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- PDB-6yih: Structure of Chromosomal Passenger Complex (CPC) bound to phospho... -

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Basic information

Entry
Database: PDB / ID: 6yih
TitleStructure of Chromosomal Passenger Complex (CPC) bound to phosphorylated Histone 3 peptide at 2.6 A.
Components
  • Baculoviral IAP repeat-containing protein 5
  • Borealin
  • Histone H3.1
  • Inner centromere protein
KeywordsCELL CYCLE
Function / homology
Function and homology information


central element / meiotic spindle midzone / survivin complex / meiotic spindle midzone assembly / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of exit from mitosis / positive regulation of mitotic cell cycle spindle assembly checkpoint ...central element / meiotic spindle midzone / survivin complex / meiotic spindle midzone assembly / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of exit from mitosis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / chromocenter / interphase microtubule organizing center / lateral element / protein-containing complex localization / chromosome passenger complex / cysteine-type endopeptidase inhibitor activity / mitotic metaphase chromosome alignment / nuclear chromosome / intercellular bridge / mitotic spindle assembly checkpoint signaling / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / cobalt ion binding / cytoplasmic microtubule / mitotic sister chromatid segregation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / SUMOylation of DNA replication proteins / chromosome, centromeric region / mitotic cytokinesis / mitotic spindle assembly / chromosome organization / spindle midzone / Chromatin modifying enzymes / pericentric heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / epigenetic regulation of gene expression / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / telomere organization / centriole / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / tubulin binding / positive regulation of mitotic cell cycle / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / molecular function activator activity / chromosome segregation / HDACs deacetylate histones / RHO GTPases Activate Formins / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / sensory perception of sound / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / spindle microtubule / PKMTs methylate histone lysines / Meiotic recombination / kinetochore / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / small GTPase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / spindle / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / mitotic cell cycle / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / midbody / protein-folding chaperone binding / Senescence-Associated Secretory Phenotype (SASP) / microtubule binding / Interleukin-4 and Interleukin-13 signaling / Oxidative Stress Induced Senescence / microtubule
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1900 / Borealin, N-terminal / Cell division protein borealin / Borealin, C-terminal / Nbl1 / Borealin N terminal / Cell division cycle-associated protein 8 / Inner centromere protein, ARK-binding domain / Chromosome passenger complex (CPC) protein INCENP N-terminal / Inner centromere protein, ARK binding region / Chromosome passenger complex (CPC) protein INCENP N terminal ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1900 / Borealin, N-terminal / Cell division protein borealin / Borealin, C-terminal / Nbl1 / Borealin N terminal / Cell division cycle-associated protein 8 / Inner centromere protein, ARK-binding domain / Chromosome passenger complex (CPC) protein INCENP N-terminal / Inner centromere protein, ARK binding region / Chromosome passenger complex (CPC) protein INCENP N terminal / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Special / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Baculoviral IAP repeat-containing protein 5 / Histone H3.1 / Borealin / Inner centromere protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSerena, M. / Elliott, P.R. / Barr, F.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC20079/A15940 United Kingdom
CitationJournal: J.Cell Biol. / Year: 2020
Title: Molecular basis of MKLP2-dependent Aurora B transport from chromatin to the anaphase central spindle.
Authors: Serena, M. / Bastos, R.N. / Elliott, P.R. / Barr, F.A.
History
DepositionApr 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 5
B: Borealin
C: Inner centromere protein
D: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5086
Polymers35,3464
Non-polymers1612
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-70 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.365, 99.365, 56.224
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Baculoviral IAP repeat-containing protein 5 / Apoptosis inhibitor 4 / Apoptosis inhibitor survivin


Mass: 16568.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC5, API4, IAP4 / Plasmid: pETDUET1 / Cell (production host): BL21 CodonPlus (DE3) RIL / Production host: Escherichia coli (E. coli) / References: UniProt: O15392
#2: Protein Borealin / Cell division cycle-associated protein 8 / Dasra-B / hDasra-B / Pluripotent embryonic stem cell- ...Cell division cycle-associated protein 8 / Dasra-B / hDasra-B / Pluripotent embryonic stem cell-related gene 3 protein


Mass: 8164.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDCA8, PESCRG3 / Plasmid: pETDuet1 / Cell (production host): BL21 CodonPlus (DE3) RIL / Production host: Escherichia coli (E. coli) / References: UniProt: Q53HL2
#3: Protein Inner centromere protein


Mass: 9224.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INCENP / Plasmid: pFAT2-His6-GST / Cell (production host): BL21 CodonPlus (DE3) RIL / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NQS7

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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 1388.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431

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Non-polymers , 3 types, 44 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 20 % (w/v) PEG 4,000, 100 mM HEPES pH 7.0, 150 mM ammonium sulphate

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.55→56.22 Å / Num. obs: 9950 / % possible obs: 96.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 52.98 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.091 / Net I/σ(I): 9.2
Reflection shellResolution: 2.55→2.66 Å / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1236 / CC1/2: 0.706

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
xia2data processing
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QFA

2qfa


Resolution: 2.55→47.07 Å / SU ML: 0.3239 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.553
RfactorNum. reflection% reflection
Rfree0.2593 489 4.97 %
Rwork0.2337 --
obs0.235 9834 94.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 79.7 Å2
Refinement stepCycle: LAST / Resolution: 2.55→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 6 42 1934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00381929
X-RAY DIFFRACTIONf_angle_d0.63912611
X-RAY DIFFRACTIONf_chiral_restr0.0376286
X-RAY DIFFRACTIONf_plane_restr0.0046340
X-RAY DIFFRACTIONf_dihedral_angle_d8.11811174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.920.33841720.28813140X-RAY DIFFRACTION95.58
2.92-3.680.30141670.27733101X-RAY DIFFRACTION94.37
3.68-47.070.21511500.20073104X-RAY DIFFRACTION92.23
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)
11.56892538481-0.7352318909520.4981342033162.47992781203-0.02650630561870.939253315332-0.0489335624698-0.07789491553680.386660269230.00675550520608-0.2196396191760.155630966038-0.270469568167-0.01272302704270.2103716311830.4169768740150.0002535163903420.005302624227270.381674310074-0.04699674379630.48718221267940.8398074658-2.28159843215-4.33914429931
21.731793019660.113433795285-0.03516138740291.128901152290.5763927874461.378132301950.00884706564066-0.4476881465820.3514336294670.285881469723-0.2656527765260.0497493260874-0.019243035301-0.2345547000740.1053770452610.426486340395-0.004396439101780.04695830112210.532703618819-0.1210777434510.36648428392740.4617781226-17.19700231738.25168670298
31.20908584759-0.358311564651-1.240908036491.271130222430.5235953153061.258375998010.0674687720476-0.8030010109050.03746969493820.406560516567-0.3738500413991.02200475137-0.0138232233852-0.3366077152360.372530334930.601390554562-0.09411169782320.1763440762621.05452368799-0.1780575579910.78005463865927.5253123861-14.735449664312.2669602713
42.72678106346-0.130274266052.984842428135.795006489180.770145019273.491791198920.280024988223-0.5043556218770.3860263344981.233513392740.01009953806760.761385944706-0.329921745669-0.616266272676-0.5118141580521.105728765090.11283744140.1642803528820.781471178784-0.06410266564460.80330012547637.25888193797.420983430183.44356366336
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 4 through 138)
2X-RAY DIFFRACTION2(chain 'B' and resid 17 through 76)
3X-RAY DIFFRACTION3(chain 'C' and resid 7 through 45)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 7)

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