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- PDB-7lbk: Crystal structure of human Survivin bound to histone H3 T3phK4me3... -

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Basic information

Entry
Database: PDB / ID: 7lbk
TitleCrystal structure of human Survivin bound to histone H3 T3phK4me3 peptide
Components
  • Baculoviral IAP repeat-containing protein 5
  • histone H3 T3phK4me3 peptide
KeywordsCELL CYCLE / lysine methylation / threonine phosphorylation / histone H3 / CPC
Function / homology
Function and homology information


survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / 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 / interphase microtubule organizing center / protein-containing complex localization ...survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / 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 / interphase microtubule organizing center / protein-containing complex localization / chromosome passenger complex / cysteine-type endopeptidase inhibitor activity / 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 / cobalt ion binding / cytoplasmic microtubule / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / SUMOylation of DNA replication proteins / chromosome, centromeric region / mitotic cytokinesis / mitotic spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Chromatin modifying enzymes / 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 / 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 / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / spindle microtubule / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / kinetochore / Meiotic recombination / 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 / gene expression / HATs acetylate histones / midbody / protein-folding chaperone binding / Senescence-Associated Secretory Phenotype (SASP) / microtubule binding / Interleukin-4 and Interleukin-13 signaling / Oxidative Stress Induced Senescence / microtubule / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / cell division / protein phosphorylation / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / DNA binding
Similarity search - Function
BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Baculoviral IAP repeat-containing protein 5 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsNiedzialkowska, E. / Minor, W. / Stukenberg, P.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM053163 United States
CitationJournal: Mol.Biol.Cell / Year: 2022
Title: Tip60 acetylation of histone H3K4 temporally controls chromosome passenger complex localization.
Authors: Niedzialkowska, E. / Liu, L. / Kuscu, C. / Mayo, Z. / Minor, W. / Strahl, B.D. / Adli, M. / Stukenberg, P.T.
History
DepositionJan 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 3, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Baculoviral IAP repeat-containing protein 5
D: histone H3 T3phK4me3 peptide
A: Baculoviral IAP repeat-containing protein 5
C: histone H3 T3phK4me3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6446
Polymers36,5134
Non-polymers1312
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-19 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.292, 71.369, 82.554
Angle α, β, γ (deg.)90.00, 129.33, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010B6 - 139
2010A6 - 139

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Components

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


Mass: 16826.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC5, API4, IAP4 / Production host: Escherichia coli (E. coli) / References: UniProt: O15392
#2: Protein/peptide histone H3 T3phK4me3 peptide / 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: 1430.548 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.62 Å3/Da / Density % sol: 66.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: The crystal was obtained by mixing 1 uL of protein at 10 mg/mL with 1 uL of mother liquor composed of 0.16 M potassium/sodium tartrate, 14% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.27822 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27822 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 13890 / % possible obs: 98.1 % / Redundancy: 14.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.5
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.756 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-3000data scaling
SCALEPACKdata scaling
HKL-3000data reduction
SHELXDphasing
DMphasing
MLPHAREphasing
HKL-3000phasing
BUCCANEERmodel building
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.7→41.04 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.875 / SU B: 21.775 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.566 / ESU R Free: 0.321
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 623 5 %RANDOM
Rwork0.212 ---
obs0.214 11791 87.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å2-0.17 Å2
2--2.03 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.7→41.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 2 34 2286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192306
X-RAY DIFFRACTIONr_bond_other_d0.0040.022118
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.9653118
X-RAY DIFFRACTIONr_angle_other_deg1.05134900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5765279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45224.775111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.74315383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8381511
X-RAY DIFFRACTIONr_chiral_restr0.0830.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212580
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02519
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6763 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 19 -
Rwork0.299 483 -
obs--49.12 %
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)
17.5476-1.2830.92810.82841.43913.57260.0712-0.16490.6669-0.15490.00330.4706-0.2078-0.1073-0.07450.1756-0.0078-0.01660.1243-0.06490.1798-40.63640.51693.397
231.3267-3.6603-4.10473.0773-0.10983.72990.2322-0.38140.2612-0.1371-0.0321-0.0672-0.388-0.2129-0.20020.3565-0.0297-0.0020.1204-0.04640.1746-73.15631.34999.617
35.7710.69430.328211.93541.44094.9657-0.10590.07570.0128-0.18940.08420.09680.02240.09250.02180.26530.02730.01510.0872-0.03630.0207-25.64111.22872.437
41.1733-0.1955-3.27180.03860.851526.6829-0.1513-0.00050.1650.00970.0006-0.02170.42920.01090.15080.4449-0.00650.01510.0298-0.00170.2558-23.03824.81160.76
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 115
2X-RAY DIFFRACTION2A116 - 142
3X-RAY DIFFRACTION3B5 - 91
4X-RAY DIFFRACTION4B92 - 140

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