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- PDB-7d0n: Crystal structure of mouse CRY2 apo form -

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Basic information

Entry
Database: PDB / ID: 7d0n
TitleCrystal structure of mouse CRY2 apo form
ComponentsCryptochrome-2
KeywordsCIRCADIAN CLOCK PROTEIN / CRY / CRY2 / cryptochrome / PHR
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
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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMiller, S.A. / Aikawa, Y. / Hirota, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJPR14LA Japan
Japan Society for the Promotion of Science (JSPS)15H05590 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structural differences in the FAD-binding pockets and lid loops of mammalian CRY1 and CRY2 for isoform-selective regulation.
Authors: Miller, S. / Srivastava, A. / Nagai, Y. / Aikawa, Y. / Tama, F. / Hirota, T.
History
DepositionSep 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cryptochrome-2


Theoretical massNumber of molelcules
Total (without water)58,8471
Polymers58,8471
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The protein is monomeric in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19700 Å2
Unit cell
Length a, b, c (Å)67.840, 67.840, 128.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein Cryptochrome-2


Mass: 58847.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cry2, Kiaa0658 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9R194
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES pH 7.0, 100 mM NaCl, 10% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→36.12 Å / Num. obs: 14322 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 45.03 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.058 / Rrim(I) all: 0.147 / Net I/σ(I): 10.9
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2112 / CC1/2: 0.746 / Rpim(I) all: 0.267 / Rrim(I) all: 0.662 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
REFMAC5.8.0257refinement
MOSFLM7.3.0data reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
Coot0.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KX8

6kx8


Resolution: 2.8→33.92 Å / SU ML: 0.5078 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.0882
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2934 678 4.74 %
Rwork0.2505 13616 -
obs0.2526 14294 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.07 Å2
Refinement stepCycle: LAST / Resolution: 2.8→33.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3359 0 0 34 3393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583460
X-RAY DIFFRACTIONf_angle_d0.78264754
X-RAY DIFFRACTIONf_chiral_restr0.0464529
X-RAY DIFFRACTIONf_plane_restr0.0053620
X-RAY DIFFRACTIONf_dihedral_angle_d15.0425490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.020.37711240.32272741X-RAY DIFFRACTION100
3.02-3.320.3371190.29082707X-RAY DIFFRACTION100
3.32-3.80.31181230.26012744X-RAY DIFFRACTION100
3.8-4.780.27651300.21752722X-RAY DIFFRACTION100
4.78-33.920.26261820.23042702X-RAY DIFFRACTION99.9
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)
11.383086667640.339463217253-0.8517594921890.935820257321-0.7729089813941.32362567433-0.818762863668-0.101144082404-1.313917761040.09003795082540.0175300730149-0.03991229727371.375757370990.325722586860.8355767473921.128579457040.2329598620620.8137093923010.4667628512620.1525158786140.8633252298465.5408434354-36.15318145934.22976487645
20.560000782309-0.133509363819-0.03953956574360.910919153497-0.1292785677241.25190512068-0.560029780264-0.696541200224-0.5629744767310.69181644292-0.1187718286310.06830122185380.5520686248420.5901023814110.06685911817040.7435615775680.2418050034090.2710699928410.7264435815060.2919755405180.4207402477522.06855638058-24.643973648318.7847557697
32.866705525960.408052934132-1.362695224470.510371234442-0.5990736470732.95543750211-0.3952559266821.04870303258-0.614081247757-0.209341500768-0.04325609672040.009896930692620.752046053694-0.8266205818550.2351780651060.503656635933-0.3391217939120.1550116402131.06626292403-0.2492757393060.500261994436-21.0350878494-24.94743665592.7860329788
42.846626690580.14787247854-0.8063566818631.132338451110.2699379118623.193434874530.2492144334960.7282103517830.284414860489-0.08684559219770.0504598697754-0.03205174922350.207873901027-0.571147204618-0.06028150390990.199281462730.04126241895370.06579068432880.2927025395860.03298008817230.198432118745-9.86828985051-11.2991151197.59431634866
51.324178976191.21216317515-0.1093439054331.27215439969-0.1338769035812.46914398409-0.05958703591740.178808998681-0.1544979801290.461523111231-0.2062703008360.6309479578140.296728920524-0.7881105616780.1324642101210.421636665283-0.165953906960.2050991837310.375512507057-0.1503440171030.504771447143-17.4713676806-18.347168043513.3631624258
60.4336278399550.0884963061086-0.8651658992350.596066638597-0.4125336308411.803124504270.6697064805990.1683891529691.060160497060.254842529557-0.01061725446710.158119704574-0.846188931431-0.335621130643-0.376258537030.567179821735-0.06200279583460.413229404140.3108023201080.05301576037270.746368045076-12.45062841492.3205217558113.7171797307
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 21 through 217 )21 - 2171 - 190
22chain 'A' and (resid 218 through 318 )218 - 318191 - 274
33chain 'A' and (resid 319 through 341 )319 - 341275 - 297
44chain 'A' and (resid 342 through 407 )342 - 407298 - 363
55chain 'A' and (resid 408 through 434 )408 - 434364 - 390
66chain 'A' and (resid 435 through 507 )435 - 507391 - 463

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