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- PDB-7luo: N-terminus of Skp2 bound to Cyclin A -

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Basic information

Entry
Database: PDB / ID: 7luo
TitleN-terminus of Skp2 bound to Cyclin A
Components
  • S-phase kinase-associated protein 2,Cyclin-A2
  • Skp2 Motif 1 uncharacterized fragment 1
  • Skp2 Motif 1 uncharacterized fragment 2
KeywordsCELL CYCLE / Complex / Cyclin / Ligase / Fusion
Function / homology
Function and homology information


Aberrant regulation of mitotic exit in cancer due to RB1 defects / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / G2/M DNA replication checkpoint / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / response to glucagon / male pronucleus / female pronucleus / cellular response to cocaine ...Aberrant regulation of mitotic exit in cancer due to RB1 defects / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / G2/M DNA replication checkpoint / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / response to glucagon / male pronucleus / female pronucleus / cellular response to cocaine / cyclin-dependent protein serine/threonine kinase regulator activity / positive regulation of DNA biosynthetic process / cellular response to insulin-like growth factor stimulus / cyclin A2-CDK2 complex / G2 Phase / SCF ubiquitin ligase complex / p53-Dependent G1 DNA Damage Response / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Regulation of APC/C activators between G1/S and early anaphase / microtubule organizing center / animal organ regeneration / G0 and Early G1 / regulation of DNA replication / cochlea development / cellular response to platelet-derived growth factor stimulus / Telomere Extension By Telomerase / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cyclin A:Cdk2-associated events at S phase entry / protein K63-linked ubiquitination / Cyclin A/B1/B2 associated events during G2/M transition / cyclin-dependent protein kinase holoenzyme complex / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / ubiquitin-like ligase-substrate adaptor activity / positive regulation of double-strand break repair via homologous recombination / cellular response to nitric oxide / protein K48-linked ubiquitination / post-translational protein modification / positive regulation of fibroblast proliferation / Regulation of BACH1 activity / cellular response to estradiol stimulus / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Orc1 removal from chromatin / Cyclin D associated events in G1 / Regulation of RUNX2 expression and activity / Regulation of TP53 Degradation / Antigen processing: Ubiquitination & Proteasome degradation / defense response to virus / Neddylation / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / proteasome-mediated ubiquitin-dependent protein catabolic process / cell division / regulation of apoptotic process / Ras protein signal transduction / innate immune response / Ub-specific processing proteases / protein domain specific binding / nucleolus / protein kinase binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SKP2 LRR domain / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / A Receptor for Ubiquitination Targets / F-box domain profile. / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / F-box-like / F-box-like domain superfamily / : ...SKP2 LRR domain / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / A Receptor for Ubiquitination Targets / F-box domain profile. / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / F-box-like / F-box-like domain superfamily / : / F-box domain / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Cyclin-A2 / S-phase kinase-associated protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsKelso, S. / Ceccarelli, D.F. / Sicheri, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN-143277 Canada
CitationJournal: Structure / Year: 2021
Title: Bipartite binding of the N terminus of Skp2 to cyclin A.
Authors: Kelso, S. / Orlicky, S. / Beenstock, J. / Ceccarelli, D.F. / Kurinov, I. / Gish, G. / Sicheri, F.
History
DepositionFeb 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 15, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-phase kinase-associated protein 2,Cyclin-A2
B: Skp2 Motif 1 uncharacterized fragment 1
C: S-phase kinase-associated protein 2,Cyclin-A2
D: Skp2 Motif 1 uncharacterized fragment 2


Theoretical massNumber of molelcules
Total (without water)77,1834
Polymers77,1834
Non-polymers00
Water00
1
A: S-phase kinase-associated protein 2,Cyclin-A2
B: Skp2 Motif 1 uncharacterized fragment 1

A: S-phase kinase-associated protein 2,Cyclin-A2
B: Skp2 Motif 1 uncharacterized fragment 1

A: S-phase kinase-associated protein 2,Cyclin-A2
B: Skp2 Motif 1 uncharacterized fragment 1

A: S-phase kinase-associated protein 2,Cyclin-A2
B: Skp2 Motif 1 uncharacterized fragment 1


Theoretical massNumber of molelcules
Total (without water)154,5378
Polymers154,5378
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area10120 Å2
ΔGint-50 kcal/mol
Surface area44120 Å2
MethodPISA
2
C: S-phase kinase-associated protein 2,Cyclin-A2
D: Skp2 Motif 1 uncharacterized fragment 2

C: S-phase kinase-associated protein 2,Cyclin-A2
D: Skp2 Motif 1 uncharacterized fragment 2

C: S-phase kinase-associated protein 2,Cyclin-A2
D: Skp2 Motif 1 uncharacterized fragment 2

C: S-phase kinase-associated protein 2,Cyclin-A2
D: Skp2 Motif 1 uncharacterized fragment 2


Theoretical massNumber of molelcules
Total (without water)154,1978
Polymers154,1978
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area9540 Å2
ΔGint-51 kcal/mol
Surface area44620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.738, 109.738, 152.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11(chain A and (resid 2078 through 4225 or (resid 4226...
21(chain C and (resid 2078 through 4193 or (resid 4194...
12(chain B and resid 1002 through 1008)
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPTYRTYR(chain A and (resid 2078 through 4225 or (resid 4226...AA2078 - 422566 - 128
121LYSLYSLYSLYS(chain A and (resid 2078 through 4225 or (resid 4226...AA4226129
131ASPASPLEULEU(chain A and (resid 2078 through 4225 or (resid 4226...AA2078 - 443266 - 335
141ASPASPLEULEU(chain A and (resid 2078 through 4225 or (resid 4226...AA2078 - 443266 - 335
151ASPASPLEULEU(chain A and (resid 2078 through 4225 or (resid 4226...AA2078 - 443266 - 335
161ASPASPLEULEU(chain A and (resid 2078 through 4225 or (resid 4226...AA2078 - 443266 - 335
171ASPASPLEULEU(chain A and (resid 2078 through 4225 or (resid 4226...AA2078 - 443266 - 335
181ASPASPLEULEU(chain A and (resid 2078 through 4225 or (resid 4226...AA2078 - 443266 - 335
211ASPASPCYSCYS(chain C and (resid 2078 through 4193 or (resid 4194...CC2078 - 419366 - 96
221LYSLYSLYSLYS(chain C and (resid 2078 through 4193 or (resid 4194...CC419497
231ASPASPLEULEU(chain C and (resid 2078 through 4193 or (resid 4194...CC2078 - 443266 - 335
241ASPASPLEULEU(chain C and (resid 2078 through 4193 or (resid 4194...CC2078 - 443266 - 335
251ASPASPLEULEU(chain C and (resid 2078 through 4193 or (resid 4194...CC2078 - 443266 - 335
261ASPASPLEULEU(chain C and (resid 2078 through 4193 or (resid 4194...CC2078 - 443266 - 335
112UNKUNKUNKUNK(chain B and resid 1002 through 1008)BB1002 - 10082 - 8
212UNKUNKUNKUNKchain DDD1002 - 10081 - 7

NCS ensembles :
ID
1
2

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Components

#1: Protein S-phase kinase-associated protein 2,Cyclin-A2 / Cyclin-A/CDK2-associated protein p45 / F-box protein Skp2 / F-box/LRR-repeat protein 1 / p45skp2 / ...Cyclin-A/CDK2-associated protein p45 / F-box protein Skp2 / F-box/LRR-repeat protein 1 / p45skp2 / Cyclin-A / Cyclin A


Mass: 37935.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Chimeric fusion protein of Skp2 17-84-GSG-cyclin A 173-432.,Chimeric fusion protein of Skp2 17-84-GSG-cyclin A 173-432.,Chimeric fusion protein of Skp2 17-84-GSG-cyclin A 173-432.,Chimeric ...Details: Chimeric fusion protein of Skp2 17-84-GSG-cyclin A 173-432.,Chimeric fusion protein of Skp2 17-84-GSG-cyclin A 173-432.,Chimeric fusion protein of Skp2 17-84-GSG-cyclin A 173-432.,Chimeric fusion protein of Skp2 17-84-GSG-cyclin A 173-432.
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP2, FBXL1, CCNA2, CCN1, CCNA / Production host: Escherichia coli (E. coli) / References: UniProt: Q13309, UniProt: P20248
#2: Protein/peptide Skp2 Motif 1 uncharacterized fragment 1


Mass: 698.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 8 amino acids from the N-terminus of Skp2, amino acid sequence unknown
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide Skp2 Motif 1 uncharacterized fragment 2


Mass: 613.749 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 8 amino acids from the N-terminus of Skp2, amino acid sequence unknown
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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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: 3.68 Å3/Da / Density % sol: 66.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 1.7 M Sodium-potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.17→109.74 Å / Num. obs: 16322 / % possible obs: 99.8 % / Redundancy: 8.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.073 / Rrim(I) all: 0.217 / Net I/σ(I): 10.3 / Num. measured all: 142882
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.17-3.399.11.6312642829090.4390.5811.7371.4100
8.97-109.747.60.03662038170.9990.0140.03942.498.9

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
XDSJun 1, 2017data reduction
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FIN

1fin


Resolution: 3.17→88.98 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2772 809 4.97 %
Rwork0.2335 15459 -
obs0.2357 16268 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.07 Å2 / Biso mean: 79.6226 Å2 / Biso min: 36.13 Å2
Refinement stepCycle: final / Resolution: 3.17→88.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4106 0 0 0 4106
Num. residues----549
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2374X-RAY DIFFRACTION2.617TORSIONAL
12C2374X-RAY DIFFRACTION2.617TORSIONAL
21B12X-RAY DIFFRACTION2.617TORSIONAL
22D12X-RAY DIFFRACTION2.617TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.17-3.370.39391330.34462497263099
3.37-3.630.37371260.281525372663100
3.63-3.990.28831320.231325552687100
3.99-4.570.28711470.208525622709100
4.57-5.760.23431340.21382588272299
5.76-88.980.24131370.22322720285798
Refinement TLS params.Method: refined / Origin x: 41.5366 Å / Origin y: -20.0752 Å / Origin z: 38.0482 Å
111213212223313233
T0.4875 Å2-0.0281 Å2-0.0002 Å2-0.3933 Å20.0155 Å2--0.4556 Å2
L0.2862 °20.0258 °20.0237 °2-0.0456 °20.0653 °2--0.5108 °2
S-0.0296 Å °-0.0168 Å °-0.1298 Å °0.0344 Å °-0.0282 Å °0.0816 Å °0.1608 Å °-0.019 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2078 - 4432
2X-RAY DIFFRACTION1allB1001 - 1008
3X-RAY DIFFRACTION1allC2078 - 4432
4X-RAY DIFFRACTION1allD1002 - 1008

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