[English] 日本語
Yorodumi
- PDB-4z61: The plant peptide hormone receptor complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z61
TitleThe plant peptide hormone receptor complex
Components
  • PTR-ILE-PTR-THR-GLN
  • Phytosulfokine receptor 1
  • Somatic embryogenesis receptor kinase 2
KeywordsTRANSFERASE / hormone receptor / complex
Function / homology
Function and homology information


microsporogenesis / pollen maturation / brassinosteroid mediated signaling pathway / response to other organism / receptor serine/threonine kinase binding / defense response / non-specific serine/threonine protein kinase / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity ...microsporogenesis / pollen maturation / brassinosteroid mediated signaling pathway / response to other organism / receptor serine/threonine kinase binding / defense response / non-specific serine/threonine protein kinase / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / lipid binding / ATP binding / nucleus / 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, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat ...: / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / : / Leucine-rich repeat region / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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 / Alpha Beta
Similarity search - Domain/homology
Phytosulfokine receptor 1 / Somatic embryogenesis receptor kinase 2
Similarity search - Component
Biological speciesDaucus carota (carrot)
Arabidopsis thaliana (thale cress)
Arabidopsis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsChai, J. / Wang, J.
CitationJournal: Nature / Year: 2015
Title: Allosteric receptor activation by the plant peptide hormone phytosulfokine
Authors: Wang, J. / Li, H. / Han, Z. / Zhang, H. / Wang, T. / Lin, G. / Chang, J. / Yang, W. / Chai, J.
History
DepositionApr 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phytosulfokine receptor 1
B: Phytosulfokine receptor 1
C: Somatic embryogenesis receptor kinase 2
D: Somatic embryogenesis receptor kinase 2
P: PTR-ILE-PTR-THR-GLN
Q: PTR-ILE-PTR-THR-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,61823
Polymers190,8576
Non-polymers3,76117
Water3,693205
1
A: Phytosulfokine receptor 1
C: Somatic embryogenesis receptor kinase 2
Q: PTR-ILE-PTR-THR-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,64113
Polymers95,4293
Non-polymers2,21210
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phytosulfokine receptor 1
D: Somatic embryogenesis receptor kinase 2
P: PTR-ILE-PTR-THR-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,97710
Polymers95,4293
Non-polymers1,5487
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)486.185, 73.495, 67.333
Angle α, β, γ (deg.)90.00, 95.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-830-

HOH

-
Components

#1: Protein Phytosulfokine receptor 1 / DcPSKR1 / Phytosulfokine LRR receptor kinase 1


Mass: 70140.000 Da / Num. of mol.: 2 / Fragment: UNP residues 24-659 / Mutation: A245E, I355L, E368A, A575S, A613D, V625A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Daucus carota (carrot) / Gene: PSKR
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q8LPB4, non-specific serine/threonine protein kinase
#2: Protein Somatic embryogenesis receptor kinase 2 / AtSERK2 / Somatic embryogenesis receptor-like kinase 2


Mass: 24441.812 Da / Num. of mol.: 2 / Fragment: UNP residues 1-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SERK2, At1g34210, F23M19.11
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9XIC7, non-specific serine/threonine protein kinase
#3: Protein/peptide PTR-ILE-PTR-THR-GLN


Mass: 846.879 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis (plant)
#4: 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.: 17
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


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium citrate pH 5.5, 0.4M KCl, 30%(v/v) Pentaerythritol propoxylate (5/4 PO/OH)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Mar 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→99 Å / Num. obs: 54303 / % possible obs: 88.8 % / Redundancy: 2 % / Net I/σ(I): 14.7

-
Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→29.87 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.262 2770 5.1 %
Rwork0.196 --
obs0.2 54303 87.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12227 0 238 205 12670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812715
X-RAY DIFFRACTIONf_angle_d1.43317285
X-RAY DIFFRACTIONf_dihedral_angle_d15.2784674
X-RAY DIFFRACTIONf_chiral_restr0.1132040
X-RAY DIFFRACTIONf_plane_restr0.0082208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7501-2.79750.34521160.2381976X-RAY DIFFRACTION68
2.7975-2.84830.37421480.23822613X-RAY DIFFRACTION89
2.8483-2.90310.31851360.22432639X-RAY DIFFRACTION91
2.9031-2.96230.2961290.2322632X-RAY DIFFRACTION90
2.9623-3.02660.31971460.23672617X-RAY DIFFRACTION90
3.0266-3.0970.34241370.23512622X-RAY DIFFRACTION90
3.097-3.17430.31631490.2462617X-RAY DIFFRACTION90
3.1743-3.260.30491370.23572611X-RAY DIFFRACTION90
3.26-3.35580.31751370.22282643X-RAY DIFFRACTION89
3.3558-3.4640.28251570.21762571X-RAY DIFFRACTION89
3.464-3.58760.27621370.19942635X-RAY DIFFRACTION90
3.5876-3.7310.26321380.18442631X-RAY DIFFRACTION89
3.731-3.90050.22841280.16552580X-RAY DIFFRACTION88
3.9005-4.10560.2021210.1562651X-RAY DIFFRACTION89
4.1056-4.36210.19451630.1492607X-RAY DIFFRACTION89
4.3621-4.69770.22911450.1462590X-RAY DIFFRACTION89
4.6977-5.16830.20961320.15082609X-RAY DIFFRACTION88
5.1683-5.91110.2231360.18752598X-RAY DIFFRACTION88
5.9111-7.42840.27261440.21062572X-RAY DIFFRACTION86
7.4284-29.87360.27371340.24332519X-RAY DIFFRACTION82

+
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