[English] 日本語
Yorodumi
- PDB-7xpc: Complex structure of D-glycerate-3-kinase(GLYK) and AVRvnt1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xpc
TitleComplex structure of D-glycerate-3-kinase(GLYK) and AVRvnt1
Components
  • D-glycerate-3-kinase (GLYK)
  • RxLR effector protein Avr-vnt11
KeywordsIMMUNE SYSTEM / D-glycerate-3-kinase and AVRvnt1 complex / plant immunity / HR response / protein binding / decoy
Function / homology
Function and homology information


mitotic cell cycle phase transition / host cell nucleolus / cyclin-dependent protein serine/threonine kinase regulator activity / regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / host cell cytoplasm / cell division / extracellular region / nucleus / cytoplasm
Similarity search - Function
Cyclin, C-terminal domain / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cyclin N-terminal domain-containing protein / RxLR effector protein Avr-vnt11
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
Phytophthora infestans T30-4 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.31 Å
AuthorsHu, Q. / Zhou, J. / Yao, D. / Xing, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Chloroplast Protein GLYK Hijacked by Phytophthora Infestans Effector AVRvnt1 in Cytoplasm to Activate NLR
Authors: Hu, Q. / Zhou, J. / Yao, D. / Xing, W.
History
DepositionMay 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-glycerate-3-kinase (GLYK)
B: RxLR effector protein Avr-vnt11
C: D-glycerate-3-kinase (GLYK)
D: RxLR effector protein Avr-vnt11


Theoretical massNumber of molelcules
Total (without water)96,7304
Polymers96,7304
Non-polymers00
Water00
1
A: D-glycerate-3-kinase (GLYK)
B: RxLR effector protein Avr-vnt11


Theoretical massNumber of molelcules
Total (without water)48,3652
Polymers48,3652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: D-glycerate-3-kinase (GLYK)
D: RxLR effector protein Avr-vnt11


Theoretical massNumber of molelcules
Total (without water)48,3652
Polymers48,3652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.285, 131.285, 121.968
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein D-glycerate-3-kinase (GLYK)


Mass: 38783.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3Q7FWS2
#2: Protein RxLR effector protein Avr-vnt11 / Avirulence protein Avr-vnt1


Mass: 9581.048 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora infestans T30-4 (eukaryote)
Strain: T30-4 / Gene: Avr-vnt1, PITG_16294 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0NTY1
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.13 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 10% w/v Polyethylene glycol 3,350, 0.1 M Tris pH 8.0, 100 mM Taurine and 10% w/v glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.31→42.97 Å / Num. obs: 35167 / % possible obs: 99.9 % / Redundancy: 10.343 % / Biso Wilson estimate: 134.62 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.144 / Rrim(I) all: 0.152 / Χ2: 0.873 / Net I/σ(I): 11.9 / Num. measured all: 363729
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.31-3.510.3472.4661.2158594567856630.5762.59599.7
3.5-3.7510.4951.2992.6755926532953290.8551.367100
3.75-4.0410.6230.7264.952425493549350.9610.764100
4.04-4.4310.1510.378.7146218455345530.9860.39100
4.43-4.9410.5230.19414.9343745415741570.9940.205100
4.94-5.6910.080.13817.9536670363836380.9960.146100
5.69-6.9510.6090.10721.7533067311731170.9960.112100
6.95-9.7110.1830.06235.2124276238423840.9980.065100
9.71-42.979.2080.05439.1412808140913910.9980.05798.7

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.31→42.97 Å / SU ML: 0.76 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 43.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3172 3526 10.05 %
Rwork0.2931 31555 -
obs0.2956 35081 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 354.38 Å2 / Biso mean: 185.241 Å2 / Biso min: 84.17 Å2
Refinement stepCycle: final / Resolution: 3.31→42.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6550 0 0 0 6550
Num. residues----816
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.31-3.350.5071350.48391233136898
3.35-3.40.49951440.480912711415100
3.4-3.450.56851470.456212631410100
3.45-3.50.43531460.420412841430100
3.5-3.560.41691400.391912171357100
3.56-3.620.44961440.369812681412100
3.62-3.690.39021420.367712851427100
3.69-3.760.38181420.3812621404100
3.76-3.840.39771400.364912751415100
3.84-3.920.37821400.331212551395100
3.92-4.010.27841380.315312651403100
4.01-4.110.40531380.322212561394100
4.11-4.220.3261480.295312731421100
4.22-4.350.40131240.300512481372100
4.35-4.490.29591500.300612961446100
4.49-4.640.34391250.255212621387100
4.65-4.830.27651450.286912871432100
4.83-5.050.32691460.278612661412100
5.05-5.320.35481380.327312611399100
5.32-5.650.291440.309612521396100
5.65-6.080.32881460.335712551401100
6.08-6.690.33841480.342912611409100
6.7-7.660.28941350.298712821417100
7.66-9.620.25951370.219812701407100
9.63-42.970.2481440.20681208135295
Refinement TLS params.Method: refined / Origin x: 22.101 Å / Origin y: -37.455 Å / Origin z: -10.9321 Å
111213212223313233
T0.8781 Å2-0.2364 Å20.0745 Å2-0.8126 Å20.1865 Å2--1.2627 Å2
L7.9147 °2-3.8744 °21.3665 °2-4.1244 °2-0.4552 °2--2.1222 °2
S0.0348 Å °-0.4924 Å °-1.6397 Å °-0.0579 Å °-0.0182 Å °1.5013 Å °0.1733 Å °-0.2194 Å °0.014 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA116 - 452
2X-RAY DIFFRACTION1allB77 - 147
3X-RAY DIFFRACTION1allC116 - 452
4X-RAY DIFFRACTION1allD77 - 147

+
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