[English] 日本語
Yorodumi
- PDB-6of7: Crystal structure of the CRY1-PER2 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6of7
TitleCrystal structure of the CRY1-PER2 complex
Components
  • Cryptochrome-1
  • Period circadian protein homolog 2
KeywordsCIRCADIAN CLOCK PROTEIN / Cryptochrome-1 / Period 2 complex
Function / homology
Function and homology information


regulation of glutamate uptake involved in transmission of nerve impulse / : / circadian regulation of translation / negative regulation of glucocorticoid secretion / negative regulation of fat cell proliferation / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of transcription regulatory region DNA binding / negative regulation of circadian rhythm / lactate biosynthetic process / negative regulation of G protein-coupled receptor signaling pathway ...regulation of glutamate uptake involved in transmission of nerve impulse / : / circadian regulation of translation / negative regulation of glucocorticoid secretion / negative regulation of fat cell proliferation / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of transcription regulatory region DNA binding / negative regulation of circadian rhythm / lactate biosynthetic process / negative regulation of G protein-coupled receptor signaling pathway / lipid storage / regulation of DNA damage checkpoint / glycogen biosynthetic process / response to glucagon / regulation of gluconeogenesis / entrainment of circadian clock by photoperiod / E-box binding / photoreceptor activity / regulation of insulin secretion / response to light stimulus / regulation of vasoconstriction / white fat cell differentiation / regulation of neurogenesis / phosphatase binding / negative regulation of gluconeogenesis / signal transduction in response to DNA damage / positive regulation of gluconeogenesis / negative regulation of protein ubiquitination / FAD binding / transcription corepressor binding / fatty acid metabolic process / response to activity / positive regulation of protein ubiquitination / response to ischemia / gluconeogenesis / nuclear receptor binding / circadian regulation of gene expression / response to insulin / regulation of circadian rhythm / kinase binding / circadian rhythm / histone deacetylase binding / Circadian Clock / glucose homeostasis / positive regulation of cold-induced thermogenesis / double-stranded DNA binding / DNA-binding transcription factor binding / transcription coactivator activity / transcription cis-regulatory region binding / regulation of cell cycle / negative regulation of DNA-templated transcription / nucleolus / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Period circadian-like, C-terminal / Period protein 2/3C-terminal region / 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 / PAS fold-3 / PAS fold ...Period circadian-like, C-terminal / Period protein 2/3C-terminal region / 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 / PAS fold-3 / PAS fold / 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 / PAS domain / PAS repeat profile. / Rossmann-like alpha/beta/alpha sandwich fold / PAS domain / PAS domain superfamily / 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
Period circadian protein homolog 2 / Cryptochrome-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsMichael, A.K. / Fribourgh, J.L. / Tripathi, S.M. / Partch, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107069 United States
CitationJournal: Elife / Year: 2020
Title: Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing.
Authors: Fribourgh, J.L. / Srivastava, A. / Sandate, C.R. / Michael, A.K. / Hsu, P.L. / Rakers, C. / Nguyen, L.T. / Torgrimson, M.R. / Parico, G.C.G. / Tripathi, S. / Zheng, N. / Lander, G.C. / ...Authors: Fribourgh, J.L. / Srivastava, A. / Sandate, C.R. / Michael, A.K. / Hsu, P.L. / Rakers, C. / Nguyen, L.T. / Torgrimson, M.R. / Parico, G.C.G. / Tripathi, S. / Zheng, N. / Lander, G.C. / Hirota, T. / Tama, F. / Partch, C.L.
History
DepositionMar 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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
B: Period circadian protein homolog 2


Theoretical massNumber of molelcules
Total (without water)71,1962
Polymers71,1962
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-38 kcal/mol
Surface area25260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.640, 81.230, 98.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cryptochrome-1 /


Mass: 56591.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cry1 / Production host: Escherichia coli (E. coli) / References: UniProt: P97784
#2: Protein Period circadian protein homolog 2 / hPER2 / Circadian clock protein PERIOD 2


Mass: 14604.450 Da / Num. of mol.: 1 / Fragment: UNP residues 1093-1212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PER2, KIAA0347 / Production host: Escherichia coli (E. coli) / References: UniProt: O15055

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium chloride, 0.1 M Bis-Tris, pH 5.5, 25% PEG3350

-
Data collection

DiffractionMean temperature: 75 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 6, 2016
RadiationMonochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.11→62.565 Å / Num. obs: 10939 / % possible obs: 100 % / Redundancy: 5.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.17 / Net I/σ(I): 7.5
Reflection shellResolution: 3.11→3.28 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3 / Num. unique obs: 1564 / CC1/2: 0.75 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4CT0

4ct0


Resolution: 3.11→62.565 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.87
RfactorNum. reflection% reflection
Rfree0.2617 555 5.09 %
Rwork0.2084 --
obs0.2113 10898 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.11→62.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 0 0 4424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024540
X-RAY DIFFRACTIONf_angle_d0.4286168
X-RAY DIFFRACTIONf_dihedral_angle_d1.8042704
X-RAY DIFFRACTIONf_chiral_restr0.037664
X-RAY DIFFRACTIONf_plane_restr0.003796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.4230.40671330.27252529X-RAY DIFFRACTION100
3.423-3.91820.28441310.22662549X-RAY DIFFRACTION100
3.9182-4.93620.22511180.18432596X-RAY DIFFRACTION100
4.9362-62.57810.23271730.19442669X-RAY DIFFRACTION100

+
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