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- PDB-6p3w: Crystal structure of the Cyclin A-CDK2-ORC1 complex -

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Basic information

Entry
Database: PDB / ID: 6p3w
TitleCrystal structure of the Cyclin A-CDK2-ORC1 complex
Components
  • Cyclin-A2
  • Cyclin-dependent kinase 2
  • ORC1 Peptide
KeywordsCELL CYCLE / Inhibitor complex
Function / homology
Function and homology information


CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / : / cyclin A2-CDK1 complex / cellular response to luteinizing hormone stimulus / cell cycle G1/S phase transition / nuclear origin of replication recognition complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus ...CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / : / cyclin A2-CDK1 complex / cellular response to luteinizing hormone stimulus / cell cycle G1/S phase transition / nuclear origin of replication recognition complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / mitotic DNA replication checkpoint signaling / male pronucleus / female pronucleus / response to glucagon / 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 A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cochlea development / 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 / G1/S-Specific Transcription / regulation of anaphase-promoting complex-dependent catabolic process / microtubule organizing center / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / regulation of DNA replication / Regulation of APC/C activators between G1/S and early anaphase / telomere maintenance in response to DNA damage / centrosome duplication / Telomere Extension By Telomerase / DNA replication origin binding / G0 and Early G1 / Activation of the pre-replicative complex / DNA replication initiation / animal organ regeneration / 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 / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / condensed chromosome / regulation of G2/M transition of mitotic cell cycle / cellular response to platelet-derived growth factor stimulus / mitotic G1 DNA damage checkpoint signaling / cellular response to nitric oxide / post-translational protein modification / Assembly of the ORC complex at the origin of replication / cyclin binding / male germ cell nucleus / regulation of mitotic cell cycle / positive regulation of DNA replication / meiotic cell cycle / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / cellular response to estradiol stimulus / 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 / positive regulation of fibroblast proliferation / G2/M transition of mitotic cell cycle / Cyclin D associated events in G1 / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / regulation of gene expression / peptidyl-serine phosphorylation / Senescence-Associated Secretory Phenotype (SASP) / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / chromosome, telomeric region / DNA replication / endosome / Ub-specific processing proteases / protein phosphorylation
Similarity search - Function
CDC6, C terminal / Cdc6, C-terminal / CDC6, C terminal winged helix domain / AAA lid domain / AAA lid domain / : / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain ...CDC6, C terminal / Cdc6, C-terminal / CDC6, C terminal winged helix domain / AAA lid domain / AAA lid domain / : / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / Cyclin, C-terminal domain / Cyclin_C / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Cyclin-A2 / Cyclin-dependent kinase 2 / Origin recognition complex subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsWang, B. / Song, J.
CitationJournal: Protein Sci. / Year: 2019
Title: Structural basis for the ORC1-Cyclin A association.
Authors: Wang, B. / Song, J.
History
DepositionMay 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclin-dependent kinase 2
B: Cyclin-A2
E: ORC1 Peptide
C: Cyclin-dependent kinase 2
D: Cyclin-A2
F: ORC1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,91918
Polymers128,7796
Non-polymers1,14012
Water90150
1
A: Cyclin-dependent kinase 2
B: Cyclin-A2
E: ORC1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7707
Polymers64,3903
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cyclin-dependent kinase 2
D: Cyclin-A2
F: ORC1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,15011
Polymers64,3903
Non-polymers7608
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.396, 186.396, 214.707
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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


Mass: 33976.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P24941, cyclin-dependent kinase
#2: Protein Cyclin-A2 / Cyclin-A / Cyclin A


Mass: 29525.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNA2, CCN1, CCNA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P20248
#3: Protein/peptide ORC1 Peptide


Mass: 888.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13415*PLUS
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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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: 4.19 Å3/Da / Density % sol: 70.66 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.49 M sodium phosphate monobasic monohydrate and 0.91 M potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.54→20.07 Å / Num. obs: 72513 / % possible obs: 99.51 % / Redundancy: 8.1 % / CC1/2: 0.997 / Rsym value: 0.1438 / Net I/σ(I): 9.84
Reflection shellResolution: 2.54→2.631 Å / Num. unique obs: 7055 / CC1/2: 0.46 / Rsym value: 2.349

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F

Resolution: 2.54→20.069 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27
RfactorNum. reflection% reflection
Rfree0.2373 3709 5.12 %
Rwork0.1981 --
obs0.2001 72395 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.54→20.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8830 0 60 50 8940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039139
X-RAY DIFFRACTIONf_angle_d0.75612437
X-RAY DIFFRACTIONf_dihedral_angle_d13.6143334
X-RAY DIFFRACTIONf_chiral_restr0.0311418
X-RAY DIFFRACTIONf_plane_restr0.0051562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5401-2.57340.41461490.36712524X-RAY DIFFRACTION98
2.5734-2.60860.41921390.34972598X-RAY DIFFRACTION99
2.6086-2.64580.31671560.32622563X-RAY DIFFRACTION100
2.6458-2.68520.35051430.31852619X-RAY DIFFRACTION100
2.6852-2.7270.32611500.3152590X-RAY DIFFRACTION100
2.727-2.77160.34341320.30282630X-RAY DIFFRACTION100
2.7716-2.81930.32681290.2862623X-RAY DIFFRACTION100
2.8193-2.87040.29841500.27792600X-RAY DIFFRACTION100
2.8704-2.92550.30141290.27572612X-RAY DIFFRACTION100
2.9255-2.9850.3041370.28392623X-RAY DIFFRACTION100
2.985-3.04970.32531280.2752631X-RAY DIFFRACTION100
3.0497-3.12040.32361270.27122640X-RAY DIFFRACTION100
3.1204-3.19810.32511480.26752603X-RAY DIFFRACTION100
3.1981-3.28420.31431430.25472626X-RAY DIFFRACTION100
3.2842-3.38040.30161330.23842644X-RAY DIFFRACTION100
3.3804-3.4890.24571250.22642637X-RAY DIFFRACTION100
3.489-3.6130.2551570.20282625X-RAY DIFFRACTION100
3.613-3.75680.23491550.20122637X-RAY DIFFRACTION100
3.7568-3.92650.2161400.1822651X-RAY DIFFRACTION100
3.9265-4.13180.21011220.17462684X-RAY DIFFRACTION100
4.1318-4.38820.19531450.16792649X-RAY DIFFRACTION100
4.3882-4.72290.18561550.15652666X-RAY DIFFRACTION100
4.7229-5.19070.21491570.15682688X-RAY DIFFRACTION100
5.1907-5.92490.23431350.17542716X-RAY DIFFRACTION100
5.9249-7.40190.18241720.18042726X-RAY DIFFRACTION100
7.4019-20.06950.20531530.14242881X-RAY DIFFRACTION100
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)
13.83781.93723.56417.908-3.30617.0706-0.4221.635-0.417-0.9923-0.4685-1.01861.4428-0.2951.02820.95120.13630.19290.9637-0.07110.7215-10.341290.773733.4585
25.5138-4.5843-4.28386.1212.25223.80890.17630.3029-0.1646-0.6809-0.39520.759-0.2095-0.51390.32220.73750.02710.07990.67630.05340.614-8.460686.087433.5734
31.59080.5548-0.55222.5081-0.61821.7253-0.1161-0.0015-0.1260.10030.02230.14340.0306-0.07180.12950.69350.05020.07270.5813-0.03290.47638.006589.523730.1511
41.91060.3738-0.18423.59580.46154.5815-0.13570.2551-0.1334-0.49830.0425-0.36550.1540.16280.090.66030.03980.11860.53820.03840.477520.459692.637515.2243
58.19470.98793.91773.4878-3.63656.97040.40690.06430.52851.5887-0.3085-0.2804-1.14960.1692-0.23280.97980.13040.04520.7634-0.10770.722720.907973.44936.2041
66.53180.2484-1.07884.0508-0.88916.7656-0.0275-1.1285-0.54380.4402-0.6642-0.18550.6714-0.11030.56230.90850.13780.24290.76940.02790.8983.203153.668542.8979
75.09720.8597-1.68923.6536-1.8114.5417-0.32880.3613-0.6642-0.3569-0.1261-0.07010.6193-0.16680.47050.7741-0.04520.17370.54-0.13060.60542.224458.173629.23
85.08632.72160.28262.5374-0.88313.4887-0.21050.16910.0631-0.20060.15250.37030.0138-0.6368-0.01040.72550.06290.09770.6263-0.10890.6794-4.450264.38127.1167
92.10170.87381.6354.40384.39924.7004-0.05251.2269-0.0814-1.10730.3469-1.2509-1.07530.6605-0.11780.9323-0.08390.23810.7655-0.02210.713325.417264.805626.2664
103.3533-1.20410.66162.92442.60633.6065-0.1661-0.2602-0.33820.26210.04860.1804-0.02980.08430.25840.83990.11410.22450.57190.01110.614821.263154.45930.1136
114.84880.2534-0.47273.32263.13533.0716-0.6645-0.5521-0.19950.54680.6519-0.47180.82220.8923-0.13281.02440.13410.10350.8268-0.02410.677232.207360.640635.6319
125.8661-1.11641.57163.69750.20753.7876-0.22360.476-0.7319-0.1988-0.0137-0.02430.89820.54880.11661.11640.10010.35740.6656-0.06880.805920.617147.067725.7092
133.80383.43680.56643.13660.51950.2089-0.431-0.2068-0.5236-0.29120.37960.9413-0.31180.29260.34261.3343-0.22980.15150.9717-0.15181.0995-5.37448.287723.0602
140.12280.94171.15913.92245.2097.00290.0763-0.0623-0.0401-0.1002-0.58240.8325-0.0026-1.10440.43580.8883-0.08960.19230.9036-0.12460.8867-20.115764.61149.4661
151.33-0.12340.07692.6886-0.31613.4842-0.2045-0.0519-0.5435-0.40320.0677-0.02330.5407-0.13350.11840.657-0.06340.26340.646-0.02020.8095-10.844357.584562.8389
163.29790.5058-0.92312.31671.43825.78950.208-0.5267-0.47740.2803-0.267-0.16860.5271-0.5690.10110.644-0.11060.12340.82120.23470.7885-12.597652.211282.2488
175.6136-3.01315.04142.0272-2.75344.5654-0.0589-0.1172-0.6002-0.0392-0.5607-0.53681.2282-0.22780.130.8879-0.03940.19970.87310.01590.99067.284468.28268.096
182.80471.89040.23576.1557-1.94966.0835-0.0821-0.1281-0.0163-0.0175-0.143-0.1946-0.3010.13880.27930.51330.00110.07450.4845-0.05450.5169-3.027289.380762.0144
190.5052-0.23250.13858.5847-6.62635.0682-0.437-0.2128-0.35081.03570.42620.4409-0.8607-1.10590.11490.87050.080.19810.9987-0.11250.8678-17.540289.06765.2973
204.3075-3.40822.88116.9227-3.2438.13050.09560.6308-0.4641-0.8205-0.18570.29550.26380.25210.17580.5728-0.07030.10070.5649-0.05970.5639-9.288181.695155.6616
215.5143-2.4161-4.69014.24234.47955.7684-0.4397-1.3451-0.27410.7567-0.3643-0.6741.52640.60830.68430.86260.00740.13080.89630.14870.78646.599475.823480.4922
224.7504-1.41610.97495.62161.17024.6348-0.3011-0.2839-0.2220.18320.1394-0.7280.04290.49930.18020.5059-0.0060.04360.59970.05450.653810.516387.711878.2572
231.252.8154-3.36996.3502-7.59719.0892-0.22060.13821.6907-0.0153-1.29291.5677-1.1707-0.98961.32860.8633-0.0268-0.1471.5763-0.14711.4758-7.2977102.152561.7478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 45 )
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 158 )
4X-RAY DIFFRACTION4chain 'A' and (resid 159 through 298 )
5X-RAY DIFFRACTION5chain 'B' and (resid 176 through 192 )
6X-RAY DIFFRACTION6chain 'B' and (resid 193 through 207 )
7X-RAY DIFFRACTION7chain 'B' and (resid 208 through 268 )
8X-RAY DIFFRACTION8chain 'B' and (resid 269 through 310 )
9X-RAY DIFFRACTION9chain 'B' and (resid 311 through 326 )
10X-RAY DIFFRACTION10chain 'B' and (resid 327 through 368 )
11X-RAY DIFFRACTION11chain 'B' and (resid 369 through 387 )
12X-RAY DIFFRACTION12chain 'B' and (resid 388 through 432 )
13X-RAY DIFFRACTION13chain 'E' and (resid 233 through 239 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 45 )
15X-RAY DIFFRACTION15chain 'C' and (resid 46 through 158 )
16X-RAY DIFFRACTION16chain 'C' and (resid 159 through 296 )
17X-RAY DIFFRACTION17chain 'D' and (resid 177 through 192 )
18X-RAY DIFFRACTION18chain 'D' and (resid 193 through 268 )
19X-RAY DIFFRACTION19chain 'D' and (resid 269 through 287 )
20X-RAY DIFFRACTION20chain 'D' and (resid 288 through 310 )
21X-RAY DIFFRACTION21chain 'D' and (resid 311 through 326 )
22X-RAY DIFFRACTION22chain 'D' and (resid 327 through 432 )
23X-RAY DIFFRACTION23chain 'F' and (resid 236 through 239 )

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