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- PDB-7dli: Crystal structure of mouse CRY1 in complex with KL001 compound -

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Basic information

Entry
Database: PDB / ID: 7dli
TitleCrystal structure of mouse CRY1 in complex with KL001 compound
ComponentsCryptochrome-1
KeywordsCIRCADIAN CLOCK PROTEIN / CRY / CRY1 / cryptochrome / PHR
Function / homology
Function and homology information


negative regulation of glucocorticoid secretion / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of circadian rhythm / lipid storage / regulation of DNA damage checkpoint / response to glucagon / negative regulation of G protein-coupled receptor signaling pathway / regulation of gluconeogenesis / entrainment of circadian clock by photoperiod / E-box binding ...negative regulation of glucocorticoid secretion / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of circadian rhythm / lipid storage / regulation of DNA damage checkpoint / response to glucagon / negative regulation of G protein-coupled receptor signaling pathway / regulation of gluconeogenesis / entrainment of circadian clock by photoperiod / E-box binding / response to light stimulus / signal transduction in response to DNA damage / photoreceptor activity / negative regulation of gluconeogenesis / phosphatase binding / negative regulation of protein ubiquitination / positive regulation of gluconeogenesis / nuclear receptor binding / positive regulation of protein ubiquitination / response to activity / gluconeogenesis / circadian regulation of gene expression / response to insulin / circadian rhythm / regulation of circadian rhythm / kinase binding / histone deacetylase binding / glucose homeostasis / double-stranded DNA binding / DNA-binding transcription factor binding / nucleotide binding / negative regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / cytosol
Similarity search - Function
DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / 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 ...DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-H8X / Cryptochrome-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionNov 27, 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-1
B: Cryptochrome-1
C: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,3737
Polymers172,1153
Non-polymers1,2574
Water7,206400
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The protein is monomeric in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.598, 134.824, 145.587
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_11(chain "A" and (resid 3 through 22 or (resid 23...
d_21(chain "B" and (resid 3 through 21 or (resid 22...
d_31(chain "C" and (resid 3 through 28 or (resid 29...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_111VALTRPA1 - 219
d_121GLYSERA239 - 393
d_131CYSTYRA396 - 472
d_141LIGLIGB
d_211VALLEUC1 - 35
d_221VALTRPC38 - 221
d_231GLYSERC241 - 395
d_241CYSTYRC397 - 473
d_251LIGLIGD
d_311VALLEUE2 - 36
d_321VALSERE46 - 384
d_331CYSTYRE392 - 468
d_341LIGLIGF

NCS oper:
IDCodeMatrixVector
1given(0.996615017718, -0.0746965914706, -0.0343354871983), (0.0786167638167, 0.988079810386, 0.132354420985), (0.0240397775668, -0.134605748502, 0.990607582025)6.87174715024, 36.9589094014, 24.8247540525
2given(0.994299321143, -0.0915638040258, -0.0546345107696), (-0.0843152057058, -0.988845977433, 0.122778577124), (-0.0652671897779, -0.117472135871, -0.990929105049)37.9601362099, 3.32056466481, -48.0247790352

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Components

#1: Protein Cryptochrome-1


Mass: 57371.734 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cry1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P97784
#2: Chemical ChemComp-H8X / N-[(2R)-3-carbazol-9-yl-2-oxidanyl-propyl]-N-(furan-2-ylmethyl)methanesulfonamide


Mass: 398.475 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H22N2O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 22% (w/v) PEG3350, 3% (v/v) ethylene glycol, 0.2 M NH4Cl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→53.38 Å / Num. obs: 78355 / % possible obs: 99.2 % / Redundancy: 5.2 % / Biso Wilson estimate: 25.72 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.036 / Rrim(I) all: 0.081 / Net I/σ(I): 12.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 11226 / CC1/2: 0.858 / Rpim(I) all: 0.188 / Rrim(I) all: 0.415 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PHENIX1.18.2_3874refinement
xia20.6.467data reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
Coot0.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KX4

6kx4


Resolution: 2.2→51.17 Å / SU ML: 0.2384 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6998
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2299 3988 5.1 %
Rwork0.1901 74153 -
obs0.1921 78141 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.16 Å2
Refinement stepCycle: LAST / Resolution: 2.2→51.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10763 0 88 400 11251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008311172
X-RAY DIFFRACTIONf_angle_d0.932415302
X-RAY DIFFRACTIONf_chiral_restr0.05591677
X-RAY DIFFRACTIONf_plane_restr0.00721965
X-RAY DIFFRACTIONf_dihedral_angle_d22.17881554
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
1d_2AX-RAY DIFFRACTIONTorsion NCS0.893876999651
1d_3AX-RAY DIFFRACTIONTorsion NCS1.11532715115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.29861360.23322515X-RAY DIFFRACTION95.7
2.23-2.260.33361400.26372580X-RAY DIFFRACTION97.46
2.26-2.290.29811230.23872629X-RAY DIFFRACTION98.82
2.29-2.320.25291340.20232590X-RAY DIFFRACTION97.49
2.32-2.350.24611360.19472625X-RAY DIFFRACTION99.5
2.35-2.390.24671430.18912586X-RAY DIFFRACTION97.36
2.39-2.420.2171660.19222598X-RAY DIFFRACTION99.57
2.42-2.460.251380.19032616X-RAY DIFFRACTION97.8
2.46-2.50.20211560.18562603X-RAY DIFFRACTION99.6
2.5-2.550.24531410.19212632X-RAY DIFFRACTION98.12
2.55-2.60.26341520.20092626X-RAY DIFFRACTION99.32
2.6-2.650.26331420.2022610X-RAY DIFFRACTION98.53
2.65-2.710.21821430.20432621X-RAY DIFFRACTION98.12
2.71-2.770.24651520.212625X-RAY DIFFRACTION99.86
2.77-2.840.25911500.20732632X-RAY DIFFRACTION98.62
2.84-2.920.25251360.20872641X-RAY DIFFRACTION98.62
2.92-3.010.23411690.19952640X-RAY DIFFRACTION99.89
3.01-3.10.24251370.20622630X-RAY DIFFRACTION99.18
3.1-3.210.23711430.20422654X-RAY DIFFRACTION99.22
3.21-3.340.2531070.20812704X-RAY DIFFRACTION99.19
3.34-3.490.24761380.19112666X-RAY DIFFRACTION99.36
3.49-3.680.22331440.17922698X-RAY DIFFRACTION99.47
3.68-3.910.16061300.16172696X-RAY DIFFRACTION99.51
3.91-4.210.19451350.15532688X-RAY DIFFRACTION99.3
4.21-4.630.20311390.15732717X-RAY DIFFRACTION99.44
4.63-5.30.20851550.17922699X-RAY DIFFRACTION99.48
5.3-6.680.22171540.19712748X-RAY DIFFRACTION99.28
6.68-51.170.22541490.18312884X-RAY DIFFRACTION99.28
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)
11.46805938811-0.664010890142-0.05443615191431.82015031407-0.0172902664921.266406874440.0549670872930.3608289528240.17660099453-0.301128256301-0.0524310548956-0.0224407906942-0.0748600255103-0.16481488978-0.0131692063450.2435650936640.0158051728744-0.01263104430030.296228741279-0.02626784374480.16951051574620.11343952486.89078609846-48.7363727669
21.426912645510.629237489908-0.5975195256551.63744497408-0.2541861180771.904329368967.98716693422E-5-0.02989575860950.1273371665310.0460732197932-0.008162496743640.139268594149-0.157167943196-0.1144694339650.02040624994860.2498201821210.059044753941-0.001821507432950.183909701588-0.05769107724010.18553884639619.357884690711.4403594703-32.2654693942
31.914562937481.537563387521.316243669452.707079798371.564433050742.12146477126-0.1337759790550.33188356897-0.1916264161530.09997371080020.229639226437-0.270286104509-0.05406563906440.42375840395-0.0845449572710.171198044354-0.002531835477330.01418024522870.281962474354-0.02427245207680.20527629379438.61039030997.88136991517-37.7137413977
41.14745305135-0.137769017128-0.955180284170.8396860989470.1158668151373.11841836203-0.0573611374841-0.196778601099-0.2064250582290.02244602736820.0513800843581-0.08983726392390.07086470484220.185568024388-0.01312681754530.1773064096510.033621446206-0.01326427837350.23187485804-0.01585269247090.2222038526424.4150184465-12.8125027204-20.8938808372
52.25008435333-0.223872148854-0.0253863447561.50198642658-0.1225044465581.292338742320.05665362361590.5195639313860.10310135679-0.2071906185370.020717183492-0.02353680931110.0656069621006-0.0931655644976-0.0676993202630.187086874708-0.00652090519712-0.02538982309370.2215956637330.01077147131120.16690969334327.810928914438.8987045669-23.7536039074
63.555754039010.7080367769440.8724140700291.618099274270.5444338788060.798399922163-0.01695921350890.2065162393430.265057622473-0.1049993138190.1529119129120.3386563468270.0158956594035-0.384503491854-0.1904491352730.1883329433380.01489519858620.01511635931840.2937090009710.08110110284960.27799152320214.354942213445.0719824864-15.5106225328
71.93680943132-0.262055119606-1.209900229051.461296814060.3375182409931.917623921740.0804383138847-0.1755003913970.1638822329860.191585886598-0.00480313395649-0.282219325124-0.1038277297230.336463319878-0.06071315578410.174973229978-0.0153728000815-0.0266982469910.1763073446640.005408703826260.18093994548741.340480692844.6037418357-7.8502646472
81.31099788344-0.0819493496399-0.3038245641051.19874577049-0.0002191742662492.5768573955-0.0349436007312-0.11184429561-0.276391629119-0.0603430888287-0.00761579505024-0.1070123730630.2120574652870.1420052607990.01477966491050.133849644551-0.004958236670460.008000163266550.1166368052350.03977399685220.23369157014332.942965641823.24655105646.55462645606
92.387608517310.716297245272-0.1544210216110.6107713367430.08192197285163.0264920304-0.0593578937608-0.0156165777436-0.2802693195280.128372377926-0.04969523850130.03732155460020.0252373408487-0.1076103338440.0822385929810.201533246467-0.01726644345090.02391939640580.1163472637660.002100221628220.2483996401452.3059658219-13.0889754521-6.44680605162
101.979714664630.7386275311640.5309840127661.495016537510.3274300660322.033852502830.0831030204679-0.511527572767-0.07730521115720.0912711996176-0.1842902030470.207318058158-0.00320365039172-0.2690989725680.09052479207450.311470073729-0.003375290355580.02447433974240.2466825735360.04751091486680.21809688928752.586610759-9.378360299724.3778135409
113.200293160251.13967042494-0.2906612109530.993079235599-0.02110338316040.87037044482-0.109250852222-0.171558811734-0.4465510064820.1039456732520.0705414219815-0.1885474359240.1068729940790.09504598545440.03673048476650.2074246858340.0432832415295-0.01729463990280.1773384369680.02042906123530.21270794400874.0723686386-8.50066180233-2.23633293272
122.23616277739-1.30134642345-0.4904483413043.56259400842-0.9407527833413.02933900156-0.1102529708520.145695253506-0.468013200815-0.03869980298010.3013440452650.4129027143140.0371374389358-0.759290665284-0.1894927832020.242391527014-0.0983876325335-0.01411526311810.213936429861-0.02167801060660.33659080506745.7554681077-14.8149727943-11.1767570855
132.113379779340.147357026455-0.3080798467891.43402341319-0.344170494041.04932406422-0.1356309203330.369478661358-0.64937867508-0.2147413343770.0371520364407-0.2757884778060.1902135540440.1906980985550.1089639767220.2254894239840.01129138873690.04949516169840.234219377197-0.06802328048760.35821521872372.2330581294-12.6023501657-16.7629542387
141.222546083450.3052690926960.8987975001861.18630777803-0.08546521290882.721294988450.02344516313710.164780937336-0.106627286264-0.09151617133360.0776332705946-0.02337741369830.1550431533790.106784690217-0.09757475857720.1729678926140.0109739687530.01277889915670.13460956899-0.03005927112440.13906513466766.092471709910.3057026437-20.8005971105
151.408635582780.411880331592-0.1044804836641.23597945510.1300241688243.34365363015-0.1028825321440.511715082384-0.100192750116-0.2804786455340.09074339060420.1348847867540.39360593249-0.230262978401-0.02506248188510.356457833305-0.0719566988984-0.04025109874660.339777331874-0.007656580864030.15155770089259.955077540810.8788003284-43.7715778867
163.507108824910.5270726750911.801901022782.105283211690.53568284596.49535517783-0.0710900346036-0.102813468793-0.1099892157910.0911778784988-0.00663015761475-0.215615448264-0.06477756447960.833611063274-0.03508898667720.302780998209-0.05364180267040.06961021422810.343805661729-0.01711271818380.27912599622679.036588688222.0580351518-20.6159660694
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 171 )AA3 - 1711 - 160
22chain 'A' and (resid 172 through 261 )AA172 - 261161 - 250
33chain 'A' and (resid 262 through 300 )AA262 - 300251 - 289
44chain 'A' and (resid 301 through 488 )AA301 - 488290 - 472
55chain 'B' and (resid 3 through 171 )BC3 - 1711 - 162
66chain 'B' and (resid 172 through 213 )BC172 - 213163 - 204
77chain 'B' and (resid 214 through 300 )BC214 - 300205 - 291
88chain 'B' and (resid 301 through 490 )BC301 - 490292 - 475
99chain 'C' and (resid 2 through 69 )CE2 - 691 - 68
1010chain 'C' and (resid 70 through 119 )CE70 - 11969 - 118
1111chain 'C' and (resid 120 through 171 )CE120 - 171119 - 170
1212chain 'C' and (resid 172 through 213 )CE172 - 213171 - 212
1313chain 'C' and (resid 214 through 300 )CE214 - 300213 - 280
1414chain 'C' and (resid 301 through 421 )CE301 - 421281 - 401
1515chain 'C' and (resid 422 through 472 )CE422 - 472402 - 452
1616chain 'C' and (resid 473 through 496 )CE473 - 496453 - 476

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  • 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

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