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- PDB-2p64: D domain of b-TrCP -

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Basic information

Entry
Database: PDB / ID: 2p64
TitleD domain of b-TrCP
ComponentsF-box/WD repeat protein 1A
KeywordsLIGASE / right handed super-helical bundle
Function / homology
Function and homology information


protein phosphorylated amino acid binding / positive regulation of circadian rhythm / regulation of cell cycle process / ubiquitin ligase activator activity / regulation of canonical Wnt signaling pathway / protein dephosphorylation / non-canonical NF-kappaB signal transduction / SCF ubiquitin ligase complex / ligase activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ...protein phosphorylated amino acid binding / positive regulation of circadian rhythm / regulation of cell cycle process / ubiquitin ligase activator activity / regulation of canonical Wnt signaling pathway / protein dephosphorylation / non-canonical NF-kappaB signal transduction / SCF ubiquitin ligase complex / ligase activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / positive regulation of proteolysis / negative regulation of T cell receptor signaling pathway / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / negative regulation of smoothened signaling pathway / Wnt signaling pathway / MAP3K8 (TPL2)-dependent MAPK1/3 activation / rhythmic process / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / protein destabilization / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of CRY and PER proteins / Activation of NF-kappaB in B cells / Deactivation of the beta-catenin transactivating complex / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / beta-catenin binding / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / regulation of circadian rhythm / Degradation of beta-catenin by the destruction complex / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Interleukin-1 signaling / Regulation of PLK1 Activity at G2/M Transition / ubiquitin protein ligase activity / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein dimerization activity / protein ubiquitination / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1840 / D domain of beta-TrCP / D domain of beta-TrCP / D domain of beta-TrCP / : / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily / F-box domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1840 / D domain of beta-TrCP / D domain of beta-TrCP / D domain of beta-TrCP / : / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily / F-box domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / F-box/WD repeat-containing protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsNeculai, D. / Orlicky, S. / Ceccarelli, D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Suprafacial orientation of the SCFCdc4 dimer accommodates multiple geometries for substrate ubiquitination.
Authors: Tang, X. / Orlicky, S. / Lin, Z. / Willems, A. / Neculai, D. / Ceccarelli, D. / Mercurio, F. / Shilton, B.H. / Sicheri, F. / Tyers, M.
History
DepositionMar 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
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.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_type.id / _struct_ref_seq_dif.details / _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: F-box/WD repeat protein 1A
B: F-box/WD repeat protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7563
Polymers12,6442
Non-polymers1121
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-37 kcal/mol
Surface area6230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.316, 71.316, 116.301
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein F-box/WD repeat protein 1A / F-box and WD repeats protein beta-TrCP / E3RSIkappaB / pIkappaBalpha-E3 receptor subunit


Mass: 6321.773 Da / Num. of mol.: 2 / Fragment: D domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTRC, BTRCP, FBW1A, FBXW1A / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9Y297
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200 mM MgCl2, 5 mM CdCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.97906 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2005 / Details: mirrors
RadiationMonochromator: double-crystal monochromator SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 12340 / Num. obs: 11999 / % possible obs: 97.2 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.246 / Net I/σ(I): 18.8
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 3.19 / Num. unique all: 1100 / % possible all: 82.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.78 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / SU B: 11.644 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26679 536 4.9 %RANDOM
Rwork0.23854 ---
obs0.23986 10345 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.936 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms868 0 1 11 880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021906
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9131215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9925103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.34225.4951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.9615163
X-RAY DIFFRACTIONr_chiral_restr0.1160.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02698
X-RAY DIFFRACTIONr_nbd_refined0.2080.2398
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2600
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3310.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3020.24
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.3590.22
X-RAY DIFFRACTIONr_mcbond_it1.2081.5536
X-RAY DIFFRACTIONr_mcangle_it1.5312830
X-RAY DIFFRACTIONr_scbond_it2.6963435
X-RAY DIFFRACTIONr_scangle_it3.4534.5385
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 40 -
Rwork0.303 728 -
obs--100 %
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)
16.027-1.7441-0.90435.60781.85215.9959-0.0871-0.21420.12680.0150.22-0.54270.20510.4123-0.133-0.0845-0.0289-0.04990.0716-0.05360.038967.319744.075555.5159
24.4588-1.53511.01993.3536-0.78054.18150.08890.0462-0.4158-0.10710.07760.02040.18010.1254-0.16660.0325-0.0424-0.0779-0.0171-0.02470.03165.151742.830656.5596
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA127 - 1772 - 52
2X-RAY DIFFRACTION2BB127 - 1772 - 52

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