[English] 日本語
Yorodumi
- PDB-5hyx: Plant peptide hormone receptor RGFR1 in complex with RGF1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hyx
TitlePlant peptide hormone receptor RGFR1 in complex with RGF1
Components
  • PTR-SER-ASN-PRO-GLY-HIS-HIS-PRO-HYP-ARG-HIS-ASN
  • Probable LRR receptor-like serine/threonine-protein kinase At4g26540
KeywordsTRANSFERASE / Plant Receptor
Function / homology
Function and homology information


maintenance of meristem identity / regulation of lateral root development / regulation of root morphogenesis / regulation of root development / maintenance of root meristem identity / regulation of root meristem growth / peptide receptor activity / regulation of asymmetric cell division / cellular response to phosphate starvation / regulation of reactive oxygen species metabolic process ...maintenance of meristem identity / regulation of lateral root development / regulation of root morphogenesis / regulation of root development / maintenance of root meristem identity / regulation of root meristem growth / peptide receptor activity / regulation of asymmetric cell division / cellular response to phosphate starvation / regulation of reactive oxygen species metabolic process / post-transcriptional regulation of gene expression / regulation of cell division / peptide binding / growth factor activity / cell differentiation / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / ATP binding / plasma membrane
Similarity search - Function
Root meristem growth factor 1/2/3 / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / 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 / Leucine-rich repeat domain superfamily ...Root meristem growth factor 1/2/3 / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / 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 / Leucine-rich repeat domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic 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
LRR receptor-like serine/threonine-protein kinase RGI3 / Protein GOLVEN 11
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Arabidopsis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.596 Å
AuthorsSong, W. / Han, Z. / Chai, J.
CitationJournal: Cell Res. / Year: 2016
Title: Signature motif-guided identification of receptors for peptide hormones essential for root meristem growth
Authors: Song, W. / Liu, L. / Wang, J. / Wu, Z. / Zhang, H. / Tang, J. / Lin, G. / Wang, Y. / Wen, X. / Li, W. / Han, Z. / Guo, H. / Chai, J.
History
DepositionFeb 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Probable LRR receptor-like serine/threonine-protein kinase At4g26540
A: PTR-SER-ASN-PRO-GLY-HIS-HIS-PRO-HYP-ARG-HIS-ASN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6975
Polymers70,8302
Non-polymers8673
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint9 kcal/mol
Surface area27040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.335, 182.335, 87.441
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein Probable LRR receptor-like serine/threonine-protein kinase At4g26540


Mass: 69202.875 Da / Num. of mol.: 1 / Fragment: UNP residues 57-689 / Mutation: V64T, G81E, M82K, D83Q, N104Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g26540, M3E9.30
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: C0LGR3, non-specific serine/threonine protein kinase
#2: Protein/peptide PTR-SER-ASN-PRO-GLY-HIS-HIS-PRO-HYP-ARG-HIS-ASN


Mass: 1627.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis (plant) / References: UniProt: Q3E880*PLUS
#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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 3.95 Å3/Da / Density % sol: 68.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES monohydrate pH 6.0, 22% (v/v) polyethylene glycol (PEG) 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 21, 2014
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.596→99 Å / Num. obs: 33085 / % possible obs: 98.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 53.39 Å2 / Net I/av σ(I): 19.5

-
Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.596→12.022 Å / FOM work R set: 0.7942 / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 27.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 1679 5.08 %
Rwork0.1906 31369 -
obs0.1928 33048 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.49 Å2 / Biso mean: 26.7 Å2 / Biso min: 4.32 Å2
Refinement stepCycle: final / Resolution: 2.596→12.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4897 0 56 79 5032
Biso mean--27.85 22.29 -
Num. residues----639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085031
X-RAY DIFFRACTIONf_angle_d1.4216827
X-RAY DIFFRACTIONf_chiral_restr0.115822
X-RAY DIFFRACTIONf_plane_restr0.008876
X-RAY DIFFRACTIONf_dihedral_angle_d15.3491900
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5955-2.67110.35061280.247526242752100
2.6711-2.75630.30791600.230125722732100
2.7563-2.85360.26311300.214826452775100
2.8536-2.96620.31351540.218725832737100
2.9662-3.0990.29451310.234326422773100
3.099-3.25930.26011420.216326282770100
3.2593-3.45890.29061330.209826302763100
3.4589-3.71860.24181260.186126212747100
3.7186-4.07950.19621470.16426232770100
4.0795-4.63990.17241560.14422576273299
4.6399-5.73790.21031340.17362623275799
5.7379-12.02190.23241380.21052602274099
Refinement TLS params.Method: refined / Origin x: 37.2409 Å / Origin y: 105.2053 Å / Origin z: -48.1996 Å
111213212223313233
T0.0328 Å20.0079 Å2-0.0099 Å2-0.2221 Å2-0.0199 Å2--0.0594 Å2
L0.2196 °20.1523 °2-0.1275 °2-0.82 °2-0.3998 °2--0.568 °2
S0.0633 Å °-0.0063 Å °-0.0116 Å °0.0044 Å °-0.1059 Å °-0.1213 Å °-0.012 Å °0.3275 Å °0.0308 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB61 - 6501
2X-RAY DIFFRACTION1allA1 - 13
3X-RAY DIFFRACTION1allS1 - 79

+
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