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- PDB-7lbo: Crystal structure of human Survivin bound to histone H3 T3phK4me1... -

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Basic information

Entry
Database: PDB / ID: 7lbo
TitleCrystal structure of human Survivin bound to histone H3 T3phK4me1 peptide
Components
  • Baculoviral IAP repeat-containing protein 5
  • histone H3 T3phK4me1 peptide
KeywordsCELL CYCLE / lysine methylation / threonine phosphorylation / histone H3 / CPC
Function / homology
Function and homology information


survivin complex / : / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of exit from mitosis / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / interphase microtubule organizing center / chromosome passenger complex ...survivin complex / : / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of exit from mitosis / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / interphase microtubule organizing center / chromosome passenger complex / protein-containing complex localization / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cobalt ion binding / nuclear chromosome / mitotic spindle assembly checkpoint signaling / spindle midzone / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / mitotic cytokinesis / SUMOylation of DNA replication proteins / chromosome, centromeric region / mitotic spindle assembly / cysteine-type endopeptidase inhibitor activity / cytoplasmic microtubule / Chromatin modifying enzymes / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / centriole / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / telomere organization / positive regulation of mitotic cell cycle / tubulin binding / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Resolution of Sister Chromatid Cohesion / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / mitotic spindle organization / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / spindle microtubule / HDACs deacetylate histones / chromosome segregation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / sensory perception of sound / RHO GTPases Activate Formins / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / kinetochore / PKMTs methylate histone lysines / Pre-NOTCH Transcription and Translation / Meiotic recombination / small GTPase binding / G2/M transition of mitotic cell cycle / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RMTs methylate histone arginines / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / Separation of Sister Chromatids / nucleosome / mitotic cell cycle / nucleosome assembly / protein-folding chaperone binding / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / Neddylation / microtubule cytoskeleton / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / midbody / Interleukin-4 and Interleukin-13 signaling / Oxidative Stress Induced Senescence / gene expression / microtubule binding / Estrogen-dependent gene expression / microtubule / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / cell division / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / apoptotic process / negative regulation of apoptotic process
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 ...: / 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 domain / 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: 2.5 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
B: Baculoviral IAP repeat-containing protein 5
C: histone H3 T3phK4me1 peptide
F: histone H3 T3phK4me1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5866
Polymers36,4554
Non-polymers1312
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-19 kcal/mol
Surface area17320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.182, 71.441, 82.786
Angle α, β, γ (deg.)90.000, 129.110, 90.000
Int Tables number5
Space group name H-MC121

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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 T3phK4me1 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: 1401.487 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.: 14 / 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: 3.68 Å3/Da / Density % sol: 66.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 1 uL of protein at 10 mg/mL was mixed with 1 uL of buffer composed of 0.16 M potassium/sodium tartrate, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 20, 2013 / Details: berrylium lenses
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 17812 / % possible obs: 99.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.026 / Rrim(I) all: 0.051 / Χ2: 1.522 / Net I/σ(I): 14.8 / Num. measured all: 67635
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.543.80.3298970.9540.1930.3820.806100
2.54-2.593.80.2788970.9680.1630.3220.83699.8
2.59-2.643.80.2368600.9750.1390.2740.84799.9
2.64-2.693.80.1938930.9830.1130.2240.812100
2.69-2.753.80.1698850.9830.0990.1960.856100
2.75-2.823.80.1488970.9870.0870.1720.886100
2.82-2.893.80.118730.990.0650.1280.964100
2.89-2.963.80.0989140.9940.0570.1131.014100
2.96-3.053.80.0879000.9940.0510.1011.242100
3.05-3.153.80.0858680.9920.050.0991.436100
3.15-3.263.80.078960.9940.0410.0821.557100
3.26-3.393.80.068890.9950.0360.071.612100
3.39-3.553.80.0499090.9960.0290.0571.64299.8
3.55-3.733.80.0438900.9980.0260.051.697100
3.73-3.973.80.0418800.9970.0240.0471.87899.7
3.97-4.273.80.0418900.9970.0240.0482.33999.3
4.27-4.73.70.0368960.9970.0220.0432.36699
4.7-5.383.70.048900.9960.0240.0462.76499.2
5.38-6.783.80.0359090.9970.0210.0412.44598.9
6.78-503.50.0288790.9980.0170.0332.70694.3

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Processing

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

3uec


Resolution: 2.5→34.34 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 15.75 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.283 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2606 910 5.1 %RANDOM
Rwork0.2071 ---
obs0.2097 16899 99.24 %-
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 max: 187.93 Å2 / Biso mean: 90.409 Å2 / Biso min: 58.91 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å2-0 Å23.89 Å2
2---6.8 Å20 Å2
3---1.04 Å2
Refinement stepCycle: final / Resolution: 2.5→34.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2233 0 2 14 2249
Biso mean--70.75 83.91 -
Num. residues----284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192292
X-RAY DIFFRACTIONr_bond_other_d0.0040.022056
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9573104
X-RAY DIFFRACTIONr_angle_other_deg0.94334755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7115280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19625.044113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77515363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3091510
X-RAY DIFFRACTIONr_chiral_restr0.0740.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212602
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02520
LS refinement shellResolution: 2.505→2.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 76 -
Rwork0.293 1204 -
all-1280 -
obs--98.23 %
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)
15.15058.3982-8.984817.0538-11.606418.5681-0.4153-0.0964-0.1638-0.2005-0.18530.1891.0818-0.1660.60070.76960.0871-0.12770.73120.18090.5083-10.81229.92147.541
27.69910.60140.42989.4592-1.4485.1084-0.16560.30861.04260.01620.0912-0.5496-0.35260.27620.07440.3058-0.0238-0.0680.23920.0830.2554-5.84142.36533.509
326.74043.2489-7.43850.4194-1.00523.68930.0302-0.0467-0.5273-0.0546-0.0102-0.12130.1808-0.031-0.01990.35110.06990.00460.18560.03840.3909-4.64325.63634.711
426.72450.5083-3.33876.1395-0.05294.87390.23050.44440.6708-0.2528-0.0571-0.1423-0.2090.2472-0.17330.4349-0.0395-0.07850.280.02450.12430.29928.97527.22
59.02199.8966-11.861814.4103-7.959523.52490.00860.18930.8798-0.56631.54960.2555-0.52181.9263-1.55820.7059-0.16820.10860.64370.05620.9344-11.28320.62449.134
65.3062-0.2967-0.405111.1385-0.08852.8351-0.0657-0.3118-0.24620.45020.02450.09310.2256-0.20430.04110.3528-0.0511-0.04330.25910.06540.0306-22.9117.0156.699
71.44640.1365-4.04540.1131-1.396522.79430.01130.09840.21520.0655-0.0038-0.0217-0.0345-0.0747-0.00750.4664-0.0043-0.03140.24090.02690.2059-23.72622.88558.661
816.2631.6457-14.27728.9599-1.434932.91470.5036-0.7651-0.04140.0617-0.11390.43470.2978-0.3005-0.38970.3783-0.0468-0.03610.254-0.00280.2904-26.78919.22294.79
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 10
2X-RAY DIFFRACTION2A11 - 93
3X-RAY DIFFRACTION3A94 - 122
4X-RAY DIFFRACTION4A123 - 141
5X-RAY DIFFRACTION5B5 - 11
6X-RAY DIFFRACTION6B12 - 90
7X-RAY DIFFRACTION7B91 - 128
8X-RAY DIFFRACTION8B129 - 140

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