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- PDB-1f3h: X-RAY CRYSTAL STRUCTURE OF THE HUMAN ANTI-APOPTOTIC PROTEIN SURVIVIN -

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Basic information

Entry
Database: PDB / ID: 1f3h
TitleX-RAY CRYSTAL STRUCTURE OF THE HUMAN ANTI-APOPTOTIC PROTEIN SURVIVIN
ComponentsSURVIVIN
KeywordsAPOPTOSIS / APOPTOSIS INHIBITOR SURVIVIN / THIOL PROTEASE INHIBITOR / ALPHA-BETA
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 / interphase microtubule organizing center / chromosome passenger complex ...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 / interphase microtubule organizing center / chromosome passenger complex / protein-containing complex localization / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cobalt ion binding / 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 / 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 / positive regulation of mitotic cell cycle / Resolution of Sister Chromatid Cohesion / mitotic spindle organization / spindle microtubule / chromosome segregation / RHO GTPases Activate Formins / sensory perception of sound / kinetochore / small GTPase binding / G2/M transition of mitotic cell cycle / Separation of Sister Chromatids / mitotic cell cycle / protein-folding chaperone binding / Neddylation / microtubule cytoskeleton / midbody / Interleukin-4 and Interleukin-13 signaling / microtubule binding / microtubule / 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 / zinc ion binding / nucleoplasm / metal ion binding / identical protein binding / nucleus / 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 / Resolution: 2.58 Å
AuthorsVerdecia, M.A. / Huang, H. / Dutil, E. / Hunter, T. / Noel, J.P.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structure of the human anti-apoptotic protein survivin reveals a dimeric arrangement.
Authors: Verdecia, M.A. / Huang, H. / Dutil, E. / Kaiser, D.A. / Hunter, T. / Noel, J.P.
History
DepositionJun 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_sheet / 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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SURVIVIN
B: SURVIVIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2857
Polymers32,8662
Non-polymers4195
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-40 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.040, 71.450, 86.630
Angle α, β, γ (deg.)90.00, 133.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SURVIVIN / APOPTOSIS INHIBITOR 4


Mass: 16432.773 Da / Num. of mol.: 2 / Mutation: L54M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHIS8-3 / Production host: Escherichia coli (E. coli) / References: UniProt: O15392
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.9 Å3/Da / Density % sol: 68.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, LITHIUMSULPHATE, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
2100 mMsodium-HEPES1reservoirpH7.5
36-8 %PEG80001reservoir
4200 mM1reservoirLi2SO4
52 mMdithiothreitol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL9-211.283
SYNCHROTRONSSRL BL9-221.2826
SYNCHROTRONSSRL BL9-231.1271
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 14, 2000
2
3
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.2831
21.28261
31.12711
ReflectionResolution: 2.58→54.12 Å / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 60.5 Å2
Reflection shellResolution: 2.58→2.64 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.388 / % possible all: 95.5
Reflection
*PLUS
Num. obs: 15366 / % possible obs: 95.5 % / Num. measured all: 29469 / Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 92 % / Rmerge(I) obs: 0.349

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
RefinementResolution: 2.58→54.12 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1711716.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.287 774 5 %RANDOM
Rwork0.228 ---
all0.228 29469 --
obs0.228 15494 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.36 Å2 / ksol: 0.3262 e/Å3
Displacement parametersBiso mean: 83.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.14 Å20 Å214.19 Å2
2---16.88 Å20 Å2
3---20.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.58→54.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2213 0 17 90 2320
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.025
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.65
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it17.661.5
X-RAY DIFFRACTIONc_mcangle_it19.332
X-RAY DIFFRACTIONc_scbond_it20.982
X-RAY DIFFRACTIONc_scangle_it24.472.5
LS refinement shellResolution: 2.58→2.74 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.448 115 4.7 %
Rwork0.406 2324 -
obs--92.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 83.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.65
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.448 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.406

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