PDB-7d19: Crystal structure of mouse Cryptochrome 1 in complex with compoun...

ID or keywords:

Entry

Database: PDB / ID: 7d19

Title

Crystal structure of mouse Cryptochrome 1 in complex with compound TH129

Components

Cryptochrome-1

Keywords

CIRCADIAN CLOCK PROTEIN / Cryptochrome / CRY / CRY1 / clock

Function / homology

Function and homology information

negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor 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 ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Miller, S.A. / Hirota, T.

Funding support

Japan, 2items

Citation

Journal: J.Am.Chem.Soc. / Year: 2021
Title: Photopharmacological Manipulation of Mammalian CRY1 for Regulation of the Circadian Clock.
Authors: Kolarski, D. / Miller, S. / Oshima, T. / Nagai, Y. / Aoki, Y. / Kobauri, P. / Srivastava, A. / Sugiyama, A. / Amaike, K. / Sato, A. / Tama, F. / Szymanski, W. / Feringa, B.L. / Itami, K. / Hirota, T.

History

Deposition	Sep 14, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 27, 2021	Provider: repository / Type: Initial release
Revision 1.1	Feb 17, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Nov 29, 2023	Group: 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 viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7d19.cif.gz	458.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7d19.ent.gz	311.1 KB	Display	PDB format
PDBx/mmJSON format	7d19.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7d19_validation.pdf.gz	1008.5 KB	Display	wwPDB validaton report
Full document	7d19_full_validation.pdf.gz	1015.2 KB	Display
Data in XML	7d19_validation.xml.gz	34.9 KB	Display
Data in CIF	7d19_validation.cif.gz	48.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d1/7d19 ftp://data.pdbj.org/pub/pdb/validation_reports/d1/7d19	HTTPS FTP

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Related structure data

Related structure data	7d1cC 6kx4S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6se9-d 7btk-2 6etz-d 6g9w-d 6h1p-d 6zjv-d 1kfu-d 6tn3-d 4mgz-d 6zju-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#97 - Jan 2008 Circadian Clock Proteins similarity (1) #91 - Jul 2007 Thymine Dimers similarity (8)

Deposited unit

A: Cryptochrome-1

B: Cryptochrome-1

hetero molecules

116 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, The protein is monomeric in solution

Unit cell

Length a, b, c (Å)	81.139, 81.139, 141.780
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	145
Space group name H-M	P3₂
Space group name Hall	P3₂
Symmetry operation	#1: x,y,z #2: -y,x-y,z+2/3 #3: -x+y,-x,z+1/3

#1: Protein	Cryptochrome-1 Mass: 57371.734 Da / Num. of mol.: 2 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-GOC / N-[2-(2,4-dimethylphenyl)-4,6-dihydrothieno[3,4-c]pyrazol-3-yl]-4-(phenylcarbonyl)benzamide Mass: 453.555 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₂₃N₃O₂S / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.3 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.15-0.35 M NH4Cl, 30% w/v PEG 3350, 3% v/v Ethylene glycol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 5, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.35→62.78 Å / Num. obs: 43127 / % possible obs: 99.9 % / Redundancy: 3.5 % / B_iso Wilson estimate: 39.49 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.087 / R_pim(I) all: 0.054 / R_rim(I) all: 0.103 / Net I/σ(I): 8.2
Reflection shell	Resolution: 2.35→2.48 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.483 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6262 / CC_1/2: 0.771 / R_pim(I) all: 0.298 / R_rim(I) all: 0.569 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
REFMAC	5.8.0257	refinement
xia2	0.6.467	data reduction
SCALA	3.3.22	data scaling
PHASER	2.8.3	phasing
Coot	0.9	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6KX4

6kx4

Resolution: 2.35→40.57 Å / SU ML: 0.2381 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.6881
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2301	2271	5.27 %
R_work	0.189	40792	-
obs	0.1912	43063	99.63 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 50.68 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→40.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7338	0	66	135	7539

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0069	7615
X-RAY DIFFRACTION	f_angle_d	0.7894	10400
X-RAY DIFFRACTION	f_chiral_restr	0.0475	1129
X-RAY DIFFRACTION	f_plane_restr	0.0053	1345
X-RAY DIFFRACTION	f_dihedral_angle_d	21.7927	1044

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.35-2.41	0.2844	122	0.2235	2532	X-RAY DIFFRACTION	96.93
2.41-2.46	0.3006	150	0.2228	2530	X-RAY DIFFRACTION	99.89
2.46-2.52	0.2509	119	0.2139	2597	X-RAY DIFFRACTION	99.85
2.52-2.59	0.2904	137	0.2108	2563	X-RAY DIFFRACTION	99.82
2.59-2.67	0.2277	192	0.2096	2447	X-RAY DIFFRACTION	99.89
2.67-2.75	0.2421	138	0.2071	2595	X-RAY DIFFRACTION	99.74
2.75-2.85	0.3046	110	0.2156	2560	X-RAY DIFFRACTION	99.63
2.85-2.97	0.267	158	0.2099	2540	X-RAY DIFFRACTION	99.82
2.97-3.1	0.2353	156	0.1974	2542	X-RAY DIFFRACTION	99.96
3.1-3.27	0.2648	144	0.2052	2575	X-RAY DIFFRACTION	99.71
3.27-3.47	0.2202	162	0.1992	2499	X-RAY DIFFRACTION	99.7
3.47-3.74	0.1774	129	0.1824	2581	X-RAY DIFFRACTION	100
3.74-4.11	0.2066	118	0.1643	2587	X-RAY DIFFRACTION	100
4.12-4.71	0.2244	124	0.1647	2579	X-RAY DIFFRACTION	100
4.71-5.93	0.224	172	0.1914	2521	X-RAY DIFFRACTION	99.89
5.94-40.57	0.2052	140	0.1728	2544	X-RAY DIFFRACTION	99.26

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.69346487659	0.189847113606	-0.929975534523	2.2928842545	0.0456603981621	1.66947548677	-0.0454515721805	-0.100397635497	-0.133532232092	-0.0222504144891	0.00791883149152	0.140791617146	0.0233783060928	0.115593205931	0.00605005757188	0.189826255441	0.00189319406348	0.0216780191052	0.180440807526	0.020932820248	0.214179522249	-10.2978759873	11.5231862748	7.6786339848
2	2.20357226615	-0.866629653914	-0.566131620509	1.35986441617	0.0619952375147	0.704936632652	0.227881059724	0.196199801508	-0.100173062732	-0.416243862019	-0.326144042494	0.443266358887	-0.143717466604	-0.242708268962	0.106441362738	0.398922322553	-0.0160434306894	-0.00186028460122	0.344203868334	-0.0184974827719	0.404876252915	-12.6253030101	13.4145870943	1.32157742933
3	2.22945253894	0.00849476957915	-0.478939732289	2.1638810418	0.0944697590614	2.1347672366	0.0255406715672	0.123519206805	0.138672644295	-0.409324378701	0.061315487422	-0.186423518827	-0.444647804377	0.226603343177	-0.111066925154	0.377867802401	-0.0702378987843	0.0352590816189	0.267369166805	0.0184783430048	0.285572475683	2.17692030746	18.7985877392	-8.74384552643
4	0.464599699909	-0.350282083802	-1.19900117241	1.7846932738	2.21648194815	4.62111139854	-0.38953872651	0.0908149264997	-0.232140815508	-0.0606678979569	0.146234163903	0.204736974382	0.405084848277	0.762932028689	0.360068095489	0.504388962578	-0.0214401697828	-0.00821204540633	0.480281687339	-0.0380656104266	0.35170920313	-4.648055059	2.33420339886	-18.9069142859
5	2.12794599265	-1.6485070086	-0.484504163998	3.32819914107	0.687414859132	1.15566147265	-0.0785690736933	-0.231164030127	0.279922713604	-0.179331074442	0.400064041075	-0.790801794837	-0.0219102990164	0.639045752107	-0.13798764385	0.278928957503	-0.0450862863306	0.0704325392844	0.570950324069	-0.172411084219	0.386675855773	20.9160734682	6.90606305499	-2.14893682549
6	2.11278944549	0.122301601133	-0.323184560884	1.44085347905	0.704165820713	1.67561270453	-0.00911465745906	-0.0581238265733	0.0459258190368	0.0921360220913	-0.0023728852941	0.0853277880018	0.0677766538444	0.0814932084861	-0.00274669023669	0.182939287778	-0.00859950857873	0.0284157790597	0.182246110854	-0.00204201188238	0.219211545026	5.63859077838	62.5019749982	31.759190026
7	0.725566048918	0.815200656358	0.149387479315	1.29243750602	0.451744298482	0.436688720648	0.0543473658604	0.121524554801	0.290925670317	0.159489274524	-0.0640879309895	0.740113265525	-0.246886530542	0.278461408041	-0.0435275822533	0.477608082697	-0.122574834444	0.0303289982822	0.422744603892	-0.092090410932	0.685715752364	-7.55607669068	47.8303835558	18.4135523014
8	1.81927135065	-0.102137208999	0.390141254684	1.63533344003	0.884896668156	2.7522787056	-0.00656076708214	0.287863782065	0.096099784246	-0.263121068128	0.110887760145	-0.0414684413315	-0.0412793069521	0.232866653665	-0.0703208894707	0.254678976111	-0.0319398297095	0.0192787323641	0.356646305869	0.0412805164828	0.270110481899	11.7496339162	57.9984618989	15.2709962361
9	1.84064865704	1.46301595705	0.675894318444	3.92260780171	0.814913881193	1.02600295449	0.102330040739	0.313349875345	-0.579667887598	0.370135788052	0.274406496245	-0.6543123958	0.494051194441	0.34999701086	-0.217002646402	0.454941744621	0.158270171457	-0.112131570203	0.388816337968	-0.159929880507	0.391597265774	16.7818406605	32.3381274712	21.5384487432

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 149 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 150 through 195 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 196 through 261 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 262 through 289 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 290 through 492 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 2 through 141 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 142 through 171 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 172 through 289 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 290 through 489 )

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