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- PDB-2b9r: Crystal Structure of Human Cyclin B1 -

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Basic information

Entry
Database: PDB / ID: 2b9r
TitleCrystal Structure of Human Cyclin B1
ComponentsHuman cyclin B1
KeywordsCELL CYCLE / cyclin
Function / homology
Function and homology information


cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / Depolymerization of the Nuclear Lamina / positive regulation of attachment of spindle microtubules to kinetochore / MASTL Facilitates Mitotic Progression / regulation of mitotic cell cycle spindle assembly checkpoint / Activation of NIMA Kinases NEK9, NEK6, NEK7 ...cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / Depolymerization of the Nuclear Lamina / positive regulation of attachment of spindle microtubules to kinetochore / MASTL Facilitates Mitotic Progression / regulation of mitotic cell cycle spindle assembly checkpoint / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Phosphorylation of Emi1 / patched binding / Nuclear Pore Complex (NPC) Disassembly / Transcriptional regulation by RUNX2 / Phosphorylation of the APC/C / outer kinetochore / mitotic cell cycle phase transition / Initiation of Nuclear Envelope (NE) Reformation / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / cyclin-dependent protein serine/threonine kinase activator activity / Condensation of Prometaphase Chromosomes / cyclin-dependent protein serine/threonine kinase regulator activity / mitotic metaphase chromosome alignment / ubiquitin-like protein ligase binding / Regulation of APC/C activators between G1/S and early anaphase / Nuclear events stimulated by ALK signaling in cancer / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Cyclin A/B1/B2 associated events during G2/M transition / Resolution of Sister Chromatid Cohesion / positive regulation of G2/M transition of mitotic cell cycle / APC/C:Cdc20 mediated degradation of Cyclin B / positive regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / mitotic spindle organization / spindle pole / G2/M transition of mitotic cell cycle / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / positive regulation of fibroblast proliferation / in utero embryonic development / mitochondrial matrix / cell division / centrosome / protein kinase binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
: / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin-like / Cyclin A; domain 1 ...: / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
G2/mitotic-specific cyclin-B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBasavappa, R. / Petri, E.
CitationJournal: Cell Cycle / Year: 2007
Title: The Crystal Structure of Human Cyclin B.
Authors: Petri, E.T. / Errico, A. / Escobedo, L. / Hunt, T. / Basavappa, R.
History
DepositionOct 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 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.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Human cyclin B1
B: Human cyclin B1


Theoretical massNumber of molelcules
Total (without water)61,6802
Polymers61,6802
Non-polymers00
Water1,69394
1
A: Human cyclin B1


Theoretical massNumber of molelcules
Total (without water)30,8401
Polymers30,8401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Human cyclin B1


Theoretical massNumber of molelcules
Total (without water)30,8401
Polymers30,8401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.169, 117.169, 197.685
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-311-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
31B
41A
51B
61A

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTHRTHRBB37 - 11437 - 114
21METMETTHRTHRAA37 - 11437 - 114
32HISHISARGARGBB116 - 143116 - 143
42HISHISARGARGAA116 - 143116 - 143
53ILEILEASPASPBB148 - 193148 - 193
63ILEILEASPASPAA148 - 193148 - 193

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Components

#1: Protein Human cyclin B1


Mass: 30840.141 Da / Num. of mol.: 2 / Fragment: Residues 165-433 / Mutation: C167S, C283S, C350S, E183A, E184A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-28 a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus RIL / References: UniProt: P14635
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 5

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.9→29.3 Å / Num. all: 18101 / Num. obs: 18101 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.39 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.59 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FIN

1fin


Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.895 / SU B: 38.658 / SU ML: 0.38 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 3.707 / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30795 1773 9.8 %RANDOM
Rwork0.243 ---
all0.24928 16278 --
obs0.24928 16278 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 88.674 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3936 0 0 94 4030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224016
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9685451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.055507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78723.831154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.40715699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9741519
X-RAY DIFFRACTIONr_chiral_restr0.0910.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022937
X-RAY DIFFRACTIONr_nbd_refined0.3160.32673
X-RAY DIFFRACTIONr_nbtor_refined0.3420.52869
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2970.5346
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.356
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3760.53
X-RAY DIFFRACTIONr_mcbond_it4.65322596
X-RAY DIFFRACTIONr_mcangle_it6.4634084
X-RAY DIFFRACTIONr_scbond_it3.63421581
X-RAY DIFFRACTIONr_scangle_it5.75331367
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
608tight positional0.050.05
613medium positional0.550.5
608tight thermal0.090.5
613medium thermal0.942
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
Num. reflection% reflection
Rfree131 -
Rwork1153 -
obs-99.69 %
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)
16.1005-2.4978-2.85494.75112.02323.5964-0.179-1.70210.95510.45250.6042-0.5360.29050.5242-0.4252-0.2930.10880.01560.5855-0.3068-0.0794-74.00159.418-5.774
23.7323-1.23310.74652.875-0.43033.1790.242-0.128-0.1278-0.09320.2272-0.26920.37090.1411-0.4692-0.2211-0.0391-0.17380.0522-0.0762-0.2794-57.86524.012-16.694
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 2607 - 260
2X-RAY DIFFRACTION2BB7 - 2607 - 260

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