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- PDB-4ct0: Crystal Structure of Mouse Cryptochrome1 in Complex with Period2 -

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Basic information

Entry
Database: PDB / ID: 4ct0
TitleCrystal Structure of Mouse Cryptochrome1 in Complex with Period2
Components
  • CRYPTOCHROME-1
  • PERIOD CIRCADIAN PROTEIN HOMOLOG 2
KeywordsCIRCADIAN CLOCK PROTEIN / CRYPTOCHROME-PERIOD COMPLEX / CRYPTOCHROME INTERACTIONS / ZINC INTERFACE / DISULFIDE BOND / REDOX REGULATION
Function / homology
Function and homology information


regulation of glutamate uptake involved in transmission of nerve impulse / Cry-Per complex / negative regulation of termination of DNA-templated transcription / negative regulation of glucocorticoid secretion / negative regulation of fat cell proliferation / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of circadian rhythm / lactate biosynthetic process / histone methyltransferase binding / lipid storage ...regulation of glutamate uptake involved in transmission of nerve impulse / Cry-Per complex / negative regulation of termination of DNA-templated transcription / negative regulation of glucocorticoid secretion / negative regulation of fat cell proliferation / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of circadian rhythm / lactate biosynthetic process / histone methyltransferase binding / lipid storage / regulation of DNA damage checkpoint / glycogen biosynthetic process / pre-mRNA binding / RNA polymerase binding / response to glucagon / negative regulation of G protein-coupled receptor signaling pathway / regulation of gluconeogenesis / entrainment of circadian clock by photoperiod / E-box binding / white fat cell differentiation / regulation of neurogenesis / response to light stimulus / photoreceptor activity / signal transduction in response to DNA damage / negative regulation of gluconeogenesis / regulation of vasoconstriction / phosphatase binding / transcription regulator inhibitor activity / negative regulation of protein ubiquitination / positive regulation of gluconeogenesis / regulation of insulin secretion / positive regulation of protein ubiquitination / response to ischemia / transcription corepressor binding / nuclear receptor binding / response to activity / gluconeogenesis / fatty acid metabolic process / response to insulin / circadian regulation of gene expression / regulation of circadian rhythm / kinase binding / histone deacetylase binding / circadian rhythm / 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 / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleotide binding / negative regulation of DNA-templated transcription / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Period circadian protein homolog bHLH-like domain / Period circadian-like, C-terminal / : / Period protein 2/3C-terminal region / Period circadian protein homolog 3-like, PAS-A domain / : / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / PAS fold-3 ...Period circadian protein homolog bHLH-like domain / Period circadian-like, C-terminal / : / Period protein 2/3C-terminal region / Period circadian protein homolog 3-like, PAS-A domain / : / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / PAS fold-3 / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSchmalen, I. / Rajan Prabu, J. / Benda, C. / Wolf, E.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: Interaction of Circadian Clock Proteins Cry1 and Per2 is Modulated by Zinc Binding and Disulfide Bond Formation.
Authors: Schmalen, I. / Reischl, S. / Wallach, T. / Klemz, R. / Grudziecki, A. / Prabu, J.R. / Benda, C. / Kramer, A. / Wolf, E.
History
DepositionMar 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRYPTOCHROME-1
B: PERIOD CIRCADIAN PROTEIN HOMOLOG 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1975
Polymers74,8142
Non-polymers3833
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-100.5 kcal/mol
Surface area24230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.736, 99.736, 178.632
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein CRYPTOCHROME-1 / CRYPTOCHROME1


Mass: 58497.980 Da / Num. of mol.: 1 / Fragment: PHOTOLYASE HOMOLOGY REGION (PHR), RESIDUES 1-496
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse)
Description: HIGH5 INSECT CELLS WERE INFECTED WITH BACULO VIRUS
Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P97784
#2: Protein PERIOD CIRCADIAN PROTEIN HOMOLOG 2 / PERIOD2 / MPER2 / CIRCADIAN CLOCK PROTEIN PERIOD 2


Mass: 16316.273 Da / Num. of mol.: 1 / Fragment: RESIDUES 1132-1252
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O54943

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Non-polymers , 4 types, 178 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growDetails: 0.2 M MGCL2, 12-13% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9716
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9716 Å / Relative weight: 1
ReflectionResolution: 2.45→45.5 Å / Num. obs: 33988 / % possible obs: 100 % / Observed criterion σ(I): 3.6 / Redundancy: 25.1 % / Biso Wilson estimate: 68.48 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 35
Reflection shellResolution: 2.45→45.5 Å / Redundancy: 26.3 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4K0R

4k0r


Resolution: 2.45→45.496 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 24.45 / Stereochemistry target values: ML
Details: CHAIN A RESIDUES 1-2 AND 233-240, CHAIN B RESIDUES 1215-1252 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2331 1695 5 %
Rwork0.186 --
obs0.1884 33913 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.8 Å2
Refinement stepCycle: LAST / Resolution: 2.45→45.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4570 0 21 175 4766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094719
X-RAY DIFFRACTIONf_angle_d1.1256421
X-RAY DIFFRACTIONf_dihedral_angle_d14.6811692
X-RAY DIFFRACTIONf_chiral_restr0.079690
X-RAY DIFFRACTIONf_plane_restr0.005826
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.52210.2681390.22922642X-RAY DIFFRACTION100
2.5221-2.60350.27861380.22572620X-RAY DIFFRACTION100
2.6035-2.69650.28451390.23132640X-RAY DIFFRACTION100
2.6965-2.80450.29671400.23122632X-RAY DIFFRACTION100
2.8045-2.93210.25911390.2232662X-RAY DIFFRACTION100
2.9321-3.08670.281400.21592638X-RAY DIFFRACTION100
3.0867-3.280.25171380.21542663X-RAY DIFFRACTION100
3.28-3.53320.28071410.20392677X-RAY DIFFRACTION100
3.5332-3.88850.19081410.17282670X-RAY DIFFRACTION100
3.8885-4.45080.1981420.16072720X-RAY DIFFRACTION100
4.4508-5.60590.23411460.17452751X-RAY DIFFRACTION100
5.6059-45.50430.2231520.17742903X-RAY DIFFRACTION100
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)
13.7448-1.99022.79133.0726-0.72364.7958-0.07880.16660.1428-0.1719-0.4301-0.6843-0.31351.13170.33860.7352-0.1380.1040.49840.17590.4612-6.81481.6143-25.3233
22.7903-0.0997-0.49152.3933-0.64444.25950.1020.20620.0895-0.3238-0.2236-0.5129-0.40751.2350.00130.3846-0.08260.03920.53470.11160.4231-2.4993-4.3168-15.4485
31.9718-0.79010.55763.5969-0.73633.4739-0.34-0.00710.4431-0.42710.0310.0207-1.27451.19290.20061.1174-0.0995-0.12050.0490.14740.4753-16.082510.2614-19.8389
42.2455-0.09110.61762.4241-1.04964.77730.0501-0.37030.0325-0.41120.32810.6894-0.4203-1.5821-0.04350.42570.1114-0.16460.69280.20350.5294-37.0405-6.7716-16.2356
51.325-0.5439-0.89396.92590.92451.47630.2837-0.0891-0.0285-0.14840.2230.3930.54650.04220.12941.1803-0.044-0.1379-0.1534-0.06040.6593-23.8184-16.6474-31.1965
67.47894.29662.66225.34684.34594.1827-0.42330.4792-0.0445-0.80020.248-0.0178-0.49680.0008-0.06041.3457-0.4604-0.46060.54640.06270.7466-34.8575-22.1355-29.9835
73.71931.19911.7640.4040.65144.75360.13010.8106-0.0992-0.4515-0.21450.1684-0.04730.0333-0.20170.7884-0.3267-1.05371.2330.42750.6423-42.965-17.6011-33.0299
87.17861.47644.11656.51544.2234.20440.134-0.2928-0.1553-0.1741-0.05140.39830.2633-1.0237-0.06141.026-0.4852-0.31041.42050.24820.7409-47.9581-20.763-21.3002
94.0293-1.9065-1.37865.5549-0.05464.08630.0602-0.7394-0.72461.13790.47680.59620.3478-2.0188-0.62970.7334-0.3736-0.18241.09140.36260.489-39.0134-26.2113-2.6714
106.5858-3.423-0.95033.5356-0.15041.8236-0.206-0.0454-0.1135-0.0464-0.0912-0.6168-0.0152-0.2455-0.1573-0.08-0.04890.04711.01490.13330.4803-26.7003-16.59524.6841
119.08661.81710.01829.4605-1.43853.02720.0297-1.14520.22811.74430.550.0906-1.0007-2.8422-0.68020.84150.01390.04561.1570.13640.5153-26.3848-5.391810.0847
120.87911.80011.28124.49542.42091.9307-0.26-1.8072-0.19122.0501-0.87511.57030.571-0.64720.68550.80650.06150.23711.66270.10380.674-34.7204-7.36647.8235
135.42780.5517-4.25812.7438-0.49763.3392-0.03580.2959-0.2001-0.0772-0.16340.42410.0002-0.6666-0.15150.01480.12430.34011.9990.58220.8205-43.2201-8.84252.4935
146.3701-7.58886.06629.1672-7.22035.77980.1446-2.3788-0.672-0.03381.30691.9515-0.0911-4.4462-1.29690.65510.1731-0.19582.08980.1710.5675-51.2828-3.9213-9.5902
150.80360.69820.20120.86810.47910.43260.04580.0165-0.6257-0.40820.2116-0.32250.61860.18980.59031.19160.0487-0.29540.17880.16880.8644-18.9413-14.875-32.7366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 3 THROUGH 69 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 70 THROUGH 149 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 150 THROUGH 283 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 284 THROUGH 495 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 1132 THROUGH 1141 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 1142 THROUGH 1146 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 1147 THROUGH 1151 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 1152 THROUGH 1159 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 1160 THROUGH 1177 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 1178 THROUGH 1182 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 1183 THROUGH 1192 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 1193 THROUGH 1198 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 1199 THROUGH 1208 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 1209 THROUGH 1214 )
15X-RAY DIFFRACTION15CHAIN B AND (RESID -12 THROUGH 0)

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