2OVQ

Structure of the Skp1-Fbw7-CyclinEdegC complex

> Summary

Summary for 2OVQ

Related2OVP 2OVR
DescriptorS-phase kinase-associated protein 1A/F-box/WD repeat protein 7/cyclinE C-terminal degron
Functional Keywordsf-box; wd40 domains; double phosphorylation, transcription-cell cycle complex, transcription/cell cycle
Biological sourceHomo sapiens (human)
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Cellular locationIsoform 1: Nucleus, nucleoplasm. Isoform 2: Cytoplasm. Isoform 4: Nucleus, nucleolus. Nucleus (By similarity) Q969H0
Total number of polymer chains3
Total molecular weight69228.02
Authors
Hao, B.,Oehlmann, S.,Sowa, M.E.,Harper, J.W.,Pavletich, N.P. (deposition date: 2007-02-14, release date: 2007-04-24, modification date: 2011-11-16)
Primary citation
Hao, B.,Oehlmann, S.,Sowa, M.E.,Harper, J.W.,Pavletich, N.P.
Structure of a Fbw7-Skp1-Cyclin E Complex: Multisite-Phosphorylated Substrate Recognition by SCF Ubiquitin Ligases
Mol.Cell, 26:131-143, 2007
PubMed: 17434132
DOI: 10.1016/j.molcel.2007.02.022
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.6 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.264242.9%6.3%3.1%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 2ovq
no rotation
Molmil generated image of 2ovq
rotated about x axis by 90°
Molmil generated image of 2ovq
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 2ovq
no rotation
Molmil generated image of 2ovq
rotated about x axis by 90°
Molmil generated image of 2ovq
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (2ovq.pdb1.gz [99.94 KB])
Coordinate files for Biological unit (2ovq.pdb2.gz [390.88 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AS-phase kinase-associated protein 1Apolymer14916853.31
UniProt (P63208)
Pfam (PF01466)
Pfam (PF03931)
Homo sapiens (human)@PDBjSkp1; Cyclin A/CDK2-associated protein p19; p19A; p19skp1; RNA polymerase II elongation factor-like protein; Organ of Corti protein 2; OCP-II protein; OCP-2; Transcription elongation factor B; SIII
BF-box/WD repeat protein 7polymer44550279.91
UniProt (Q969H0)
Pfam (PF00400)
Pfam (PF12937)
Homo sapiens (human)@PDBjFbw7; F-box and WD-40 domain protein 7; F-box protein FBX30; hCdc4; Archipelago homolog; hAgo; SEL-10
CcyclinE C-terminal degronpolymer121326.31
SULFATE IONnon-polymer96.18
waterwater18.0178

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains3
Total molecular weight68459.6
Non-Polymers*Number of molecules8
Total molecular weight768.5
All*Total molecular weight69228.0
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.6 Å)

Cell axes233.066233.066107.563
Cell angles90.0090.0090.00
SpacegroupI 41 2 2
Resolution limits19.76 - 2.60
the highest resolution shell value2.760 - 2.600
R-factor0.232
R-work0.23200
the highest resolution shell value0.352
R-free0.26600
the highest resolution shell value0.379
RMSD bond length0.007
RMSD bond angle1.500

Data Collection Statistics

Resolution limits20.00 - 2.60
the highest resolution shell value -
Number of reflections44674
Rmerge_l_obs0.091
the highest resolution shell value0.363
Completeness97.6
Redundancy6.2
the highest resolution shell value5.5
I/sigma(I)0

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP9294

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0005730cellular_componentnucleolus
B0005654cellular_componentnucleoplasm
B1990452cellular_componentParkin-FBXW7-Cul1 ubiquitin ligase complex
B0043234cellular_componentprotein complex
B0019005cellular_componentSCF ubiquitin ligase complex
B0030332molecular_functioncyclin binding
B0042802molecular_functionidentical protein binding
B0050816molecular_functionphosphothreonine binding
B0030674molecular_functionprotein binding, bridging
B0031625molecular_functionubiquitin protein ligase binding
B0097027molecular_functionubiquitin-protein transferase activator activity
B0004842molecular_functionubiquitin-protein transferase activity
B0006974biological_processcellular response to DNA damage stimulus
B0034644biological_processcellular response to UV
B0055088biological_processlipid homeostasis
B0032876biological_processnegative regulation of DNA endoreduplication
B2000346biological_processnegative regulation of hepatocyte proliferation
B0045746biological_processnegative regulation of Notch signaling pathway
B2000639biological_processnegative regulation of SREBP signaling pathway
B0010868biological_processnegative regulation of triglyceride biosynthetic process
B0045741biological_processpositive regulation of epidermal growth factor-activated receptor activity
B0070374biological_processpositive regulation of ERK1 and ERK2 cascade
B1903378biological_processpositive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway
B1901800biological_processpositive regulation of proteasomal protein catabolic process
B1903955biological_processpositive regulation of protein targeting to mitochondrion
B0031398biological_processpositive regulation of protein ubiquitination
B2000060biological_processpositive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process
B0051443biological_processpositive regulation of ubiquitin-protein transferase activity
B0000209biological_processprotein polyubiquitination
B0050821biological_processprotein stabilization
B0016567biological_processprotein ubiquitination
B1902806biological_processregulation of cell cycle G1/S phase transition
B0010883biological_processregulation of lipid storage
B1903146biological_processregulation of mitophagy
B0032880biological_processregulation of protein localization
B0031146biological_processSCF-dependent proteasomal ubiquitin-dependent protein catabolic process
B0007062biological_processsister chromatid cohesion
B0001944biological_processvasculature development
B0016032biological_processviral process
A0031467cellular_componentCul7-RING ubiquitin ligase complex
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0070062cellular_componentextracellular exosome
A0005654cellular_componentnucleoplasm
A0005634cellular_componentnucleus
A0019005cellular_componentSCF ubiquitin ligase complex
A0008013molecular_functionbeta-catenin binding
A0097602molecular_functioncullin family protein binding
A0004842molecular_functionubiquitin-protein transferase activity
A0038095biological_processFc-epsilon receptor signaling pathway
A0000086biological_processG2/M transition of mitotic cell cycle
A0035518biological_processhistone H2A monoubiquitination
A0038061biological_processNIK/NF-kappaB signaling
A0051437biological_processpositive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition
A0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
A0000209biological_processprotein polyubiquitination
A0016567biological_processprotein ubiquitination
A0031146biological_processSCF-dependent proteasomal ubiquitin-dependent protein catabolic process
A0002223biological_processstimulatory C-type lectin receptor signaling pathway
A0051403biological_processstress-activated MAPK cascade
A0050852biological_processT cell receptor signaling pathway
A0016055biological_processWnt signaling pathway
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC15BINDING SITE FOR RESIDUE SO4 B 901
ChainResidue
BHOH51
BHOH93
BHOH134
BARG2505
BARG2674

AC23BINDING SITE FOR RESIDUE SO4 B 902
ChainResidue
BGLN2388
BGLN2428
BARG2676

AC33BINDING SITE FOR RESIDUE SO4 B 903
ChainResidue
BHOH41
BARG2415
BTHR2416

AC43BINDING SITE FOR RESIDUE SO4 B 904
ChainResidue
BASN2392
BARG2393
BSER2407

AC53BINDING SITE FOR RESIDUE SO4 B 905
ChainResidue
BHOH3
BARG2441
BGLN2618

AC64BINDING SITE FOR RESIDUE SO4 B 906
ChainResidue
BHOH24
BARG2357
BASN2679
BTHR2680

AC73BINDING SITE FOR RESIDUE SO4 B 907
ChainResidue
BHOH96
BHIS2379
BASP2380

AC81BINDING SITE FOR RESIDUE SO4 B 908
ChainResidue
BARG2415

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails
CSA11Annotated By Reference To The Literature 1g72
ChainResidueDetails
BSER2407

CSA21Annotated By Reference To The Literature 1g72
ChainResidueDetails
BASP2567

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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb2ovq.ent.gz (106.42 KB)
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all (no-compress)pdb2ovq.ent (447.56 KB)
header onlypdb2ovq.ent.gz (9 KB)
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PDBx/mmCIF2ovq.cif.gz (134.72 KB)
PDBMLall2ovq.xml.gz (202.85 KB)
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no-atom2ovq-noatom.xml.gz (33.9 KB)
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ext-atom2ovq-extatom.xml.gz (115.48 KB)
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PDBMLplusall2ovq-plus.xml.gz (205.78 KB)
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no-atom2ovq-plus-noatom.xml.gz (36.83 KB)
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add only2ovq-add.xml.gz (2.93 KB)
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RDF2ovq.rdf.gz (67.11 KB)
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Structure factorsr2ovqsf.ent.gz (498.02 KB)
Biological unit (PDB format)2ovq.pdb1.gz (99.94 KB) (A,B,C)
*author and software defined assembly, 3 molecule(s) (trimeric)
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2ovq.pdb2.gz (390.88 KB) (A,B,C)
*software defined assembly, 12 molecule(s) (dodecameric)
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Validation reportsPDF2ovq​_validation.pdf.gz (301.33 KB)
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PDF-full2ovq​_full​_validation.pdf.gz (325.08 KB)
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XML2ovq​_validation.xml.gz (29.56 KB)
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PNG2ovq​_multipercentile​_validation.png.gz (155.55 KB)
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SVG2ovq​_multipercentile​_validation.svg.gz (950 B)
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Sequence (fasta)2ovq​_seq.txt
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