[English] 日本語
Yorodumi
- PDB-5hzg: The crystal structure of the strigolactone-induced AtD14-D3-ASK1 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hzg
TitleThe crystal structure of the strigolactone-induced AtD14-D3-ASK1 complex
Components
  • F-box/LRR-repeat MAX2 homolog
  • SKP1-like protein 1A
  • Strigolactone esterase D14
KeywordsHYDROLASE/SIGNALING PROTEIN/PROTEIN BINDING / F-box protein / receptor / HYDROLASE-SIGNALING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


cellular response to strigolactone / bud dilation / regulation of shoot system morphogenesis / shoot system morphogenesis / regulation of meristem structural organization / negative regulation of seed germination / positive regulation of response to water deprivation / strigolactone biosynthetic process / secondary shoot formation / phragmoplast ...cellular response to strigolactone / bud dilation / regulation of shoot system morphogenesis / shoot system morphogenesis / regulation of meristem structural organization / negative regulation of seed germination / positive regulation of response to water deprivation / strigolactone biosynthetic process / secondary shoot formation / phragmoplast / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / auxin polar transport / response to jasmonic acid / response to auxin / auxin-activated signaling pathway / response to water deprivation / negative regulation of DNA recombination / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / response to light stimulus / chromosome segregation / microtubule cytoskeleton organization / spindle / ubiquitin-dependent protein catabolic process / Hydrolases; Acting on ester bonds / hydrolase activity / protein ubiquitination / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Alpha/beta hydrolase family ...Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Alpha/beta hydrolase family / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Alpha/beta hydrolase fold-1 / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat domain superfamily / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2Z)-2-methylbut-2-ene-1,4-diol / SKP1-like protein 1A / F-box/LRR-repeat MAX2 homolog / Strigolactone esterase D14
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Oryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsYao, R.F. / Ming, Z.H. / Yan, L.M. / Rao, Z.H. / Lou, Z.Y. / Xie, D.X.
Funding support China, 4items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31230008 China
the National Natural Science Foundation of China81322023 China
Ministry of Science and Technology2011CB915404 China
Ministry of Science and Technology2013CB911100 China
CitationJournal: Nature / Year: 2016
Title: DWARF14 is a non-canonical hormone receptor for strigolactone
Authors: Yao, R. / Ming, Z. / Yan, L. / Li, S. / Wang, F. / Ma, S. / Yu, C. / Yang, M. / Chen, L. / Chen, L. / Li, Y. / Yan, C. / Miao, D. / Sun, Z. / Yan, J. / Sun, Y. / Wang, L. / Chu, J. / Fan, S. ...Authors: Yao, R. / Ming, Z. / Yan, L. / Li, S. / Wang, F. / Ma, S. / Yu, C. / Yang, M. / Chen, L. / Chen, L. / Li, Y. / Yan, C. / Miao, D. / Sun, Z. / Yan, J. / Sun, Y. / Wang, L. / Chu, J. / Fan, S. / He, W. / Deng, H. / Nan, F. / Li, J. / Rao, Z. / Lou, Z. / Xie, D.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Strigolactone esterase D14
B: F-box/LRR-repeat MAX2 homolog
C: SKP1-like protein 1A
E: Strigolactone esterase D14
F: F-box/LRR-repeat MAX2 homolog
G: SKP1-like protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,8288
Polymers259,6236
Non-polymers2042
Water43224
1
A: Strigolactone esterase D14
B: F-box/LRR-repeat MAX2 homolog
C: SKP1-like protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,9144
Polymers129,8123
Non-polymers1021
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-34 kcal/mol
Surface area42590 Å2
MethodPISA
2
E: Strigolactone esterase D14
F: F-box/LRR-repeat MAX2 homolog
G: SKP1-like protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,9144
Polymers129,8123
Non-polymers1021
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-33 kcal/mol
Surface area42500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.397, 172.979, 186.845
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Strigolactone esterase D14 / Protein DWARF 14 / AtD14


Mass: 29653.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: D14, At3g03990, T11I18.10 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12
References: UniProt: Q9SQR3, Hydrolases; Acting on ester bonds
#2: Protein F-box/LRR-repeat MAX2 homolog / F-box and leucine-rich repeat MAX2 homolog / Protein DWARF 3


Mass: 81153.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: D3, Os06g0154200, LOC_Os06g06050, OSJNBa0085L11.6-1
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q5VMP0
#3: Protein SKP1-like protein 1A / SKP1-like 1 / UFO-binding protein 1


Mass: 19004.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SKP1A, ASK1, SKP1, UIP1, At1g75950, T4O12.17
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q39255
#4: Chemical ChemComp-6OM / (2Z)-2-methylbut-2-ene-1,4-diol


Mass: 102.132 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.85 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 16% PEG 3350, 16mM BICINE pH 9.0, 20mM HEPES pH 7.5, 4.4% w/v Polyacrylic Acid 5100 Sodium salt, 10mM Praseodymium (III) acetate hydrate, 100 mM NDSB-256

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 49674 / % possible obs: 99.9 % / Redundancy: 19.82 % / Net I/σ(I): 12.6
Reflection shellResolution: 3.3→3.4 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.3→49.07 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.801 / SU B: 31.208 / SU ML: 0.504 / Cross valid method: THROUGHOUT / ESU R Free: 0.597 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31585 2669 5.1 %RANDOM
Rwork0.24623 ---
obs0.24969 49674 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 89.173 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2---0.02 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 3.3→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15638 0 14 24 15676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01915976
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215363
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.9721701
X-RAY DIFFRACTIONr_angle_other_deg1.151335275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.66251985
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9323.014700
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.179152628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.01315134
X-RAY DIFFRACTIONr_chiral_restr0.1490.22506
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02117847
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023655
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.5028.8528000
X-RAY DIFFRACTIONr_mcbond_other5.4948.8537999
X-RAY DIFFRACTIONr_mcangle_it9.0313.2639965
X-RAY DIFFRACTIONr_mcangle_other9.03213.2629966
X-RAY DIFFRACTIONr_scbond_it4.8689.0877976
X-RAY DIFFRACTIONr_scbond_other4.8679.0877974
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.26413.50511736
X-RAY DIFFRACTIONr_long_range_B_refined13.77369.37717662
X-RAY DIFFRACTIONr_long_range_B_other13.77269.37817663
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 194 -
Rwork0.363 3640 -
obs--99.9 %

+
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