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- PDB-7lbq: Crystal structure of human Survivin bound to histone H3 T3phK4me2... -

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Basic information

Entry
Database: PDB / ID: 7lbq
TitleCrystal structure of human Survivin bound to histone H3 T3phK4me2 peptide
Components
  • Baculoviral IAP repeat-containing protein 5
  • histone H3 T3phK4me2 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 / cobalt ion binding / 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 / 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 / positive regulation of mitotic cell cycle / tubulin binding / 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 / RHO GTPases Activate Formins / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / sensory perception of sound / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / spindle microtubule / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / kinetochore / small GTPase binding / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / 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 / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / 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 / Oxidative Stress Induced Senescence / Interleukin-4 and Interleukin-13 signaling / 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 / MOLECULAR REPLACEMENT / Resolution: 2.69 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
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 5
E: histone H3 T3phK4me2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3073
Polymers18,2422
Non-polymers651
Water1267
1
A: Baculoviral IAP repeat-containing protein 5
E: histone H3 T3phK4me2 peptide
hetero molecules

A: Baculoviral IAP repeat-containing protein 5
E: histone H3 T3phK4me2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6146
Polymers36,4834
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_757-x+2,y,-z+21
Buried area2240 Å2
ΔGint-19 kcal/mol
Surface area16620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.343, 70.162, 89.447
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-307-

HOH

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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.: 1
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 T3phK4me2 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: 1415.514 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 uL of protein was mixed with 1uL of buffer composed of 2.25 mM spermine, 9 mM MgCl2, 0.9 mM spermidine, 1.8 mM cobalt (III)hexamine chloride, 0.05 sodium cacodylate pH 7.0, 5% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 6766 / % possible obs: 99.1 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.075 / Χ2: 2.916 / Net I/σ(I): 18.2 / Num. measured all: 43026
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.6-2.644.80.7583560.9731100
2.64-2.6950.7013220.8971100
2.69-2.745.60.5453351.0031100
2.74-2.85.90.4923241.0291100
2.8-2.866.10.393481.1271100
2.86-2.936.60.3063161.2811100
2.93-37.20.2783451.3631100
3-3.087.20.2473281.4491100
3.08-3.177.30.1933431.7741100
3.17-3.287.20.1693381.9521100
3.28-3.397.20.1413332.5051100
3.39-3.536.90.1083422.9551100
3.53-3.6970.0923353.2821100
3.69-3.886.80.0773484.231100
3.88-4.136.60.0663394.251100
4.13-4.456.40.0613444.7361100
4.45-4.896.20.0573434.808199.4
4.89-5.66.30.0623495.599199.7
5.6-7.0560.063535.798199.7
7.05-505.10.0593257.479184.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UEC

3uec


Resolution: 2.69→29.36 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.874 / SU B: 23.639 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.569 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2684 292 4.8 %RANDOM
Rwork0.2485 ---
obs0.2494 5805 96.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.21 Å2 / Biso mean: 53.655 Å2 / Biso min: 15.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0 Å2-0 Å2
2---0.4 Å20 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 2.69→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 33 7 1092
Biso mean--53.32 31.77 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191082
X-RAY DIFFRACTIONr_bond_other_d0.0010.02983
X-RAY DIFFRACTIONr_angle_refined_deg2.0631.9511465
X-RAY DIFFRACTIONr_angle_other_deg0.93832258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3865136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.79723.77845
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.27315163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.583155
X-RAY DIFFRACTIONr_chiral_restr0.1130.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211218
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02251
LS refinement shellResolution: 2.69→2.759 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 18 -
Rwork0.363 291 -
all-309 -
obs--67.17 %
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)
121.2707-3.7463.9389.2793-6.39046.9209-0.4995-0.75281.28980.77280.87571.0374-1.0613-0.5989-0.37610.41810.0479-0.03040.15430.19360.541151.9716.37575.99
214.9958-4.297613.37735.6584-7.151615.06520.18620.27020.1523-0.81020.05280.63920.62730.0675-0.2390.3003-0.0054-0.10990.0450.08490.363560.1627.45176.285
30.5232-3.02915.675119.1718-35.826267.3772-0.27080.24470.19350.662-1.5007-1.2045-1.2052.26661.77150.6416-0.19-0.13080.79320.69250.718766.97920.56465.632
48.61613.8868-11.17512.715-11.667460.566-0.069-0.042-0.5467-0.12880.0221-0.13660.3743-0.13040.0470.4328-0.09190.03540.02520.03850.383864.31330.79241.439
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 66
2X-RAY DIFFRACTION2A67 - 106
3X-RAY DIFFRACTION3A107 - 124
4X-RAY DIFFRACTION4A125 - 141

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