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- PDB-3uii: crystal structure of human Survivin in complex with H3(1-10) peptide -

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Basic information

Entry
Database: PDB / ID: 3uii
Titlecrystal structure of human Survivin in complex with H3(1-10) peptide
Components
  • Baculoviral IAP repeat-containing protein 5
  • histone H3(1-10) peptide
KeywordsAPOPTOSIS/APOPTOSIS INHIBITOR / BIR domain / mitosis / T3 phosphorylated H3 binding / Smac/Diablo binding/H3 peptide / APOPTOSIS-APOPTOSIS INHIBITOR complex
Function / homology
Function and homology information


survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of exit from mitosis / positive regulation of mitotic cytokinesis / 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 exit from mitosis / positive regulation of mitotic cytokinesis / 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 / cobalt ion binding / 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 / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / SUMOylation of DNA replication proteins / mitotic cytokinesis / chromosome, centromeric region / mitotic spindle assembly / cytoplasmic microtubule / 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 / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / RHO GTPases Activate Formins / HDACs deacetylate histones / spindle microtubule / 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 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / spindle / kinetochore / PKMTs methylate histone lysines / small GTPase binding / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / Separation of Sister Chromatids / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / nucleosome / mitotic cell cycle / gene expression / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / midbody / protein-folding chaperone binding / Senescence-Associated Secretory Phenotype (SASP) / microtubule binding / Oxidative Stress Induced Senescence / Interleukin-4 and Interleukin-13 signaling / Estrogen-dependent gene expression / microtubule / cadherin binding / Amyloid fiber formation / 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 / DNA binding
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 / Histone H3/CENP-A ...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 / 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: 2.6 Å
AuthorsDu, J. / Patel, D.J.
CitationJournal: Structure / Year: 2012
Title: Structural Basis for Recognition of H3T3ph and Smac/DIABLO N-terminal Peptides by Human Survivin.
Authors: Du, J. / Kelly, A.E. / Funabiki, H. / Patel, D.J.
History
DepositionNov 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.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

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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: Baculoviral IAP repeat-containing protein 5
P: histone H3(1-10) peptide
Q: histone H3(1-10) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3756
Polymers35,2444
Non-polymers1312
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-0 kcal/mol
Surface area9390 Å2
Unit cell
Length a, b, c (Å)115.250, 71.256, 81.636
Angle α, β, γ (deg.)90.00, 128.46, 90.00
Int Tables number5
Space group name H-MC121
Detailsthe biological assembly is the same as the asymmetric unit

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Components

#1: Protein Baculoviral IAP repeat-containing protein 5 / Apoptosis inhibitor 4 / Apoptosis inhibitor survivin


Mass: 16471.787 Da / Num. of mol.: 2 / Fragment: unp residues 1-142 / Mutation: K139E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC5, API4, IAP4 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE)3RIL / References: UniProt: O15392
#2: Protein/peptide histone H3(1-10) peptide


Mass: 1150.332 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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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: 3.72 Å3/Da / Density % sol: 66.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M ammonium citrate tribasic, pH 7.0, 12% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 11, 2011
RadiationMonochromator: SI MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 16594 / Num. obs: 16412 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 10.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2 / Rsym value: 0.529 / % possible all: 96.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F3H

1f3h


Resolution: 2.6→29.272 Å / SU ML: 0.46 / σ(F): 1.34 / σ(I): 0 / Phase error: 33.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2734 811 5.11 %RANDOM
Rwork0.2217 ---
obs0.2247 15872 98.87 %-
all-16683 --
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.224 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.8234 Å20 Å216.1418 Å2
2---10.3216 Å20 Å2
3---5.4982 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 2 17 2293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132330
X-RAY DIFFRACTIONf_angle_d1.433128
X-RAY DIFFRACTIONf_dihedral_angle_d20.448898
X-RAY DIFFRACTIONf_chiral_restr0.099320
X-RAY DIFFRACTIONf_plane_restr0.008410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.76290.39561360.33092462X-RAY DIFFRACTION98
2.7629-2.9760.32011340.27732510X-RAY DIFFRACTION100
2.976-3.27520.33051330.24432522X-RAY DIFFRACTION100
3.2752-3.74820.28161110.23152562X-RAY DIFFRACTION100
3.7482-4.71920.23061550.19212499X-RAY DIFFRACTION99
4.7192-29.27370.27181420.21152506X-RAY DIFFRACTION97
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)
11.3994-0.5412-1.63670.24911.07394.27890.5555-1.75055.576-0.07511.6271-0.7593-1.8561-0.4499-0.06140.43250.2532-0.3151.0803-0.53151.808416.55345.623114.785
21.0530.4895-1.11014.9565-2.21061.1798-0.1346-0.2546-0.3560.42620.27090.34350.6104-0.0415-0.1210.55510.0109-0.02250.4781-0.06110.293724.3987-10.710211.0289
30.41530.16860.72230.4160.32961.1572-0.69712.6234-0.43780.00851.27322.2866-1.7870.0098-0.06641.2642-0.2084-0.31141.201-0.16090.799721.309-10.8228-4.5527
44.40252.0209-1.3292.06860.03351.52460.00320.5139-0.2323-1.1334-0.054-0.77690.02330.0532-0.12430.70710.1014-0.08010.4598-0.1750.393130.7832-8.33014.0248
52.7023-0.73670.60560.9914-0.66790.2596-0.2988-0.33440.3264-0.08140.6498-0.9926-0.17151.0655-0.00750.62490.0638-0.03040.8264-0.16070.733637.3842-3.09449.3567
61.4745-1.2139-0.65481.11030.3460.3336-2.4621-1.1841-2.96080.7590.69971.28861.0919-0.1889-0.02660.93090.3543-0.07361.21410.05861.153428.61311.931923.6905
70.4945-0.1401-0.5055-3.583-0.43275.23890.03670.04670.3539-0.20740.1802-0.1931-0.1977-0.2174-0.0330.98960.03320.04020.3483-0.05780.542229.13227.8047-1.0395
86.81320.1948-1.96430.35280.64583.16320.6597-0.0605-1.33490.7511-1.1328-0.28652.26180.9306-0.02390.7070.07930.0680.96280.05640.690231.21782.8101-31.8815
90.2352-0.27980.05370.6356-0.0329-0.0179-0.06690.3313-1.94222.64121.0425-1.98722.6177-0.3641-0.0671.17420.175-0.38571.0435-0.01480.628815.708914.217616.3293
101.3831.00341.26984.20411.19080.64110.31830.5489-0.1295-1.6944-0.7351-0.4538-0.22630.6688-0.05890.84160.08420.11210.62910.01170.783615.956123.01822.6671
110.0710.2131-0.16520.78190.71241.6731.47140.5814-0.5679-0.44620.37240.3672-0.46060.941-0.16920.73290.0856-0.16720.7072-0.1321.73510.634736.484126.4282
121.24831.33080.62181.7240.85111.1301-1.4297-0.52561.31560.86051.5731-0.1525-0.07480.6048-0.06740.54450.04370.08350.5289-0.21551.187515.534830.93331.7408
130.2985-0.2508-0.5041-0.2119-0.07630.39770.1852-0.85170.21011.7087-0.14123.1291-0.96180.7836-0.0280.750.1462-0.26750.6359-0.2721.52911.096230.687426.341
143.46420.6431.1792.5631-0.63082.967-0.0431-0.68450.50430.6283-0.01051.29170.0576-0.59-0.0340.42960.12290.13310.5731-0.19550.87219.74524.281436.3049
154.6149-2.12831.57151.76581.98014.4802-0.5752-1.2083-1.23030.54480.10360.19480.72190.2247-0.04280.62830.0817-0.08340.6716-0.15160.839520.598811.248428.6365
163.39720.66491.67830.3111-0.8935-1.2312-0.0594-0.51820.68320.10590.1635-0.764-0.1269-0.1227-0.02890.7166-0.06290.19910.5882-0.07890.7168-13.358912.407334.3928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:10)
2X-RAY DIFFRACTION2(chain A and resid 11:45)
3X-RAY DIFFRACTION3(chain A and resid 46:52)
4X-RAY DIFFRACTION4(chain A and resid 53:74)
5X-RAY DIFFRACTION5(chain A and resid 75:90)
6X-RAY DIFFRACTION6(chain A and resid 91:96)
7X-RAY DIFFRACTION7(chain A and resid 97:131)
8X-RAY DIFFRACTION8(chain A and resid 132:139)
9X-RAY DIFFRACTION9(chain B and resid 5:10)
10X-RAY DIFFRACTION10(chain B and resid 11:21)
11X-RAY DIFFRACTION11(chain B and resid 22:29)
12X-RAY DIFFRACTION12(chain B and resid 30:43)
13X-RAY DIFFRACTION13(chain B and resid 44:54)
14X-RAY DIFFRACTION14(chain B and resid 55:88)
15X-RAY DIFFRACTION15(chain B and resid 89:108)
16X-RAY DIFFRACTION16(chain B and resid 109:139)

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