[English] 日本語
Yorodumi
- PDB-6lz7: Tetrameric structure of ZmCRY1a PHR domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lz7
TitleTetrameric structure of ZmCRY1a PHR domain
ComponentsCryptochrome-1
KeywordsPLANT PROTEIN / Cryptochrome / photoreceptor / photosignaling
Function / homology
Function and homology information


blue light photoreceptor activity / : / entrainment of circadian clock by photoperiod / FAD binding / circadian regulation of gene expression / DNA binding / nucleus / cytoplasm
Similarity search - Function
Cryptochrome C-terminal / Blue/Ultraviolet sensing protein C terminal / Cryptochrome, plant / DNA photolyases class 1 signature 2. / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / Cryptochrome/DNA photolyase class 1 ...Cryptochrome C-terminal / Blue/Ultraviolet sensing protein C terminal / Cryptochrome, plant / DNA photolyases class 1 signature 2. / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Cryptochrome-1 / Cryptochrome-1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59936165826 Å
AuthorsShao, K. / Zhang, X. / Zhang, P.
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: The oligomeric structures of plant cryptochromes.
Authors: Kai Shao / Xue Zhang / Xu Li / Yahui Hao / Xiaowei Huang / Miaolian Ma / Minhua Zhang / Fang Yu / Hongtao Liu / Peng Zhang /
Abstract: Cryptochromes (CRYs) are a group of evolutionarily conserved flavoproteins found in many organisms. In plants, the well-studied CRY photoreceptor, activated by blue light, plays essential roles in ...Cryptochromes (CRYs) are a group of evolutionarily conserved flavoproteins found in many organisms. In plants, the well-studied CRY photoreceptor, activated by blue light, plays essential roles in plant growth and development. However, the mechanism of activation remains largely unknown. Here, we determined the oligomeric structures of the blue-light-perceiving PHR domain of Zea mays CRY1 and an Arabidopsis CRY2 constitutively active mutant. The structures form dimers and tetramers whose functional importance is examined in vitro and in vivo with Arabidopsis CRY2. Structure-based analysis suggests that blue light may be perceived by CRY to cause conformational changes, whose precise nature remains to be determined, leading to oligomerization that is essential for downstream signaling. This photoactivation mechanism may be widely used by plant CRYs. Our study reveals a molecular mechanism of plant CRY activation and also paves the way for design of CRY as a more efficient optical switch.
History
DepositionFeb 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5852
Polymers57,7991
Non-polymers7861
Water0
1
A: Cryptochrome-1
hetero molecules

A: Cryptochrome-1
hetero molecules

A: Cryptochrome-1
hetero molecules

A: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,3398
Polymers231,1974
Non-polymers3,1424
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area16440 Å2
ΔGint-48 kcal/mol
Surface area79350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.023, 154.023, 141.072
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

-
Components

#1: Protein Cryptochrome-1 /


Mass: 57799.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 100384475, ZEAMMB73_Zm00001d016915 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A1D6HB66, UniProt: A0A1D6HB67*PLUS
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.27 Å3/Da / Density % sol: 71.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20%(w/v) PEG 3350, 0.2M sodium thiocyanate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.599→30.61 Å / Num. obs: 15933 / % possible obs: 99.9 % / Redundancy: 15.1 % / Biso Wilson estimate: 63.1281446645 Å2 / CC1/2: 0.99 / Net I/σ(I): 11
Reflection shellResolution: 3.599→3.728 Å / Num. unique obs: 596 / CC1/2: 0.525

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PHENIX1.10_2155refinement
HKL-3000data collection
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U3C

1u3c


Resolution: 3.59936165826→30.6012670848 Å / SU ML: 0.455975310619 / Cross valid method: THROUGHOUT / σ(F): 1.33792184465 / Phase error: 26.6927274577
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.273492457464 1600 10.0420510889 %
Rwork0.231943314541 14333 -
obs0.236119008145 15933 73.4544281038 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.7565723716 Å2
Refinement stepCycle: LAST / Resolution: 3.59936165826→30.6012670848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4048 0 0 0 4048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01513560786644180
X-RAY DIFFRACTIONf_angle_d1.698297590495709
X-RAY DIFFRACTIONf_chiral_restr0.075576237465586
X-RAY DIFFRACTIONf_plane_restr0.013173039157733
X-RAY DIFFRACTIONf_dihedral_angle_d18.10232220392427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5994-3.71530.337681968241500.332352090181442X-RAY DIFFRACTION25.1148545176
3.7153-3.84790.3576600931111000.323166781897907X-RAY DIFFRACTION50.6030150754
3.8479-4.00160.3479013697091050.285506545064944X-RAY DIFFRACTION53.3570701933
4.0016-4.18330.2491301974811070.265167414816959X-RAY DIFFRACTION54.1391569325
4.1833-4.40330.28777671831100.257745695548996X-RAY DIFFRACTION56.1991869919
4.4033-4.67830.279464325371470.22857528711288X-RAY DIFFRACTION73.0279898219
4.6783-5.0380.2574398655811960.2205617184841751X-RAY DIFFRACTION98.9832231825
5.038-5.54230.2976525841381970.2337025917041777X-RAY DIFFRACTION99.8987854251
5.5423-6.33810.2967118582212030.2450422581161769X-RAY DIFFRACTION99.8481012658
6.3381-7.9620.2682260492291900.2322129273781765X-RAY DIFFRACTION99.3394308943
7.962-30.60120.2169376499441950.1693983189571735X-RAY DIFFRACTION97.1313537997

+
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