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- PDB-9q3o: Crystal structure of human CDK5-cyclinB1 complex bound to AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 9q3o
TitleCrystal structure of human CDK5-cyclinB1 complex bound to AMP-PNP
Components
  • Cyclin-dependent kinase 5
  • G2/mitotic-specific cyclin-B1
KeywordsCELL CYCLE / Kinase / CDK / Cyclin / complex
Function / homology
Function and homology information


positive regulation of presynaptic cytosolic calcium concentration / negative regulation of calcium ion-dependent exocytosis of neurotransmitter / acetylcholine receptor activator activity / protein kinase 5 complex / response to DDT / regulation of chromosome condensation / ErbB-2 class receptor binding / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase ...positive regulation of presynaptic cytosolic calcium concentration / negative regulation of calcium ion-dependent exocytosis of neurotransmitter / acetylcholine receptor activator activity / protein kinase 5 complex / response to DDT / regulation of chromosome condensation / ErbB-2 class receptor binding / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / ventricular cardiac muscle cell development / E2F-enabled inhibition of pre-replication complex formation / Depolymerization of the Nuclear Lamina / positive regulation of mRNA 3'-end processing / regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of attachment of spindle microtubules to kinetochore / MASTL Facilitates Mitotic Progression / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Activated NTRK2 signals through CDK5 / tissue regeneration / patched binding / Phosphorylation of Emi1 / oocyte maturation / Transcriptional regulation by RUNX2 / axon extension / Nuclear Pore Complex (NPC) Disassembly / G2/M DNA replication checkpoint / Phosphorylation of the APC/C / oligodendrocyte differentiation / outer kinetochore / NGF-stimulated transcription / CRMPs in Sema3A signaling / signaling receptor inhibitor activity / ErbB-3 class receptor binding / regulation of dendritic spine morphogenesis / digestive tract development / Initiation of Nuclear Envelope (NE) Reformation / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / cellular response to fatty acid / Phosphorylation and nuclear translocation of BMAL1 (ARNTL) and CLOCK / cyclin-dependent protein serine/threonine kinase activator activity / cellular response to iron(III) ion / Condensation of Prometaphase Chromosomes / cyclin-dependent protein serine/threonine kinase regulator activity / regulation of synaptic vesicle recycling / tau-protein kinase activity / Phosphorylation and nuclear translocation of the CRY:PER:kinase complex / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of cell cycle phase transition / synaptic vesicle transport / positive regulation of cardiac muscle cell proliferation / synaptic vesicle exocytosis / Regulation of APC/C activators between G1/S and early anaphase / microtubule organizing center / ubiquitin-like protein ligase binding / negative regulation of proteolysis / DARPP-32 events / cyclin-dependent protein kinase holoenzyme complex / response to mechanical stimulus / mitotic metaphase chromosome alignment / cyclin-dependent protein serine/threonine kinase activity / neuron apoptotic process / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / synaptic vesicle endocytosis / regulation of synaptic transmission, glutamatergic / regulation of protein localization to plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / Cyclin A/B1/B2 associated events during G2/M transition / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of mitotic cell cycle / regulation of macroautophagy / axonogenesis / NPAS4 regulates expression of target genes / Nuclear events stimulated by ALK signaling in cancer / synapse assembly / ionotropic glutamate receptor binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / APC/C:Cdc20 mediated degradation of Cyclin B / Resolution of Sister Chromatid Cohesion / mitotic spindle organization / Condensation of Prophase Chromosomes / filopodium / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / neuromuscular junction / neuron migration / regulation of synaptic plasticity / Hsp90 protein binding / microtubule cytoskeleton organization / tau protein binding / neuron projection development / cellular response to amyloid-beta / spindle pole / positive regulation of neuron apoptotic process / p53 binding / kinase activity / actin cytoskeleton organization / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition
Similarity search - Function
: / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal 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 / : / 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
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / polyethylene glycol / G2/mitotic-specific cyclin-B1 / Cyclin-dependent kinase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSyed, A. / Arvai, A.S. / Chowdhury, D. / Tainer, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 CA220430 United States
CitationJournal: To Be Published
Title: Crystal structure of human CDK5-cyclinB1 complex bound to AMP-PNP
Authors: Syed, A. / Arvai, A.S. / Chowdhury, D. / Tainer, J.A.
History
DepositionAug 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Cyclin-dependent kinase 5
C: G2/mitotic-specific cyclin-B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,59411
Polymers66,1202
Non-polymers3,4749
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-33 kcal/mol
Surface area25340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.859, 120.859, 116.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 2 molecules BC

#1: Protein Cyclin-dependent kinase 5 / Cell division protein kinase 5 / Cyclin-dependent-like kinase 5 / Serine/threonine-protein kinase ...Cell division protein kinase 5 / Cyclin-dependent-like kinase 5 / Serine/threonine-protein kinase PSSALRE / Tau protein kinase II catalytic subunit / TPKII catalytic subunit


Mass: 33622.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK5, CDKN5, PSSALRE / Production host: Escherichia coli (E. coli)
References: UniProt: Q00535, non-specific serine/threonine protein kinase
#2: Protein G2/mitotic-specific cyclin-B1


Mass: 32497.691 Da / Num. of mol.: 1 / Mutation: C167S, C238S, C350S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNB1, CCNB / Production host: Escherichia coli (E. coli) / References: UniProt: P14635

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Non-polymers , 5 types, 80 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-P4K / polyethylene glycol / 3,6,9,12,15,18,21,24,27,30,33,36,39,42-tetradecaoxatetratetracontan-1-ol


Mass: 662.804 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H62O15
#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.7 Å3/Da / Density % sol: 66.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% PEG 3350 200 mM Imidazole/Malate pH 6.0 5% Mg Formate (saturated) 2.3 mM AMP-PNP was added to the protein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.5→39.56 Å / Num. obs: 34310 / % possible obs: 99.9 % / Redundancy: 10.4 % / CC1/2: 0.998 / Net I/σ(I): 9.4
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 10.1 % / Num. unique obs: 3800 / CC1/2: 0.287 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→39.56 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 1441 4.98 %
Rwork0.1945 --
obs0.1972 28950 84.37 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4497 0 124 71 4692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.528
X-RAY DIFFRACTIONf_dihedral_angle_d14.831812
X-RAY DIFFRACTIONf_chiral_restr0.038704
X-RAY DIFFRACTIONf_plane_restr0.004800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.590.52731060.39732071X-RAY DIFFRACTION65
2.59-2.690.38911100.37752165X-RAY DIFFRACTION67
2.69-2.820.44341250.33752349X-RAY DIFFRACTION73
2.82-2.960.34341380.30072494X-RAY DIFFRACTION78
2.96-3.150.33521340.25362657X-RAY DIFFRACTION81
3.15-3.390.32671550.24222862X-RAY DIFFRACTION89
3.39-3.730.2531580.19273082X-RAY DIFFRACTION94
3.73-4.270.20861640.16293179X-RAY DIFFRACTION97
4.27-5.380.19251710.15013254X-RAY DIFFRACTION99
5.39-39.560.19021800.14613396X-RAY DIFFRACTION99

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