[English] 日本語
Yorodumi
- PDB-6brp: F-box protein form 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6brp
TitleF-box protein form 2
Components
  • F-box/LRR-repeat MAX2 homolog
  • SKP1-like protein 1A
KeywordsLIGASE / Ubiquitin ligase / F-box
Function / homology
Function and homology information


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 / cuticle development / phragmoplast / auxin polar transport / jasmonic acid mediated signaling pathway ...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 / cuticle development / phragmoplast / auxin polar transport / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to jasmonic acid / response to auxin / auxin-activated signaling pathway / response to water deprivation / negative regulation of DNA recombination / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / response to light stimulus / chromosome segregation / spindle / microtubule cytoskeleton organization / ubiquitin-dependent protein catabolic process / protein ubiquitination / mitochondrion / nucleus / cytosol
Similarity search - Function
Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Potassium Channel Kv1.1; Chain A ...Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / 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 / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SKP1-like protein 1A / F-box/LRR-repeat MAX2 homolog
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.39 Å
AuthorsShabek, N. / Zheng, N. / Mao, H. / Hinds, T.R. / Ticchiarelli, F. / Leyser, O.
CitationJournal: Nature / Year: 2018
Title: Structural plasticity of D3-D14 ubiquitin ligase in strigolactone signalling.
Authors: Shabek, N. / Ticchiarelli, F. / Mao, H. / Hinds, T.R. / Leyser, O. / Zheng, N.
History
DepositionNov 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: F-box/LRR-repeat MAX2 homolog
A: SKP1-like protein 1A
D: F-box/LRR-repeat MAX2 homolog
C: SKP1-like protein 1A


Theoretical massNumber of molelcules
Total (without water)187,4104
Polymers187,4104
Non-polymers00
Water8,899494
1
B: F-box/LRR-repeat MAX2 homolog
A: SKP1-like protein 1A


Theoretical massNumber of molelcules
Total (without water)93,7052
Polymers93,7052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-25 kcal/mol
Surface area32990 Å2
MethodPISA
2
D: F-box/LRR-repeat MAX2 homolog
C: SKP1-like protein 1A


Theoretical massNumber of molelcules
Total (without water)93,7052
Polymers93,7052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-25 kcal/mol
Surface area33220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.451, 130.471, 94.316
Angle α, β, γ (deg.)90.000, 99.380, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein F-box/LRR-repeat MAX2 homolog / F-box and leucine-rich repeat MAX2 homolog / Protein DWARF 3


Mass: 75828.922 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: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q5VMP0
#2: Protein SKP1-like protein 1A / SKP1-like 1 / UFO-binding protein 1


Mass: 17876.043 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: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q39255
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 80 mM Tris-HCl, pH 7.0, 24% MPD, 24% PEG1000, 24% P3350; 15 mM Sodium Citrate tribasic dihydrate pH 5.6; 0.5 M 1,6-Hexanediol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→93.06 Å / Num. obs: 73476 / % possible obs: 98.9 % / Redundancy: 7.2 % / Rsym value: 0.179 / Net I/σ(I): 26.4
Reflection shellResolution: 2.392→2.478 Å / Num. unique obs: 7246 / Rsym value: 0.939

-
Processing

Software
NameVersionClassification
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementResolution: 2.39→93.06 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.218 3783 RANDOM
Rwork0.192 --
obs-73464 -
Displacement parametersBiso max: 129.1 Å2 / Biso mean: 35.3522 Å2 / Biso min: 8.09 Å2
Refinement stepCycle: LAST / Resolution: 2.39→93.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11737 0 0 494 12231
LS refinement shellResolution: 2.392→2.478 Å / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.243
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)
10.383-0.1716-0.01750.10160.04760.50870.0219-0.008-0.0462-0.00390.01330.00730.0108-0.0256-0.03510.08530.0036-0.01810.1167-0.00650.06718.186-34.4514-51.6386
21.42940.89540.40162.9108-0.00450.8883-0.16350.31490.2-0.3360.12460.3345-0.26480.30560.03890.1243-0.0852-0.04410.18670.04480.047336.7793-12.0169-55.7519
30.570.12820.07660.05810.10660.66760.0237-0.05650.04810.0017-0.0268-0.0191-0.001-0.12760.00310.0834-0.009-0.0170.126-0.01050.062-31.1105-8.4543-12.8801
40.5253-0.2305-0.47812.0162-1.02091.3827-0.1625-0.21320.0254-0.0470.0748-0.03890.28490.19310.08770.15070.04060.01090.153-0.00420.0507-3.4241-30.6632-6.7101
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B13 - 720
2X-RAY DIFFRACTION2A4 - 160
3X-RAY DIFFRACTION3D13 - 720
4X-RAY DIFFRACTION4C4 - 160

+
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