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- PDB-3uef: Crystal structure of human Survivin bound to histone H3 (C2 space... -

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Basic information

Entry
Database: PDB / ID: 3uef
TitleCrystal structure of human Survivin bound to histone H3 (C2 space group).
Components
  • Baculoviral IAP repeat-containing protein 5
  • N-terminal fragment of histone H3
KeywordsCELL CYCLE / ZINC FINGER MOTIF / BIR DOMAIN / chromosomal passenger complex / cell division / mitosis
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 / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / centriole / tubulin binding / telomere organization / positive regulation of mitotic cell cycle / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Resolution of Sister Chromatid Cohesion / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / epigenetic regulation of gene expression / 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 / chromosome segregation / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / sensory perception of sound / 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 / kinetochore / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / small GTPase binding / Meiotic recombination / Pre-NOTCH Transcription and Translation / G2/M transition of mitotic cell cycle / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / Separation of Sister Chromatids / structural constituent of chromatin / nucleosome / mitotic cell cycle / nucleosome assembly / protein-folding chaperone binding / Neddylation / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / microtubule cytoskeleton / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / midbody / Interleukin-4 and Interleukin-13 signaling / Oxidative Stress Induced Senescence / microtubule binding / gene expression / 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
: / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 ...: / 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 / 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 / Orthogonal Bundle / Mainly Alpha
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: 2.45 Å
AuthorsNiedzialkowska, E. / Porebski, P.J. / Wang, F. / Higgins, J.M. / Stukenberg, P.T. / Minor, W.
CitationJournal: Mol.Biol.Cell / Year: 2012
Title: Molecular basis for phosphospecific recognition of histone H3 tails by Survivin paralogues at inner centromeres.
Authors: Niedzialkowska, E. / Wang, F. / Porebski, P.J. / Minor, W. / Higgins, J.M. / Stukenberg, P.T.
History
DepositionOct 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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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
C: Baculoviral IAP repeat-containing protein 5
B: N-terminal fragment of histone H3
D: N-terminal fragment of histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5248
Polymers36,2694
Non-polymers2554
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-11 kcal/mol
Surface area17430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.737, 71.092, 82.762
Angle α, β, γ (deg.)90.00, 129.77, 90.00
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: API4, BIRC5, IAP4 / Plasmid: p8HIS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O15392
#2: Protein/peptide N-terminal fragment of histone H3


Mass: 1308.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: UniProt: P68431*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsE129K REPRESENTS A NATURAL VARIANT

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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: 3.55 Å3/Da / Density % sol: 65.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG 3350, 0.2 M potassium/sodium tartate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 6, 2011 / Details: beryllium lens
RadiationMonochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 18747 / Num. obs: 18747 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 68.3 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 33.9
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.3 / Num. unique all: 939 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
HKL-3000phasing
MOLREPphasing
REFMAC5.6.0117refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UEC

3uec


Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 13.047 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21415 958 5.1 %RANDOM
Rwork0.18816 ---
all0.18953 17712 --
obs0.18953 17712 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.507 Å2
Baniso -1Baniso -2Baniso -3
1-3.03 Å20 Å23.3 Å2
2---0.87 Å20 Å2
3---2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 10 47 2274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022279
X-RAY DIFFRACTIONr_bond_other_d0.0050.021621
X-RAY DIFFRACTIONr_angle_refined_deg1.8861.9533068
X-RAY DIFFRACTIONr_angle_other_deg1.25933946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7815278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21624.231104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.24915392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6541512
X-RAY DIFFRACTIONr_chiral_restr0.1110.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212510
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02470
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 75 -
Rwork0.331 1273 -
obs--99.85 %
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)
13.0476-0.33160.42886.2414-0.85561.579-0.03330.0276-0.02250.4887-0.0236-0.04270.1374-0.05420.05690.362-0.04990.01820.10980.0730.2571-53.151-68.84623.53
21.71510.2656-3.67380.0419-0.617520.5308-0.11960.08320.2378-0.0070.01730.04660.1511-0.40980.10230.52530.00830.04230.00980.01310.3784-55.937-55.04334.339
37.06950.27351.60529.288-0.91922.777-0.07660.16440.82480.2449-0.0543-0.8851-0.02860.23270.13090.1777-0.0274-0.00460.06340.07620.5171-36.477-35.0671.972
423.09981.1611-4.62960.092-0.40982.0758-0.0070.4919-0.0462-0.03960.04460.00690.0175-0.1486-0.03760.28960.02750.07090.04150.02690.6603-25.142-49.65-0.088
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 90
2X-RAY DIFFRACTION2A91 - 140
3X-RAY DIFFRACTION3C5 - 90
4X-RAY DIFFRACTION4C91 - 141

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