[English] 日本語
Yorodumi
- PDB-6yif: Structure of Chromosomal Passenger Complex (CPC) bound to phospho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yif
TitleStructure of Chromosomal Passenger Complex (CPC) bound to phosphorylated Histone 3 peptide at 1.8 A.
Components
  • Baculoviral IAP repeat-containing protein 5
  • Borealin
  • Inner centromere protein
  • Phosphorylated (Thr3) Histone H3
KeywordsCELL CYCLE
Function / homology
Function and homology information


meiotic spindle midzone / meiotic spindle midzone assembly / central element / survivin complex / 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 ...meiotic spindle midzone / meiotic spindle midzone assembly / central element / survivin complex / 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 / chromosome passenger complex / protein-containing complex localization / cobalt ion binding / mitotic metaphase chromosome alignment / cysteine-type endopeptidase inhibitor activity / intercellular bridge / nuclear chromosome / mitotic spindle assembly checkpoint signaling / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / cytoplasmic microtubule / mitotic sister chromatid segregation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / mitotic cytokinesis / SUMOylation of DNA replication proteins / chromosome, centromeric region / mitotic spindle assembly / chromosome organization / spindle midzone / Chromatin modifying enzymes / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / pericentric heterochromatin / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / telomere organization / centriole / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / tubulin binding / positive regulation of mitotic cell cycle / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / : / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / molecular function activator activity / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / chromosome segregation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / spindle microtubule / 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 / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / kinetochore / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / small GTPase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / spindle / HCMV Early Events / 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 / mitotic cell cycle / protein-folding chaperone binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / midbody / Senescence-Associated Secretory Phenotype (SASP) / microtubule binding
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: 1.81 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 5
B: Borealin
C: Inner centromere protein
D: Phosphorylated (Thr3) Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6528
Polymers32,2984
Non-polymers3544
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-78 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.863, 98.863, 56.067
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

-
Components

-
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus (RIL) / 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 BL21(DE3) (bacteria) / Variant (production host): CodonPlus (RIL) / References: UniProt: Q53HL2
#3: Protein Inner centromere protein


Mass: 6176.117 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 BL21(DE3) (bacteria) / Variant (production host): CodonPlus (RIL) / References: UniProt: Q9NQS7

-
Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide Phosphorylated (Thr3) Histone H3


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

-
Non-polymers , 3 types, 232 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.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 20 % (w/v) PEG 4,000, 200 mM Lithium sulphate, 50 mM MES pH 6.5

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96859 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96859 Å / Relative weight: 1
ReflectionResolution: 1.81→49.43 Å / Num. obs: 28454 / % possible obs: 99.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 25.37 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.8
Reflection shellResolution: 1.81→1.86 Å / Rmerge(I) obs: 0.953 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2126 / CC1/2: 0.544

-
Processing

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

2qfa


Resolution: 1.81→49.43 Å / SU ML: 0.1901 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.8182
RfactorNum. reflection% reflection
Rfree0.2227 1436 5.08 %
Rwork0.1807 --
obs0.1828 28270 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.23 Å2
Refinement stepCycle: LAST / Resolution: 1.81→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1859 0 16 228 2103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111927
X-RAY DIFFRACTIONf_angle_d1.14852603
X-RAY DIFFRACTIONf_chiral_restr0.0516275
X-RAY DIFFRACTIONf_plane_restr0.0087338
X-RAY DIFFRACTIONf_dihedral_angle_d5.40831570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.870.35331350.31152657X-RAY DIFFRACTION98.07
1.87-1.950.3421400.30232646X-RAY DIFFRACTION97.96
1.95-2.040.24351260.23242682X-RAY DIFFRACTION98.6
2.04-2.150.24231350.19812705X-RAY DIFFRACTION99.23
2.15-2.280.24641610.18892619X-RAY DIFFRACTION98.48
2.28-2.460.18931510.16552692X-RAY DIFFRACTION99.44
2.46-2.70.20351540.15992688X-RAY DIFFRACTION99.2
2.7-3.090.18931470.16442695X-RAY DIFFRACTION99.2
3.09-3.90.23181390.16242712X-RAY DIFFRACTION99.06
3.9-49.430.20651480.1692738X-RAY DIFFRACTION98.1
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)
13.606847900951.01937869149-1.61988826341.365482132770.07163285311750.764228211377-0.04242366520390.0105405679697-0.146712957778-0.0561430469983-0.06982859200790.2955868281690.108791593673-0.259975190270.1077982283130.172761676406-0.021095348128-0.007403623678410.228100651375-0.008534019442340.25007257406722.3713451714-34.77832673395.04422556125
23.31182557368-0.4729312333560.8429324012432.08349339080.5759535914943.374601623530.0328585348050.4777465974020.0334805681642-0.460196945074-0.1855553894730.272294130918-0.197516596804-0.1007566643370.09945186674840.1992844276460.0190885226301-0.04989029291820.170471343596-0.01167484035190.14604504738736.0585208916-26.48091005-6.81773611808
35.90490646717-0.9668910620495.475473997731.31715472511-2.147851898568.36646928354-0.3136050763740.4706552641260.708622323529-0.622008465585-0.1576955067320.37705001792-1.02258440772-0.4508723889210.4787722760890.715057710840.223017987942-0.2078247563080.423873828663-0.02923284824550.43505788959226.5138058596-16.454218758-12.1917149122
42.00818347679-0.156878149286-3.171096361382.00892815043-3.466971554222.014731856080.2819852985011.200422769140.45763819685-0.4789213590840.3268968560290.72952628771-0.20299602893-1.74212045362-0.562546646470.327964243752-0.06353578184170.02876609968680.6984614649470.03198112058680.42710125154712.5167435939-37.3104175232-2.63669952616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 5 through 134)
2X-RAY DIFFRACTION2(chain 'B' and resid 21 through 76)
3X-RAY DIFFRACTION3(chain 'C' and resid 7 through 43)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 5)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more