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- PDB-4u8h: Crystal Structure of Mammalian Period-Cryptochrome Complex -

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Basic information

Entry
Database: PDB / ID: 4u8h
TitleCrystal Structure of Mammalian Period-Cryptochrome Complex
Components
  • Cryptochrome-2
  • Period circadian protein homolog 2
KeywordsCIRCADIAN CLOCK PROTEIN/TRANSCRIPTION / transcriptional repression / zinc-binding / CIRCADIAN CLOCK PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


regulation of glutamate uptake involved in transmission of nerve impulse / regulation of sodium-dependent phosphate transport / circadian regulation of translation / negative regulation of termination of DNA-templated transcription / negative regulation of glucocorticoid secretion / negative regulation of fat cell proliferation / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of transcription regulatory region DNA binding / negative regulation of circadian rhythm / lactate biosynthetic process ...regulation of glutamate uptake involved in transmission of nerve impulse / regulation of sodium-dependent phosphate transport / circadian regulation of translation / negative regulation of termination of DNA-templated transcription / negative regulation of glucocorticoid secretion / negative regulation of fat cell proliferation / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of transcription regulatory region DNA binding / negative regulation of circadian rhythm / lactate biosynthetic process / histone methyltransferase binding / lipid storage / pre-mRNA binding / glycogen biosynthetic process / RNA polymerase binding / entrainment of circadian clock by photoperiod / photoreceptor activity / regulation of insulin secretion / response to light stimulus / regulation of vasoconstriction / white fat cell differentiation / regulation of neurogenesis / phosphatase binding / negative regulation of protein ubiquitination / FAD binding / transcription corepressor binding / fatty acid metabolic process / response to activity / response to ischemia / gluconeogenesis / nuclear receptor binding / circadian regulation of gene expression / response to insulin / regulation of circadian rhythm / kinase binding / protein import into nucleus / circadian rhythm / histone deacetylase binding / single-stranded DNA binding / glucose homeostasis / positive regulation of cold-induced thermogenesis / DNA-binding transcription factor binding / damaged DNA binding / transcription coactivator activity / transcription cis-regulatory region binding / regulation of cell cycle / nuclear speck / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Period circadian protein homolog 3-like, PAS-A domain / Period circadian-like, C-terminal / Period protein 2/3C-terminal region / 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 ...: / Period circadian protein homolog 3-like, PAS-A domain / Period circadian-like, C-terminal / Period protein 2/3C-terminal region / 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 / PAS fold-3 / 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-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.798 Å
AuthorsNangle, S.N. / Rosensweig, C. / Koike, N. / Tei, H. / Takahashi, J.S. / Green, C.B. / Zheng, N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-CA107134 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM007750 United States
CitationJournal: Elife / Year: 2014
Title: Molecular assembly of the period-cryptochrome circadian transcriptional repressor complex.
Authors: Nangle, S.N. / Rosensweig, C. / Koike, N. / Tei, H. / Takahashi, J.S. / Green, C.B. / Zheng, N.
History
DepositionAug 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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 / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_symmetry / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cryptochrome-2
C: Cryptochrome-2
B: Period circadian protein homolog 2
D: Period circadian protein homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,7396
Polymers144,6094
Non-polymers1312
Water86548
1
A: Cryptochrome-2
B: Period circadian protein homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3703
Polymers72,3042
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-80 kcal/mol
Surface area26380 Å2
MethodPISA
2
C: Cryptochrome-2
D: Period circadian protein homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3703
Polymers72,3042
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-75 kcal/mol
Surface area26450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.675, 97.675, 163.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Cryptochrome-2 /


Mass: 58368.676 Da / Num. of mol.: 2
Fragment: Photolyase/cryptochrome alpha/beta domain, residues 1-510
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: Protein Period circadian protein homolog 2 / mPER2 / Circadian clock protein PERIOD 2


Mass: 13935.588 Da / Num. of mol.: 2 / Fragment: CRY binding domain, residues 1095-1215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Per2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O54943
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.31 % / Description: Diamond
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 0.2 M NaCl, 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2013
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.798→42.738 Å / Num. obs: 37522 / % possible obs: 99.59 % / Redundancy: 4.2 % / Net I/σ(I): 18.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MLP

4mlp


Resolution: 2.798→42.738 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2778 1880 5.01 %Random selection
Rwork0.2052 ---
obs0.2088 37522 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.798→42.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9292 0 2 48 9342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099550
X-RAY DIFFRACTIONf_angle_d1.34512954
X-RAY DIFFRACTIONf_dihedral_angle_d16.4573556
X-RAY DIFFRACTIONf_chiral_restr0.0891356
X-RAY DIFFRACTIONf_plane_restr0.0071672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.798-2.87390.4441430.32112687X-RAY DIFFRACTION98
2.8739-2.95840.39321400.28082751X-RAY DIFFRACTION100
2.9584-3.05390.33551420.2452739X-RAY DIFFRACTION100
3.0539-3.1630.30871470.23712734X-RAY DIFFRACTION100
3.163-3.28960.30571460.21512747X-RAY DIFFRACTION100
3.2896-3.43930.32291480.22192730X-RAY DIFFRACTION100
3.4393-3.62050.28731360.22282770X-RAY DIFFRACTION100
3.6205-3.84720.28941460.19632743X-RAY DIFFRACTION100
3.8472-4.1440.29441450.18712730X-RAY DIFFRACTION100
4.144-4.56060.22881470.17332756X-RAY DIFFRACTION100
4.5606-5.21950.23571430.18492755X-RAY DIFFRACTION100
5.2195-6.57220.29121430.22022768X-RAY DIFFRACTION99
6.5722-42.74270.25091540.19542732X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 65.4943 Å / Origin y: 24.4242 Å / Origin z: -8.6096 Å
111213212223313233
T0.1807 Å2-0.0119 Å2-0.0383 Å2-0.6269 Å20.1965 Å2--0.3263 Å2
L0.5384 °20.1447 °20.2689 °2-0.2193 °2-0.152 °2--0.2928 °2
S0.1652 Å °0.0778 Å °0.0691 Å °-0.1713 Å °0.0343 Å °-0.0545 Å °0.0674 Å °-0.1498 Å °0.1233 Å °
Refinement TLS groupSelection details: all

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