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- PDB-7e34: Crystal structure of SUN1-Speedy A-CDK2 -

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Basic information

Entry
Database: PDB / ID: 7.0E+34
TitleCrystal structure of SUN1-Speedy A-CDK2
Components
  • Cyclin-dependent kinase 2
  • SUN domain-containing protein 1
  • Speedy protein A
KeywordsCELL CYCLE / Telomere / Meiosis / Kinase
Function / homology
Function and homology information


nuclear matrix anchoring at nuclear membrane / nucleokinesis involved in cell motility in cerebral cortex radial glia guided migration / cytoskeleton-nuclear membrane anchor activity / meiotic attachment of telomere to nuclear envelope / meiotic nuclear membrane microtubule tethering complex / establishment of protein localization to telomere / male meiotic nuclear division / homologous chromosome pairing at meiosis / lamin binding / XY body ...nuclear matrix anchoring at nuclear membrane / nucleokinesis involved in cell motility in cerebral cortex radial glia guided migration / cytoskeleton-nuclear membrane anchor activity / meiotic attachment of telomere to nuclear envelope / meiotic nuclear membrane microtubule tethering complex / establishment of protein localization to telomere / male meiotic nuclear division / homologous chromosome pairing at meiosis / lamin binding / XY body / telomere capping / nuclear inner membrane / centrosome localization / oogenesis / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / cyclin-dependent protein kinase activity / G2 Phase / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / X chromosome / PTK6 Regulates Cell Cycle / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / telomere maintenance in response to DNA damage / centrosome duplication / protein kinase activator activity / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / positive regulation of protein kinase activity / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cajal body / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / response to mechanical stimulus / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / protein-membrane adaptor activity / condensed chromosome / regulation of G2/M transition of mitotic cell cycle / mitotic G1 DNA damage checkpoint signaling / Meiotic synapsis / cellular response to nitric oxide / post-translational protein modification / ossification / cyclin binding / regulation of mitotic cell cycle / male germ cell nucleus / positive regulation of DNA replication / meiotic cell cycle / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / Orc1 removal from chromatin / G2/M transition of mitotic cell cycle / Cyclin D associated events in G1 / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / peptidyl-serine phosphorylation / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / nuclear membrane / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / chromosome, telomeric region / DNA replication / endosome / protein phosphorylation / chromatin remodeling / protein domain specific binding / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / intracellular membrane-bounded organelle / DNA-templated transcription / positive regulation of cell population proliferation / centrosome / DNA damage response
Similarity search - Function
Cell cycle regulatory protein Speedy / : / Cell cycle regulatory protein / SUN coiled coil domain 2 / SUN2 helix-turn-helix domain / SUN domain-containing protein 1, N-terminal / Mitochondrial RNA binding protein MRP / SUN domain-containing protein 1-5 / SUN domain profile. / SUN domain ...Cell cycle regulatory protein Speedy / : / Cell cycle regulatory protein / SUN coiled coil domain 2 / SUN2 helix-turn-helix domain / SUN domain-containing protein 1, N-terminal / Mitochondrial RNA binding protein MRP / SUN domain-containing protein 1-5 / SUN domain profile. / SUN domain / Sad1 / UNC-like C-terminal / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SUN domain-containing protein 1 / Cyclin-dependent kinase 2 / Speedy protein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsChen, Y. / Huang, C. / Wu, J. / Lei, M.
CitationJournal: Nat Commun / Year: 2021
Title: The SUN1-SPDYA interaction plays an essential role in meiosis prophase I.
Authors: Chen, Y. / Wang, Y. / Chen, J. / Zuo, W. / Fan, Y. / Huang, S. / Liu, Y. / Chen, G. / Li, Q. / Li, J. / Wu, J. / Bian, Q. / Huang, C. / Lei, M.
History
DepositionFeb 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclin-dependent kinase 2
B: Speedy protein A
C: SUN domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7275
Polymers57,5693
Non-polymers1582
Water55831
1
A: Cyclin-dependent kinase 2
B: Speedy protein A
C: SUN domain-containing protein 1
hetero molecules

A: Cyclin-dependent kinase 2
B: Speedy protein A
C: SUN domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,45310
Polymers115,1386
Non-polymers3154
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area13870 Å2
ΔGint-173 kcal/mol
Surface area41440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.340, 183.525, 103.829
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-202-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Cyclin-dependent kinase 2 / Cell division protein kinase 2 / p33 protein kinase


Mass: 33932.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P24941, cyclin-dependent kinase
#2: Protein Speedy protein A / Rapid inducer of G2/M progression in oocytes A / hSpy/Ringo A / Speedy-1 / Spy1


Mass: 18564.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPDYA, SPDY1, SPY1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5MJ70

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide SUN domain-containing protein 1 / Protein unc-84 homolog A / Sad1/unc-84 protein-like 1


Mass: 5072.433 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUN1, KIAA0810, UNC84A / Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O94901

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Non-polymers , 3 types, 33 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 49.9 % / Mosaicity: 0.441 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.15M ammonium citrate tribasic, pH7.0, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.91905 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91905 Å / Relative weight: 1
ReflectionResolution: 3.19→50 Å / Num. obs: 9795 / % possible obs: 99.3 % / Redundancy: 5.2 % / Biso Wilson estimate: 75.95 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.051 / Rrim(I) all: 0.12 / Χ2: 0.99 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.3140.5739280.8080.3140.6570.97694.3
3.31-3.455.10.4499630.8960.2170.5010.955100
3.45-3.65.50.3449510.9610.1580.3791.005100
3.6-3.795.60.289670.9660.1270.3081.053100
3.79-4.035.50.1929850.9810.0890.2121.103100
4.03-4.345.10.149680.9850.0680.1561.19299.9
4.34-4.785.70.1049820.9950.0470.1151.116100
4.78-5.475.60.0939970.9920.0430.1020.99399.9
5.47-6.895.10.0729940.9950.0350.0810.829100
6.89-5050.04610600.9970.0230.0510.66299.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UQ2

5uq2


Resolution: 3.19→42.59 Å / Cor.coef. Fo:Fc: 0.857 / Cor.coef. Fo:Fc free: 0.791 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.627 / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.3 472 5.19 %RANDOM
Rwork0.252 ---
obs0.254 9095 92.5 %-
Displacement parametersBiso max: 189.85 Å2 / Biso mean: 70 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0.7076 Å20 Å20 Å2
2--3.4716 Å20 Å2
3----4.1791 Å2
Refine analyzeLuzzati coordinate error obs: 0.52 Å
Refinement stepCycle: final / Resolution: 3.19→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3777 0 7 31 3815
Biso mean--79.37 31.08 -
Num. residues----459
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1346SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes641HARMONIC5
X-RAY DIFFRACTIONt_it3883HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion494SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4380SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3883HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg5263HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion1.89
X-RAY DIFFRACTIONt_other_torsion21.11
LS refinement shellResolution: 3.19→3.27 Å / Rfactor Rfree error: 0 / Total num. of bins used: 23
RfactorNum. reflection% reflection
Rfree0.4215 21 5.3 %
Rwork0.2427 375 -
all0.2518 396 -
obs--53.31 %
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)
13.96280.4757-0.25632.29550.76685.52820.1863-0.46620.2362-0.13020.3488-0.0587-0.1311.0388-0.5351-0.3098-0.18580.08330.2417-0.304-0.35358.582-31.087311.9362
23.6216-1.29160.26156.4786-0.17397.2550.0932-0.05780.1948-0.1630.29430.2984-0.6059-0.115-0.38750.1178-0.05380.304-0.25740.0161-0.0912-11.2659-14.7787-7.1272
30.70991.8872-2.45921.89361.43132.21290.01180.10170.0374-0.01390.0047-0.0122-0.02920.0173-0.01650.1109-0.1055-0.0873-0.0364-0.0153-0.1276-4.189-22.1432-20.5759
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|298 }A1 - 298
2X-RAY DIFFRACTION2{ B|61 - B|201 }B61 - 201
3X-RAY DIFFRACTION3{ C|137 - C|154 }C137 - 154

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