[English] 日本語
Yorodumi
- PDB-4k03: Crystal structure of Drosophila Cryprochrome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4k03
TitleCrystal structure of Drosophila Cryprochrome
ComponentsCryptochrome-1
KeywordsCIRCADIAN CLOCK PROTEIN / Rossmann fold / photoreceptor / FAD
Function / homology
Function and homology information


UV-A, blue light phototransduction / magnetoreception / detection of light stimulus involved in magnetoreception / gravitaxis / Phosphorylation of PER and TIM / Degradation of CRY / Degradation of TIM / blue light signaling pathway / response to magnetism / response to blue light ...UV-A, blue light phototransduction / magnetoreception / detection of light stimulus involved in magnetoreception / gravitaxis / Phosphorylation of PER and TIM / Degradation of CRY / Degradation of TIM / blue light signaling pathway / response to magnetism / response to blue light / regulation of circadian sleep/wake cycle, sleep / cellular response to light stimulus / blue light photoreceptor activity / entrainment of circadian clock / circadian behavior / entrainment of circadian clock by photoperiod / locomotor rhythm / photoreceptor activity / phototransduction / response to light stimulus / FAD binding / circadian regulation of gene expression / regulation of circadian rhythm / circadian rhythm / flavin adenine dinucleotide binding / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
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. ...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
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBerndt, A. / Wolf, E.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Structures of Drosophila cryptochrome and mouse cryptochrome1 provide insight into circadian function.
Authors: Czarna, A. / Berndt, A. / Singh, H.R. / Grudziecki, A. / Ladurner, A.G. / Timinszky, G. / Kramer, A. / Wolf, E.
History
DepositionApr 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cryptochrome-1
B: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,2904
Polymers128,7192
Non-polymers1,5712
Water93752
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-17 kcal/mol
Surface area43260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.120, 121.810, 79.720
Angle α, β, γ (deg.)90.00, 114.78, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cryptochrome-1 / / DmCRY1 / dcry / Blue light photoreceptor


Mass: 64359.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: cry, CG3772 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O77059
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM TrisHCl pH 8.0, 17% PEG 3350, 120 mM Mg-Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.2→46 Å / Num. all: 20433 / Num. obs: 20372 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.2→3.37 Å / % possible all: 99.6

-
Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→40.486 Å / SU ML: 0.44 / σ(F): 1.36 / Phase error: 27.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 1041 5.11 %random
Rwork0.1878 ---
obs0.1922 20357 99.68 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.825 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2501 Å20 Å20.4499 Å2
2--1.1577 Å2-0 Å2
3---0.0924 Å2
Refinement stepCycle: LAST / Resolution: 3.2→40.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8588 0 106 52 8746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118943
X-RAY DIFFRACTIONf_angle_d1.51912192
X-RAY DIFFRACTIONf_dihedral_angle_d18.8873289
X-RAY DIFFRACTIONf_chiral_restr0.0931304
X-RAY DIFFRACTIONf_plane_restr0.0071654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.36870.34011440.24082746X-RAY DIFFRACTION100
3.3687-3.57960.28441510.21812748X-RAY DIFFRACTION100
3.5796-3.85580.29771550.18582725X-RAY DIFFRACTION100
3.8558-4.24350.22991150.16432792X-RAY DIFFRACTION100
4.2435-4.85660.22811590.15562755X-RAY DIFFRACTION100
4.8566-6.11540.29421580.20032761X-RAY DIFFRACTION100
6.1154-40.48880.25531590.1852789X-RAY DIFFRACTION99

+
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