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- PDB-3uij: Crystal structure of human Survivin K62Y/H80W mutant in complex w... -

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Basic information

Entry
Database: PDB / ID: 3uij
TitleCrystal structure of human Survivin K62Y/H80W mutant in complex with Smac/DIABLO(1-15) peptide
Components
  • Baculoviral IAP repeat-containing protein 5
  • Diablo homolog, mitochondrial
KeywordsAPOPTOSIS/APOPTOSIS INHIBITOR / BIR domain / mitosis / T3 phosphorylated H3 binding / Smac/Diablo binding / 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 / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / interphase microtubule organizing center ...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 / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / interphase microtubule organizing center / Release of apoptotic factors from the mitochondria / CD40 receptor complex / protein-containing complex localization / chromosome passenger complex / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cobalt ion binding / intrinsic apoptotic signaling pathway in response to oxidative stress / 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 / extrinsic apoptotic signaling pathway via death domain receptors / mitotic spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / centriole / positive regulation of mitotic cell cycle / tubulin binding / intrinsic apoptotic signaling pathway / RHO GTPases Activate Formins / spindle microtubule / sensory perception of sound / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / mitochondrial intermembrane space / cytoplasmic side of plasma membrane / kinetochore / spindle / small GTPase binding / Separation of Sister Chromatids / activation of cysteine-type endopeptidase activity involved in apoptotic process / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / mitotic cell cycle / Neddylation / midbody / protein-folding chaperone binding / microtubule binding / neuron apoptotic process / Interleukin-4 and Interleukin-13 signaling / microtubule / positive regulation of apoptotic process / 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 / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Smac/DIABLO-like superfamily / Smac/DIABLO protein / Second Mitochondria-derived Activator of Caspases / 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 / Diablo IAP-binding mitochondrial protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.705 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
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

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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: Diablo homolog, mitochondrial
Q: Diablo homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3446
Polymers36,2134
Non-polymers1312
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-17 kcal/mol
Surface area17410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.358, 70.965, 82.348
Angle α, β, γ (deg.)90.00, 129.16, 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: 16553.844 Da / Num. of mol.: 2 / Fragment: unp residues 1-142 / Mutation: K62Y, H80W, 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 Diablo homolog, mitochondrial / / Direct IAP-binding protein with low pI / Second mitochondria-derived activator of caspase / Smac


Mass: 1552.727 Da / Num. of mol.: 2 / Fragment: unp residues 1-15 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NR28
#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.: 15 / 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: 3.58 Å3/Da / Density % sol: 65.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M sodium bromide, 12% PEG 3350, pH 7, 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: Jun 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: 2.7→50 Å / Num. all: 14031 / Num. obs: 13947 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 23.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.512 / % possible all: 97.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F3H

1f3h


Resolution: 2.705→35.483 Å / SU ML: 0.73 / σ(F): 1.35 / Phase error: 29.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2417 690 4.95 %
Rwork0.2049 --
obs0.2066 13932 98.99 %
all-14622 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.178 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.0345 Å20 Å217.1109 Å2
2---13.9572 Å20 Å2
3---3.0046 Å2
Refinement stepCycle: LAST / Resolution: 2.705→35.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 2 15 2297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042342
X-RAY DIFFRACTIONf_angle_d0.7283157
X-RAY DIFFRACTIONf_dihedral_angle_d15.942887
X-RAY DIFFRACTIONf_chiral_restr0.051322
X-RAY DIFFRACTIONf_plane_restr0.003413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7051-2.91390.39321270.33282562X-RAY DIFFRACTION97
2.9139-3.2070.33151440.25882663X-RAY DIFFRACTION100
3.207-3.67060.30241340.23332655X-RAY DIFFRACTION100
3.6706-4.6230.19661610.1722643X-RAY DIFFRACTION100
4.623-35.48550.20661240.18492719X-RAY DIFFRACTION99
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)
17.74191.38670.19648.8124-1.2623.8931-0.1446-0.059-0.31260.79730.0383-0.0590.06070.04020.11980.5351-0.0481-0.0670.49870.02970.423-27.3926-7.3894-9.0625
20.43880.6503-1.1234-0.3855-0.01533.1324-0.0749-0.07490.2445-0.2073-0.10270.21420.7869-0.01640.11310.7668-0.00330.05770.48640.00210.7007-29.51076.01847.6473
34.24853.077-3.12124.2714-0.09334.45761.083-1.52361.59962.5707-0.4128-0.14031.6874-0.9385-0.44590.998-0.2557-0.0721.0147-0.17830.7966-14.631914.9737-19.704
40.99551.3768-1.84873.371-3.9745.41320.0228-0.29653.11391.73920.0436-1.6108-1.6385-0.01140.14130.9444-0.02750.04570.5906-0.07161.8888-12.512631.9099-25.9894
56.2987-0.36361.69627.8565-2.84888.0177-0.22970.47551.0671-0.53820.01-1.4896-0.42030.591-0.13310.464-0.02260.0320.66520.19471.1305-10.514323.8877-32.8223
63.31280.1941-0.1485-1.8656-0.6259-0.4227-0.00770.6150.0226-0.3659-0.0193-0.0101-0.1615-0.061-0.05570.816-0.00010.12340.62490.00941.08726.234410.5249-32.9435
79.9154-5.2654-6.65987.3381-0.9118.83031.09360.50121.00691.3744-0.1072-1.3099-0.603-0.9256-0.63351.3386-0.07310.07050.9366-0.130.7099-33.2564-9.94953.5598
80.8198-0.05090.18820.2376-0.00720.0417-1.0272-1.1199-1.78520.54770.80350.02631.4430.0307-0.15931.85660.35190.95850.99050.68391.4877-0.681627.8864-38.3345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:97)
2X-RAY DIFFRACTION2chain 'A' and (resseq 98:140)
3X-RAY DIFFRACTION3chain 'B' and (resseq 6:14)
4X-RAY DIFFRACTION4chain 'B' and (resseq 15:34)
5X-RAY DIFFRACTION5chain 'B' and (resseq 35:97)
6X-RAY DIFFRACTION6chain 'B' and (resseq 98:140)
7X-RAY DIFFRACTION7chain 'P'
8X-RAY DIFFRACTION8chain 'Q'

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