[English] 日本語
Yorodumi
- PDB-8wee: Crystal structure of Arabidopsis thaliana MIK2 ectodomain in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wee
TitleCrystal structure of Arabidopsis thaliana MIK2 ectodomain in complex with SCOOP12
Components
  • MDIS1-interacting receptor like kinase 2
  • SERINE-RICH ENDOGENOUS PEPTIDE (SCOOP)
KeywordsPLANT PROTEIN / LRR receptor-like serine/threonine-protein kinase
Function / homology
Function and homology information


indole glucosinolate biosynthetic process / positive regulation of defense response / pollen tube / pollen tube guidance / response to herbivore / defense response to insect / peptide receptor activity / jasmonic acid biosynthetic process / cellular response to peptide / plasmodesma ...indole glucosinolate biosynthetic process / positive regulation of defense response / pollen tube / pollen tube guidance / response to herbivore / defense response to insect / peptide receptor activity / jasmonic acid biosynthetic process / cellular response to peptide / plasmodesma / peptide binding / response to molecule of bacterial origin / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / ATP binding / plasma membrane
Similarity search - Function
: / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / : / Leucine-rich repeat region / Leucine Rich Repeat / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...: / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / : / Leucine-rich repeat region / Leucine Rich Repeat / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
MDIS1-interacting receptor like kinase 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsWan, L.H. / Hu, Y.X. / Wu, H.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000900 China
CitationJournal: Nat.Plants / Year: 2024
Title: Mechanistic study of SCOOPs recognition by MIK2-BAK1 complex reveals the role of N-glycans in plant ligand-receptor-coreceptor complex formation.
Authors: Wu, H. / Wan, L. / Liu, Z. / Jian, Y. / Zhang, C. / Mao, X. / Wang, Z. / Wang, Q. / Hu, Y. / Xiong, L. / Xia, Z. / Xue, J. / Li, S. / He, P. / Shan, L. / Xu, S.
History
DepositionSep 17, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MDIS1-interacting receptor like kinase 2
B: SERINE-RICH ENDOGENOUS PEPTIDE (SCOOP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,41315
Polymers80,1722
Non-polymers4,24113
Water11,043613
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint57 kcal/mol
Surface area28260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.803, 108.135, 164.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Protein/peptide / Non-polymers , 3 types, 615 molecules AB

#1: Protein MDIS1-interacting receptor like kinase 2 / AtMIK2 / Probable LRR receptor-like serine/threonine-protein kinase At4g08850


Mass: 78853.930 Da / Num. of mol.: 1 / Mutation: L137E/D164K/S564F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MIK2, At4g08850, T32A17.160 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q8VZG8, non-specific serine/threonine protein kinase
#2: Protein/peptide SERINE-RICH ENDOGENOUS PEPTIDE (SCOOP)


Mass: 1318.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / Source method: isolated from a natural source / Formula: H2O

-
Sugars , 3 types, 13 molecules

#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 67.41 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 7.4
Details: 0.2 M Sodium acetate, 0.1 M Tris pH 7.4 and 18% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 56428 / % possible obs: 98.4 % / Redundancy: 5.2 % / CC1/2: 0.98 / Net I/σ(I): 13.9
Reflection shellResolution: 2.19→2.28 Å / Num. unique obs: 5279 / CC1/2: 0.92

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→34.19 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1991 2728 4.85 %
Rwork0.1756 --
obs0.1767 56225 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.19→34.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5111 0 276 613 6000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.176
X-RAY DIFFRACTIONf_dihedral_angle_d15.3832066
X-RAY DIFFRACTIONf_chiral_restr0.09920
X-RAY DIFFRACTIONf_plane_restr0.011951
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.230.23211330.18792276X-RAY DIFFRACTION80
2.23-2.270.21041460.18172774X-RAY DIFFRACTION97
2.27-2.310.20951340.17772798X-RAY DIFFRACTION97
2.31-2.360.21991390.17922776X-RAY DIFFRACTION98
2.36-2.420.1991360.16822791X-RAY DIFFRACTION98
2.42-2.480.1961400.16762813X-RAY DIFFRACTION98
2.48-2.550.22581450.17382810X-RAY DIFFRACTION98
2.55-2.620.23781440.17572790X-RAY DIFFRACTION98
2.62-2.710.18961540.18212843X-RAY DIFFRACTION99
2.71-2.80.22641660.18232787X-RAY DIFFRACTION99
2.8-2.920.23211470.18062842X-RAY DIFFRACTION99
2.92-3.050.22341450.19762849X-RAY DIFFRACTION99
3.05-3.210.2311560.1992836X-RAY DIFFRACTION98
3.21-3.410.24181430.19042877X-RAY DIFFRACTION99
3.41-3.670.21591400.18042890X-RAY DIFFRACTION99
3.67-4.040.16491550.1562854X-RAY DIFFRACTION99
4.04-4.630.1291230.13642928X-RAY DIFFRACTION99
4.63-5.820.16671420.16392937X-RAY DIFFRACTION99
5.82-34.190.20781400.2053026X-RAY DIFFRACTION97
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)
11.68091.3621-0.16754.3781-0.88751.60830.0869-0.0884-0.06390.07990.01470.24030.153-0.1289-0.08380.20230.01120.00150.2021-0.02370.125719.9657-26.942227.8152
22.00071.2936-0.91231.901-1.92142.97120.0488-0.095-0.04480.1655-0.1225-0.1249-0.09270.24260.0730.2180.0051-0.01630.2191-0.03080.167337.9006-5.592415.4157
30.910.25810.01080.8948-0.8962.86430.0047-0.01570.01540.0005-0.0128-0.0378-0.020.17960.01420.1477-0.00410.0060.1996-0.01070.212839.58121.6009-6.8787
42.8889-0.49381.43811.0078-0.29261.07520.05910.1222-0.0724-0.06180.0056-0.04480.07330.1104-0.07140.2129-0.01540.0370.20960.00140.204824.8574.4059-25.4858
53.6536-0.9304-1.42162.48250.19371.95430.05460.0362-0.044-0.0877-0.04640.1964-0.0244-0.0329-0.01480.153-0.0485-0.03420.1870.01130.1566-0.861214.2227-26.6142
65.4293-1.96081.45324.6425-1.764.97780.0971-0.42960.95610.37890.11560.372-0.5673-0.2811-0.20660.3722-0.01090.11990.2843-0.06170.518-9.902132.7587-17.4819
73.8328-1.552-0.747.4444-4.96174.203-0.74491.2136-0.4658-1.51141.49361.05031.59120.1929-0.6890.7811-0.1156-0.02470.8667-0.05850.555627.5249-12.51876.8889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 47 through 207 )
2X-RAY DIFFRACTION2chain 'A' and (resid 208 through 308 )
3X-RAY DIFFRACTION3chain 'A' and (resid 309 through 409 )
4X-RAY DIFFRACTION4chain 'A' and (resid 410 through 512 )
5X-RAY DIFFRACTION5chain 'A' and (resid 513 through 644 )
6X-RAY DIFFRACTION6chain 'A' and (resid 645 through 696 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 10 )

+
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