00050.2172-0.02210.2179-4.47658.443148.1167
184.30520.21490.43571.64280.20888.63890.1624-0.5566-0.03660.4905-0.1596-0.15360.25250.0578-0.00280.2367-0.01-0.00070.20670.00010.1509-7.91073.626954.9412
197.4794-2.6509-1.93354.33721.99656.7614-0.012-0.2181-0.01570.11980.1171-0.1928-0.18130.1934-0.10510.2412-0.02750.00420.21290.03180.226-9.312-4.486251.3441
208.4197-0.26550.36722.2578-0.13736.2202-0.0726-0.1637-0.17360.12970.02560.38980.1528-0.47040.0470.2092-0.00840.01890.23180.0110.2974-15.8766-3.84848.3577
214.6497-0.04520.98822.2665-2.37977.43290.0860.12560.1224-0.1083-0.05910.6822-0.0617-0.4145-0.02690.30270.04150.0010.2995-0.00110.3398-19.70524.988649.666
221.42-1.96753.24148.0337-7.20878.8852-0.0267-0.25590.09150.24130.08530.2513-0.0022-0.4666-0.05860.35260.04510.00070.24830.00970.236-14.284211.500848.4759
237.97320.30136.01098.7255.83188.1376-0.09260.0457-0.1113-0.07540.09030.1109-0.12390.06980.00220.228-0.00090.00750.24560.02130.2146-14.01658.071542.0485
242.21872.3946-2.555611.74242.32965.77940.06150.09750.06620.0284-0.0280.2091-0.0765-0.161-0.03350.1792-0.0004-0.01620.208-0.00160.2234-14.3638-1.305339.7372
256.68561.0718-1.03289.2339-2.91328.4584-0.1284-0.3533-0.13860.2920.06010.55230.1297-0.46820.06840.1884-0.00310.00030.2038-0.00180.2362-15.6542-8.992640.1982
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A919 - 924
2X-RAY DIFFRACTION2A925 - 930
3X-RAY DIFFRACTION3A931 - 936
4X-RAY DIFFRACTION4A937 - 940
5X-RAY DIFFRACTION5A941 - 948
6X-RAY DIFFRACTION6A949 - 953
7X-RAY DIFFRACTION7A954 - 959
8X-RAY DIFFRACTION8A960 - 964
9X-RAY DIFFRACTION9A965 - 971
10X-RAY DIFFRACTION10A972 - 977
11X-RAY DIFFRACTION11A978 - 983
12X-RAY DIFFRACTION12A984 - 989
13X-RAY DIFFRACTION13B912 - 916
14X-RAY DIFFRACTION14B917 - 922
15X-RAY DIFFRACTION15B923 - 928
16X-RAY DIFFRACTION16B929 - 937
17X-RAY DIFFRACTION17B938 - 941
18X-RAY DIFFRACTION18B942 - 948
19X-RAY DIFFRACTION19B949 - 953
20X-RAY DIFFRACTION20B954 - 959
21X-RAY DIFFRACTION21B960 - 964
22X-RAY DIFFRACTION22B965 - 972
23X-RAY DIFFRACTION23B973 - 978
24X-RAY DIFFRACTION24B979 - 984
25X-RAY DIFFRACTION25B985 - 990

+
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