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- PDB-3ued: Crystal structure of human Survivin bound to histone H3 phosphory... -

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Basic information

Entry
Database: PDB / ID: 3ued
TitleCrystal structure of human Survivin bound to histone H3 phosphorylated on threonine-3 (C2 space group).
Components
  • Baculoviral IAP repeat-containing protein 5
  • N-terminal fragment of histone H3
KeywordsCELL CYCLE / zinc finger / BIR domain / phosphorylation / chromosomal passenger complex / cell division / mitosis
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 / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / centriole / tubulin binding / positive regulation of mitotic cell cycle / RHO GTPases Activate Formins / sensory perception of sound / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / spindle microtubule / kinetochore / small GTPase binding / spindle / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / Neddylation / mitotic cell cycle / midbody / protein-folding chaperone binding / microtubule binding / Interleukin-4 and Interleukin-13 signaling / microtubule / protein heterodimerization activity / 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 / zinc ion binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Baculoviral IAP repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_leaving_atom_flag / _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
B: N-terminal fragment of histone H3
C: Baculoviral IAP repeat-containing protein 5
D: N-terminal fragment of histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5606
Polymers36,4294
Non-polymers1312
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-14 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.415, 71.276, 83.136
Angle α, β, γ (deg.)90.00, 129.91, 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: 1388.468 Da / Num. of mol.: 2 / Source method: obtained synthetically
#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.: 17 / 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: 3.54 Å3/Da / Density % sol: 65.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 3350, 0.16 M sodium citrate, 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-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 20, 2011 / Details: beryllium lens
RadiationMonochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 14102 / Num. obs: 14102 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 87.3 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 32.3
Reflection shellResolution: 2.7→2.72 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.1 / Num. unique all: 334 / % possible all: 100

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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: 2.7→41.28 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.944 / SU B: 22.276 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24086 709 5 %RANDOM
Rwork0.19209 ---
all0.19469 13346 --
obs0.19469 13346 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.55 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å21.52 Å2
2---0.31 Å20 Å2
3---1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.7→41.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 2 17 2273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192311
X-RAY DIFFRACTIONr_bond_other_d0.0120.021597
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.9563129
X-RAY DIFFRACTIONr_angle_other_deg3.9413.0023886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1845284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53424.862109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79915376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7081510
X-RAY DIFFRACTIONr_chiral_restr0.0880.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212574
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02462
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 41 -
Rwork0.316 938 -
obs--99.59 %
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)
14.08630.4683-0.19146.0128-0.36872.1098-0.1017-0.0721-0.03430.36620.0705-0.05160.0885-0.16230.03110.188-0.0302-0.03410.11320.07040.0554-26.504-3.503-8.025
21.44710.1996-3.16390.0309-0.279318.8571-0.17630.02890.2663-0.0184-0.00440.04420.1802-0.38630.18070.33760.0401-0.01510.06230.02870.1358-29.44210.4122.791
34.47130.68580.97217.7092-1.19511.3629-0.01880.19580.42810.2272-0.0232-0.6267-0.05170.29170.0420.0722-0.043-0.06590.12670.03970.206-9.50230.755-29.592
416.70420.2242-1.31650.0552-0.2391.16320.11330.70680.1713-0.01640.00960.0244-0.0429-0.101-0.12290.13450.04020.00360.04680.0150.30732.01216.291-32.059
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 90
2X-RAY DIFFRACTION2A91 - 141
3X-RAY DIFFRACTION3C5 - 90
4X-RAY DIFFRACTION4C91 - 141

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