[English] 日本語
Yorodumi
- PDB-8z1j: SFX structure of dark adapted CraCRY -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8z1j
TitleSFX structure of dark adapted CraCRY
ComponentsAnimal-like cryptochrome
KeywordsFLAVOPROTEIN / photoreceptor / time-resolved crystallography / resting state
Function / homology
Function and homology information


deoxyribodipyrimidine photo-lyase activity / entrainment of circadian clock by photoperiod / FAD binding / circadian regulation of gene expression / DNA binding / nucleus / cytoplasm
Similarity search - Function
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 / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Uncharacterized protein
Similarity search - Component
Biological speciesChlamydomonas reinhardtii CC3269 (plant)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsMaestre-Reyna, M. / Hosokawa, Y. / Wang, P.-H. / Saft, M. / Caramello, N. / Engilberge, S. / Franz-Badur, S. / Ngura Putu, E.P.G. / Nakamura, M. / Wu, W.-J. ...Maestre-Reyna, M. / Hosokawa, Y. / Wang, P.-H. / Saft, M. / Caramello, N. / Engilberge, S. / Franz-Badur, S. / Ngura Putu, E.P.G. / Nakamura, M. / Wu, W.-J. / Wu, H.-Y. / Lee, C.-C. / Huang, W.-C. / Huang, K.-F. / Chang, Y.-K. / Yang, C.-H. / Lin, W.-T. / Yang, K.-C. / Ban, Y. / Imura, T. / Kazuoka, A. / Tanida, E. / Owada, S. / Joti, Y. / Tanaka, R. / Tanaka, T. / Luo, F. / Tono, K. / Kiontke, S. / Korf, L. / Umena, Y. / Tosha, T. / Bessho, Y. / Nango, E. / Iwata, S. / Royant, A. / Tsai, M.-D. / Yamamoto, J. / Essen, L.-O.
Funding support Taiwan, Japan, 7items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)AS-KPQ-105-TPP Taiwan
Ministry of Science and Technology (MoST, Taiwan)AS-KPQ-109-TPP2 Taiwan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP20H05442 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP22H04751 Japan
Japan Science and TechnologyJPMJFR2057 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05776 Japan
National Science Council (NSC, Taiwan)111-2113-M-002-029-MY3 Taiwan
CitationJournal: Sci Adv / Year: 2025
Title: Capturing structural intermediates in an animal-like cryptochrome photoreceptor by time-resolved crystallography.
Authors: Maestre-Reyna, M. / Hosokawa, Y. / Wang, P.H. / Saft, M. / Caramello, N. / Engilberge, S. / Franz-Badur, S. / Gusti Ngurah Putu, E.P. / Nakamura, M. / Wu, W.J. / Wu, H.Y. / Lee, C.C. / ...Authors: Maestre-Reyna, M. / Hosokawa, Y. / Wang, P.H. / Saft, M. / Caramello, N. / Engilberge, S. / Franz-Badur, S. / Gusti Ngurah Putu, E.P. / Nakamura, M. / Wu, W.J. / Wu, H.Y. / Lee, C.C. / Huang, W.C. / Huang, K.F. / Chang, Y.K. / Yang, C.H. / Fong, M.I. / Lin, W.T. / Yang, K.C. / Ban, Y. / Imura, T. / Kazuoka, A. / Tanida, E. / Owada, S. / Joti, Y. / Tanaka, R. / Tanaka, T. / Kang, J. / Luo, F. / Tono, K. / Kiontke, S. / Korf, L. / Umena, Y. / Tosha, T. / Bessho, Y. / Nango, E. / Iwata, S. / Royant, A. / Tsai, M.D. / Yamamoto, J. / Essen, L.O.
History
DepositionApr 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Animal-like cryptochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6283
Polymers57,8071
Non-polymers8212
Water5,837324
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.840, 65.600, 153.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Animal-like cryptochrome


Mass: 57807.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii CC3269 (plant)
Gene: CHLRE_06g278251v5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8J8W0
#2: Chemical ChemComp-FAD / 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
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 5.6
Details: 50 mM sodium phosphate, pH 7.8, 250 mM NaCl, 20% glycerol

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: May 25, 2021 / Frequency: 30
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.64→33.09 Å / Num. obs: 63708 / % possible obs: 99.98 % / Redundancy: 909.6 % / Biso Wilson estimate: 26.22 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.505
Reflection shellResolution: 1.64→1.83 Å / Redundancy: 110.5 % / Mean I/σ(I) obs: 1.37 / Num. unique obs: 3083 / CC1/2: 0.506 / % possible all: 100
Serial crystallography measurementFocal spot size: 1.77 µm2 / Pulse duration: 10 fsec. / Pulse photon energy: 10 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: grease / Description: High viscosity injector / Filter size: 50 µm / Flow rate: 1 µL/min / Injector diameter: 75 µm / Injector temperature: 293 K

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrystFELdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FN3

6fn3


Resolution: 1.64→33.06 Å / SU ML: 0.1906 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.5717
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1573 1986 3.12 %
Rwork0.1399 61597 -
obs0.1404 63583 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.29 Å2
Refinement stepCycle: LAST / Resolution: 1.64→33.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3914 0 54 324 4292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01074173
X-RAY DIFFRACTIONf_angle_d0.99945709
X-RAY DIFFRACTIONf_chiral_restr0.0633594
X-RAY DIFFRACTIONf_plane_restr0.0105737
X-RAY DIFFRACTIONf_dihedral_angle_d13.93721517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.680.28821520.25954288X-RAY DIFFRACTION99.73
1.68-1.730.26351450.2354331X-RAY DIFFRACTION99.89
1.73-1.780.31281270.26084352X-RAY DIFFRACTION99.89
1.78-1.830.26351440.22334345X-RAY DIFFRACTION99.93
1.83-1.90.21241250.18144347X-RAY DIFFRACTION99.84
1.9-1.980.18121510.14784387X-RAY DIFFRACTION99.91
1.98-2.070.16351290.13644337X-RAY DIFFRACTION99.98
2.07-2.180.16731480.14414372X-RAY DIFFRACTION99.98
2.18-2.310.14631430.12964410X-RAY DIFFRACTION99.98
2.31-2.490.13531330.12254377X-RAY DIFFRACTION100
2.49-2.740.14921490.13114433X-RAY DIFFRACTION99.96
2.74-3.140.17111560.14184422X-RAY DIFFRACTION99.98
3.14-3.950.13591440.12134505X-RAY DIFFRACTION100
3.95-33.060.12791400.12784691X-RAY DIFFRACTION99.98
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)
12.319675623290.144858270122-0.5600335833473.47869626069-0.1122241487112.516095148460.0253342156069-0.0257602036040.213464752652-0.0592499569806-0.05635090037580.17482440016-0.131217117184-0.1272900827660.05685089449930.1663960250120.012671854754-0.00247471258550.15203162131-0.0343323169140.14534221930719.233094724611.1497601187-12.5426846353
20.67709816573-0.0313603066845-0.0610901335131.14573703040.2625867382260.4294705983630.00992833206612-0.03377821298460.0395996881820.0535934129648-0.02800248708620.0057110078303-0.05732218300280.007524158656540.01567718946090.203182381279-0.004481177015060.001328261004890.219896207759-0.001214018865180.18579721346322.2919004974-0.115771321956-16.8149127789
31.42226971490.587179633938-0.265142325321.79246125585-0.2287219770070.770074389157-0.02618742439150.14206272774-0.0650914752053-0.1114945423410.002080919039620.1724731435640.0433194729553-0.0840619731950.01496128600740.1707325753930.0167564792389-0.0182432348820.219015253106-0.03202136713910.2230600584045.28908313152-20.2905008577-28.6023502308
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 52 )3 - 521 - 47
22chain 'A' and (resid 53 through 304 )53 - 30448 - 299
33chain 'A' and (resid 305 through 494 )305 - 494300 - 489

+
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