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- PDB-6k8k: Crystal structure of Arabidopsis thaliana BIC2-CRY2 complex -

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Basic information

Entry
Database: PDB / ID: 6k8k
TitleCrystal structure of Arabidopsis thaliana BIC2-CRY2 complex
Components
  • Cryptochrome-2
  • Protein BIC2
KeywordsSIGNALING PROTEIN / Cryptochromes / BICs / inactivation
Function / homology
Function and homology information


flavin adenine dinucleotide metabolic process / long-day photoperiodism, flowering / response to absence of light / circadian regulation of calcium ion oscillation / response to strigolactone / regulation of meristem growth / response to low fluence blue light stimulus by blue low-fluence system / response to karrikin / regulation of leaf morphogenesis / regulation of photoperiodism, flowering ...flavin adenine dinucleotide metabolic process / long-day photoperiodism, flowering / response to absence of light / circadian regulation of calcium ion oscillation / response to strigolactone / regulation of meristem growth / response to low fluence blue light stimulus by blue low-fluence system / response to karrikin / regulation of leaf morphogenesis / regulation of photoperiodism, flowering / blue light signaling pathway / regulation of flower development / positive regulation of flower development / phototropism / stomatal movement / response to blue light / blue light photoreceptor activity / response to water deprivation / plant-type vacuole / response to light stimulus / FAD binding / regulation of circadian rhythm / PML body / circadian rhythm / positive regulation of reactive oxygen species metabolic process / chromatin organization / defense response to virus / nuclear body / chromatin remodeling / protein homodimerization activity / ATP binding / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Protein BIC / Cryptochrome, plant / DNA photolyases class 1 signature 2. / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / 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 ...Protein BIC / Cryptochrome, plant / DNA photolyases class 1 signature 2. / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / 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 / 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 / Rossmann-like alpha/beta/alpha sandwich fold / 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
ADENOSINE MONOPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / Cryptochrome-2 / Protein BIC2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, X. / Ma, L. / Guan, Z. / Yin, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2020
Title: Structural insights into BIC-mediated inactivation of Arabidopsis cryptochrome 2.
Authors: Ma, L. / Wang, X. / Guan, Z. / Wang, L. / Wang, Y. / Zheng, L. / Gong, Z. / Shen, C. / Wang, J. / Zhang, D. / Liu, Z. / Yin, P.
History
DepositionJun 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cryptochrome-2
E: Protein BIC2
B: Cryptochrome-2
C: Protein BIC2
D: Cryptochrome-2
F: Protein BIC2
G: Cryptochrome-2
H: Protein BIC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,62820
Polymers309,9998
Non-polymers4,62812
Water2,036113
1
A: Cryptochrome-2
E: Protein BIC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6575
Polymers77,5002
Non-polymers1,1573
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-48 kcal/mol
Surface area23140 Å2
MethodPISA
2
B: Cryptochrome-2
C: Protein BIC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6334
Polymers77,5002
Non-polymers1,1332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-36 kcal/mol
Surface area22520 Å2
MethodPISA
3
D: Cryptochrome-2
F: Protein BIC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6816
Polymers77,5002
Non-polymers1,1814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-58 kcal/mol
Surface area22530 Å2
MethodPISA
4
G: Cryptochrome-2
H: Protein BIC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6575
Polymers77,5002
Non-polymers1,1573
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-49 kcal/mol
Surface area23000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.552, 142.552, 526.434
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 2 types, 8 molecules ABDGECFH

#1: Protein
Cryptochrome-2 / / Atcry2 / Blue light photoreceptor / Protein PHR homolog 1 / AtPHH1 / Protein SUPPRESSOR OF elf3 20


Mass: 69579.930 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CRY2, PHH1, SEL20, At1g04400, F19P19.14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96524
#2: Protein
Protein BIC2 / BLUE-LIGHT INHIBITOR OF CRYPTOCHROMES 2


Mass: 7919.887 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BIC2, At3g44450, T22K7.130 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9M280

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Non-polymers , 4 types, 125 molecules

#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Sequence detailsThese conflicts are derived from GenBank AAB04996.

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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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: Tris, Calcium acetate hydrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 109254 / % possible obs: 99.2 % / Redundancy: 19.2 % / Biso Wilson estimate: 45.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.024 / Rrim(I) all: 0.104 / Net I/σ(I): 21.3
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.784 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 5043 / CC1/2: 0.92 / Rpim(I) all: 0.186 / Rrim(I) all: 0.807 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U3C

1u3c


Resolution: 2.5→48.425 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2232 5437 4.98 %
Rwork0.1706 --
obs0.1733 109130 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→48.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17459 0 308 113 17880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818292
X-RAY DIFFRACTIONf_angle_d0.98924882
X-RAY DIFFRACTIONf_dihedral_angle_d20.92210699
X-RAY DIFFRACTIONf_chiral_restr0.0532631
X-RAY DIFFRACTIONf_plane_restr0.0063093
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4998-2.52820.32761760.25743157X-RAY DIFFRACTION93
2.5282-2.55790.28871730.22033300X-RAY DIFFRACTION97
2.5579-2.58910.28261900.21343353X-RAY DIFFRACTION97
2.5891-2.62190.30591820.21593351X-RAY DIFFRACTION98
2.6219-2.65640.30381790.21663418X-RAY DIFFRACTION99
2.6564-2.69270.31091750.2183422X-RAY DIFFRACTION100
2.6927-2.73120.2911610.22573419X-RAY DIFFRACTION99
2.7312-2.7720.3051750.20963426X-RAY DIFFRACTION100
2.772-2.81530.26791780.19983422X-RAY DIFFRACTION100
2.8153-2.86140.2482020.20293402X-RAY DIFFRACTION100
2.8614-2.91080.28861860.20323440X-RAY DIFFRACTION100
2.9108-2.96370.3181890.22793426X-RAY DIFFRACTION100
2.9637-3.02070.32462030.22953407X-RAY DIFFRACTION100
3.0207-3.08230.28781930.23563434X-RAY DIFFRACTION100
3.0823-3.14930.32791940.22613409X-RAY DIFFRACTION100
3.1493-3.22260.30411940.22293458X-RAY DIFFRACTION100
3.2226-3.30320.27691700.20873352X-RAY DIFFRACTION96
3.3032-3.39250.2561730.19313488X-RAY DIFFRACTION100
3.3925-3.49230.231700.18433458X-RAY DIFFRACTION100
3.4923-3.60490.21461640.173480X-RAY DIFFRACTION100
3.6049-3.73370.2031780.15973513X-RAY DIFFRACTION100
3.7337-3.88320.19151730.14993485X-RAY DIFFRACTION100
3.8832-4.05980.19251710.13993533X-RAY DIFFRACTION100
4.0598-4.27370.18121850.13963511X-RAY DIFFRACTION100
4.2737-4.54130.1882020.13373509X-RAY DIFFRACTION100
4.5413-4.89160.16711710.13193459X-RAY DIFFRACTION97
4.8916-5.38330.18091770.14343565X-RAY DIFFRACTION100
5.3833-6.1610.20641690.15793626X-RAY DIFFRACTION100
6.161-7.7570.19971920.1623670X-RAY DIFFRACTION100
7.757-48.43360.17361920.14493800X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 55.5794 Å / Origin y: -12.9522 Å / Origin z: -67.4519 Å
111213212223313233
T0.4104 Å2-0.0391 Å2-0.0138 Å2-0.2542 Å20.0265 Å2--0.4159 Å2
L0.4494 °20.0323 °2-0.0955 °2-0.0959 °20.0167 °2--0.2531 °2
S0.0396 Å °-0.0597 Å °0.0121 Å °0.0036 Å °-0.0517 Å °-0.0323 Å °-0.011 Å °0.0249 Å °0.0123 Å °
Refinement TLS groupSelection details: all

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