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- PDB-7lbp: Crystal structure of human Survivin bound to histone H3T3phK4ac p... -

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Basic information

Entry
Database: PDB / ID: 7lbp
TitleCrystal structure of human Survivin bound to histone H3T3phK4ac peptide
Components
  • Baculoviral IAP repeat-containing protein 5
  • histone H3T3phK4ac peptide
KeywordsCELL CYCLE / lysine acetylation / 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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: histone H3T3phK4ac peptide
C: Baculoviral IAP repeat-containing protein 5
D: histone H3T3phK4ac peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6426
Polymers36,5114
Non-polymers1312
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-18 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.117, 70.988, 83.322
Angle α, β, γ (deg.)90.000, 130.040, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 5 - 140 / Label seq-ID: 9 - 144

Dom-IDAuth asym-IDLabel asym-ID
1AA
2CC

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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 H3T3phK4ac 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: 1429.497 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.: 5 / 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: 3.59 Å3/Da / Density % sol: 65.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 1 uL of protein at 10mg/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: beryllium lenses
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 15604 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.032 / Rrim(I) all: 0.062 / Χ2: 1.565 / Net I/σ(I): 12 / Num. measured all: 58042
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6430.4277530.8790.2960.5210.70799.1
2.64-2.693.20.347930.9380.2250.4090.69299.5
2.69-2.743.50.2967610.9450.1880.3520.695100
2.74-2.83.80.2817960.9410.1680.3280.762100
2.8-2.863.80.2057530.9740.120.2380.782100
2.86-2.933.90.1657900.9830.0970.1910.854100
2.93-33.80.1427640.9880.0830.1650.882100
3-3.083.90.1257980.9890.0730.1450.878100
3.08-3.173.90.1057810.9910.0610.1210.96699.9
3.17-3.283.80.0867460.9930.0510.11.051100
3.28-3.393.80.0757910.9930.0440.0871.075100
3.39-3.533.80.0667920.9950.0390.0771.43599.9
3.53-3.693.80.067720.9970.0350.071.73100
3.69-3.883.80.0587840.9950.0340.0672.0499.9
3.88-4.133.80.0517850.9960.030.0592.01199.9
4.13-4.453.80.0477880.9960.0280.0541.99100
4.45-4.893.80.0467810.9970.0270.0542.263100
4.89-5.63.80.0467940.9960.0270.0542.275100
5.6-7.053.80.0447850.9970.0260.0512.42799.6
7.05-503.60.047970.9910.0250.0475.50997.1

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Processing

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

3uec


Resolution: 2.6→35.49 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 22.202 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.347 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 780 5 %RANDOM
Rwork0.2121 ---
obs0.2139 14821 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 171.5 Å2 / Biso mean: 105.743 Å2 / Biso min: 67.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å2-0 Å20.12 Å2
2---0.59 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 2.6→35.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2230 0 2 5 2237
Biso mean--91.22 101.34 -
Num. residues----287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192286
X-RAY DIFFRACTIONr_bond_other_d0.0030.022032
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9583101
X-RAY DIFFRACTIONr_angle_other_deg0.89234691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5055283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52525108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68615349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.545159
X-RAY DIFFRACTIONr_chiral_restr0.0740.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212604
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02517
Refine LS restraints NCS

Ens-ID: 1 / Number: 6691 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2C
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 58 -
Rwork0.341 1045 -
all-1103 -
obs--95.58 %
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)
118.515615.233-12.630712.9903-10.97399.371-0.03880.17750.7496-0.203-0.23050.00860.25850.39390.26930.67190.12310.03150.78850.37750.968414.287-4.22617.171
24.07890.5503-1.43668.1206-0.71242.3256-0.0502-0.1524-0.08670.18190.10370.25570.1867-0.1343-0.05360.3992-0.0177-0.12110.43240.060.05752.348-17.523.573
31.81490.0977-3.01150.2942-1.985419.3306-0.03960.03670.3230.15060.0305-0.0037-0.3213-0.20650.00920.4791-0.007-0.07620.37740.03240.19111.649-1.15424.52
46.72760.5215-0.55418.0262-0.586317.0318-0.0844-0.26780.0721-0.14210.10960.04590.34890.1797-0.02520.27180.0402-0.13290.4468-0.02830.2207-1.976-4.82358.263
511.70499.281-11.25588.8472-5.926420.82870.0619-0.6512-0.21590.4723-0.46270.09420.597-0.52970.40070.7416-0.018-0.13610.55420.01260.399515.3055.51814.994
65.04880.05360.30527.4428-0.60332.2919-0.13710.12960.5965-0.05340.1338-0.5856-0.20640.39370.00340.3598-0.0174-0.14160.46120.06980.196620.57181.248
722.17493.2622-4.90850.6207-0.72192.43480.0342-0.5351-0.2344-0.0375-0.0215-0.22640.07360.0826-0.01280.40350.042-0.07990.37490.00520.342520.5191.7632.941
810.00627.28821.934611.3842-2.00822.7795-0.33681.54730.241-0.23770.2167-0.0603-0.1980.47390.12010.489-0.0306-0.1020.66440.04670.207156.8964.142-5.105
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 11
2X-RAY DIFFRACTION2A12 - 93
3X-RAY DIFFRACTION3A94 - 122
4X-RAY DIFFRACTION4A123 - 141
5X-RAY DIFFRACTION5C5 - 11
6X-RAY DIFFRACTION6C12 - 91
7X-RAY DIFFRACTION7C92 - 123
8X-RAY DIFFRACTION8C124 - 142

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