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- PDB-3uih: crystal structure of human Survivin in complex with Smac/DIABLO(1... -

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Basic information

Entry
Database: PDB / ID: 3uih
Titlecrystal structure of human Survivin 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 / : / 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 / Release of apoptotic factors from the mitochondria / interphase microtubule organizing center ...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 / Release of apoptotic factors from the mitochondria / interphase microtubule organizing center / CD40 receptor complex / chromosome passenger complex / protein-containing complex localization / SMAC, XIAP-regulated apoptotic response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / 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 / 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 / extrinsic apoptotic signaling pathway via death domain receptors / chromosome, centromeric region / mitotic spindle assembly / cysteine-type endopeptidase inhibitor activity / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / centriole / tubulin binding / intrinsic apoptotic signaling pathway / positive regulation of mitotic cell cycle / Resolution of Sister Chromatid Cohesion / mitotic spindle organization / spindle microtubule / chromosome segregation / apoptotic signaling pathway / RHO GTPases Activate Formins / sensory perception of sound / kinetochore / mitochondrial intermembrane space / small GTPase binding / G2/M transition of mitotic cell cycle / cytoplasmic side of plasma membrane / Separation of Sister Chromatids / mitotic cell cycle / protein-folding chaperone binding / Neddylation / microtubule cytoskeleton / neuron apoptotic process / midbody / Interleukin-4 and Interleukin-13 signaling / microtubule binding / microtubule / positive regulation of apoptotic process / protein heterodimerization activity / cell division / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / apoptotic process / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
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 ...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: 2.4 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 1.1Sep 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: Diablo homolog, mitochondrial
Q: Diablo homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1806
Polymers36,0494
Non-polymers1312
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-15 kcal/mol
Surface area17220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.246, 71.308, 81.095
Angle α, β, γ (deg.)90.00, 127.49, 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: 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 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


Mass: 18.015 Da / Num. of mol.: 23 / 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: 66.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M potassium thiocyanate, 10% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.29 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2011
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.29 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 20506 / Num. obs: 20178 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 22.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.595 / % possible all: 90

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F3H

1f3h


Resolution: 2.4→27.821 Å / SU ML: 0.3 / σ(F): 1.35 / σ(I): 0 / Phase error: 27.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 1027 5.12 %RANDOM
Rwork0.2093 ---
obs0.211 20056 98.67 %-
all-21083 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.273 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.8294 Å20 Å213.2378 Å2
2---12.0948 Å20 Å2
3---5.2654 Å2
Refinement stepCycle: LAST / Resolution: 2.4→27.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 2 23 2292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052325
X-RAY DIFFRACTIONf_angle_d0.8173128
X-RAY DIFFRACTIONf_dihedral_angle_d17.668890
X-RAY DIFFRACTIONf_chiral_restr0.061322
X-RAY DIFFRACTIONf_plane_restr0.007411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.52650.34171480.32332559X-RAY DIFFRACTION94
2.5265-2.68460.30421350.28912737X-RAY DIFFRACTION100
2.6846-2.89170.31621610.25762707X-RAY DIFFRACTION100
2.8917-3.18240.28271320.23892782X-RAY DIFFRACTION100
3.1824-3.6420.27191570.22832734X-RAY DIFFRACTION100
3.642-4.58520.21021570.17892761X-RAY DIFFRACTION100
4.5852-27.82330.2251370.19252749X-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)
13.4161-2.9821.76664.442-0.55263.6144-0.33780.643-0.2995-0.1580.2925-0.75850.34390.0137-0.00870.5308-0.043-0.00740.62130.05660.5401-23.1494-8.9011-12.0707
23.15360.79570.1693.16320.23521.25070.1301-0.5517-0.36991.17180.01990.26590.118-0.3657-0.0850.8389-0.0905-0.02320.65960.13390.514-30.9019-7.6057-4.511
32.77670.2682-1.29680.77160.78472.0376-0.23460.43250.62010.39670.29090.25210.8161-0.5884-0.06520.6026-0.1257-0.15050.62780.15140.7443-29.58987.0063-16.8814
4-0.95620.5020.66680.6274-1.70532.44840.2276-0.0369-0.2352-0.53910.18120.00670.71230.5905-0.20110.81040.05890.05710.6072-0.03310.7164-29.04695.491112.4459
51.03360.269-1.07942.58131.36562.5360.5938-0.4026-2.26840.365-0.48681.58023.93080.0190.0460.6743-0.09130.07170.75460.00040.7869-30.00482.057434.1038
67.0117-4.4187-5.27346.4267-1.02919.53740.62940.82631.63810.54090.6833-1.37322.46850.63630.11161.1647-0.2278-0.36970.73330.01430.6555-15.952514.9199-17.4328
73.2631-0.22880.4441.8523-0.62122.9086-0.5750.20861.3890.79060.7034-0.751-1.1173-0.78470.04620.65290.0507-0.09540.54190.05061.028-14.664730.2507-27.4113
82.5732-1.97720.72044.8964-1.50771.9526-0.14120.70380.9507-0.5474-0.1127-2.3397-0.30050.68830.30340.5434-0.09110.1430.68770.24481.2003-8.638224.9155-34.2584
90.90840.7513-1.36840.31430.19782.1417-0.06320.0689-0.1166-0.47610.2612-0.29950.2485-0.0863-0.11620.55810.04550.02020.55070.19691.05-12.22810.775-29.5164
104.53832.01370.05062.285-1.31112.50780.10280.97431.8249-0.15110.16311.1049-0.5521-0.1516-0.21830.7161-0.03560.18030.5230.01850.767822.713312.8797-37.0357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:40)
2X-RAY DIFFRACTION2(chain A and resid 41:89)
3X-RAY DIFFRACTION3(chain A and resid 90:110)
4X-RAY DIFFRACTION4(chain A and resid 111:132)
5X-RAY DIFFRACTION5(chain A and resid 133:140)
6X-RAY DIFFRACTION6(chain B and resid 6:11)
7X-RAY DIFFRACTION7(chain B and resid 12:40)
8X-RAY DIFFRACTION8(chain B and resid 41:89)
9X-RAY DIFFRACTION9(chain B and resid 90:122)
10X-RAY DIFFRACTION10(chain B and resid 123:140)

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