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- PDB-3uig: crystal structure of human Survivin in complex with T3 phosphoryl... -

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Basic information

Entry
Database: PDB / ID: 3uig
Titlecrystal structure of human Survivin in complex with T3 phosphorylated H3(1-15) peptide
Components
  • Baculoviral IAP repeat-containing protein 5
  • T3 phosphorylated H3(1-15) peptide
KeywordsAPOPTOSIS/APOPTOSIS INHIBITOR / BIR domain / mitosis / T3 phosphorylated H3 binding / Smac/Diablo binding / Phosphorylation / 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 / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule / 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 / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / 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 / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / kinetochore / spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / small GTPase binding / 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 / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / gene expression / 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 / 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
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: 2.4 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 1.1Dec 12, 2012Group: Other
Revision 1.2Apr 24, 2013Group: Other
Revision 1.3Sep 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
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_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.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

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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: T3 phosphorylated H3(1-15) peptide
Q: T3 phosphorylated H3(1-15) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3666
Polymers36,2354
Non-polymers1312
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-16 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.778, 71.042, 82.287
Angle α, β, γ (deg.)90.00, 128.81, 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(DE3)RIL / References: UniProt: O15392
#2: Protein/peptide T3 phosphorylated H3(1-15) peptide


Mass: 1645.777 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.: 22 / 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: 3.64 Å3/Da / Density % sol: 66.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M DL-malic acid, 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-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2010
RadiationMonochromator: SI MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 20678 / Num. obs: 20244 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 17.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2 / Rsym value: 0.527 / % possible all: 86.9

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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: 2.4→31.072 Å / SU ML: 0.44 / σ(F): 1.34 / σ(I): 0 / Phase error: 34.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2501 1021 5.09 %RANDOM
Rwork0.2132 ---
obs0.2151 20063 97.94 %-
all-20484 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.478 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.852 Å20 Å218.7977 Å2
2---15.705 Å20 Å2
3---5.853 Å2
Refinement stepCycle: LAST / Resolution: 2.4→31.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 2 22 2329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012361
X-RAY DIFFRACTIONf_angle_d1.2243173
X-RAY DIFFRACTIONf_dihedral_angle_d19.449911
X-RAY DIFFRACTIONf_chiral_restr0.079323
X-RAY DIFFRACTIONf_plane_restr0.007415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.52650.48781350.40522482X-RAY DIFFRACTION90
2.5265-2.68470.38411200.34992734X-RAY DIFFRACTION99
2.6847-2.89180.32411350.26692765X-RAY DIFFRACTION100
2.8918-3.18260.31651410.26142770X-RAY DIFFRACTION100
3.1826-3.64250.30721790.24382743X-RAY DIFFRACTION100
3.6425-4.58680.20551470.1762802X-RAY DIFFRACTION100
4.5868-31.07430.20711640.18282746X-RAY DIFFRACTION98
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)
10.5611-0.0916-0.24451.2799-0.25740.4049-0.01810.19531.8499-0.58270.7239-3.06321.0850.4427-0.12270.57230.0451-0.00590.8356-0.15910.66416.31294.280914.9251
20.41930.0288-0.14060.4959-0.36150.31950.0242-0.446-0.24830.91370.04431.09910.13370.1453-0.0860.65280.00970.04190.6177-0.07840.616321.0606-6.380512.7658
30.63560.3203-1.24580.4456-0.35120.7756-0.4005-0.4266-0.4280.2710.3714-0.00630.66280.0772-0.07330.76710.05680.00660.5944-0.07730.573227.0173-15.344410.4177
42.33380.1995-0.69230.9424-1.08971.073-0.28690.6797-0.3245-1.20370.4702-0.3284-0.17990.5258-0.0680.90270.0609-0.03560.6488-0.10740.552825.7905-6.66880.8891
52.2070.3539-0.91470.9246-1.39571.5535-0.00290.432-0.5674-0.5160.3798-1.18120.46160.4819-0.0610.60520.1483-0.00960.5576-0.15280.633535.9293-8.42517.7206
63.793-1.855-0.4040.88290.44381.2871-0.16280.01690.4062-0.6520.3219-0.57210.5143-0.07-0.12090.56970.0553-0.00050.4055-0.1240.587328.90616.746514.4084
70.96110.4915-0.25650.34060.22251.1961-0.2454-0.4126-0.0351-0.28280.7099-0.8737-0.0334-1.2728-0.15640.956-0.03420.07110.69150.0160.77229.49086.1288-8.0633
81.5072-0.6595-0.49980.11150.13471.39590.16220.2221-0.36730.5980.1602-0.53810.17741.0816-0.10520.5576-0.01410.03180.66850.04480.583130.72173.2146-25.4116
90.55680.1737-0.10610.20550.12560.27920.00130.26660.51230.7612-0.3582-1.7151.3319-0.7251-0.14550.91470.1090.090.9436-0.03920.618615.36614.181216.9979
100.4730.25750.53850.2972-0.06620.36610.08730.4093-0.0091-1.9478-0.1789-0.74540.47880.65-0.16720.72320.05120.03370.62730.03170.732514.134725.214522.7636
110.5050.18990.32770.5615-0.13960.6721-1.892-0.82913.19120.78891.36420.6267-1.03090.7667-0.17650.9023-0.00680.00860.5496-0.15441.956914.441633.836430.4106
120.70340.90281.10341.08780.80511.363-0.0408-0.32610.19710.7036-0.60382.2008-0.4096-0.3138-0.16850.48090.09650.0440.6553-0.32981.31044.807125.990929.8801
131.27830.52420.95730.13980.47750.5527-0.2881-1.39931.72311.63811.05670.2374-0.1705-0.0089-0.16230.9994-0.08450.28440.7747-0.28140.988812.611223.755938.8572
140.79350.1725-0.25820.13040.0890.2571-0.5978-0.79512.32180.72631.0475-0.6756-0.64520.8099-0.12320.92450.0858-0.21290.9261-0.38750.899925.408515.910328.961
150.7759-0.1998-0.34311.17311.60781.1443-0.4779-0.3675-0.5151.10820.26060.62390.8789-0.0294-0.12380.8131-0.02970.10390.614-0.09060.928911.01168.730929.4701
161.52570.31750.02590.58990.2071.73640.0325-1.37251.1672-0.2880.1631-1.0681-0.36090.4225-0.1690.8721-0.11310.24060.6296-0.06570.7613-20.817112.636436.2018
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:11)
2X-RAY DIFFRACTION2(chain A and resid 12:23)
3X-RAY DIFFRACTION3(chain A and resid 24:43)
4X-RAY DIFFRACTION4(chain A and resid 44:65)
5X-RAY DIFFRACTION5(chain A and resid 66:89)
6X-RAY DIFFRACTION6(chain A and resid 90:115)
7X-RAY DIFFRACTION7(chain A and resid 116:122)
8X-RAY DIFFRACTION8(chain A and resid 123:139)
9X-RAY DIFFRACTION9(chain B and resid 5:11)
10X-RAY DIFFRACTION10(chain B and resid 12:24)
11X-RAY DIFFRACTION11(chain B and resid 25:40)
12X-RAY DIFFRACTION12(chain B and resid 41:68)
13X-RAY DIFFRACTION13(chain B and resid 69:89)
14X-RAY DIFFRACTION14(chain B and resid 90:95)
15X-RAY DIFFRACTION15(chain B and resid 96:118)
16X-RAY DIFFRACTION16(chain B and resid 119:140)

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