[English] 日本語
Yorodumi
- PDB-4mlp: Mammalian cryptochrome in complex with a small molecule competito... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mlp
TitleMammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase
ComponentsCryptochrome-2
KeywordsTRANSCRIPTION / photolyase homology region / transcriptional repressor / PERIOD / FBXL3 / CLOCK / nucleus
Function / homology
Function and homology information


regulation of sodium-dependent phosphate transport / Cry-Per complex / negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of circadian rhythm / lipid storage / entrainment of circadian clock by photoperiod / photoreceptor activity / response to light stimulus / phosphatase binding ...regulation of sodium-dependent phosphate transport / Cry-Per complex / negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of circadian rhythm / lipid storage / entrainment of circadian clock by photoperiod / photoreceptor activity / response to light stimulus / phosphatase binding / FAD binding / response to activity / nuclear receptor binding / circadian regulation of gene expression / response to insulin / regulation of circadian rhythm / kinase binding / circadian rhythm / protein import into nucleus / glucose homeostasis / single-stranded DNA binding / damaged DNA binding / transcription cis-regulatory region binding / nuclear speck / negative regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / extracellular region / 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
Chem-2CX / Cryptochrome-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.943 Å
AuthorsNangle, S. / Xing, W. / Zheng, N.
CitationJournal: Cell Res. / Year: 2013
Title: Crystal structure of mammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase.
Authors: Nangle, S. / Xing, W. / Zheng, N.
History
DepositionSep 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Cryptochrome-2
A: Cryptochrome-2
B: Cryptochrome-2
D: Cryptochrome-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,3508
Polymers234,7564
Non-polymers1,5944
Water27,9951554
1
C: Cryptochrome-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0882
Polymers58,6891
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Cryptochrome-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0882
Polymers58,6891
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Cryptochrome-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0882
Polymers58,6891
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cryptochrome-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0882
Polymers58,6891
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.210, 93.651, 141.179
Angle α, β, γ (deg.)89.94, 90.09, 90.25
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Cryptochrome-2


Mass: 58689.047 Da / Num. of mol.: 4 / Fragment: photolyase homology region UNP residues 1-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cry2, Kiaa0658 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9R194
#2: Chemical
ChemComp-2CX / N-[(2S)-3-(9H-carbazol-9-yl)-2-hydroxypropyl]-N-(furan-2-ylmethyl)methanesulfonamide


Mass: 398.475 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H22N2O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1554 / 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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES and 4-5% PEG8K, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. all: 175262 / Num. obs: 170540 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 %
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
1.95-1.980.601195.1
1.98-2.020.496195
2.02-2.060.417195.7
2.06-2.10.369195.2
2.1-2.150.297196.3
2.15-2.20.239195.8
2.2-2.250.22196.4
2.25-2.310.18196.6
2.31-2.380.151196.8
2.38-2.460.131197.3
2.46-2.540.112197.4
2.54-2.650.099197.7
2.65-2.770.092197.9
2.77-2.910.081197.9
2.91-3.10.074198.3
3.1-3.330.068198.3
3.33-3.670.061198.5
3.67-4.20.054198.1
4.2-5.290.048198.1
5.29-500.045198.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4I6J

4i6j


Resolution: 1.943→44.458 Å / SU ML: 0.17 / σ(F): 0.08 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 1499 88 %random
Rwork0.1795 ---
obs0.1798 170540 --
all-175262 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.943→44.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16060 0 112 1554 17726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716656
X-RAY DIFFRACTIONf_angle_d1.08722612
X-RAY DIFFRACTIONf_dihedral_angle_d15.0946184
X-RAY DIFFRACTIONf_chiral_restr0.082320
X-RAY DIFFRACTIONf_plane_restr0.0042908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9433-2.0060.27151220.207613134X-RAY DIFFRACTION80
2.006-2.07770.25031250.205214782X-RAY DIFFRACTION90
2.0777-2.16090.24561360.198414908X-RAY DIFFRACTION91
2.1609-2.25920.20981290.190615265X-RAY DIFFRACTION93
2.2592-2.37840.24961430.191815386X-RAY DIFFRACTION94
2.3784-2.52730.23091330.185515704X-RAY DIFFRACTION95
2.5273-2.72250.20731420.189415700X-RAY DIFFRACTION96
2.7225-2.99640.23641410.18815973X-RAY DIFFRACTION97
2.9964-3.42980.2611410.184616058X-RAY DIFFRACTION98
3.4298-4.32060.19761410.159416032X-RAY DIFFRACTION98
4.3206-44.46940.17791460.168316099X-RAY DIFFRACTION98

+
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