9tph

Survivin 1-127 in complex with a molecular tweezer-Histone-H3-peptide conjugate

Method: X-RAY DIFFRACTION D_max: 81.1 Å Quality: REASONABLE

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Baculoviral IAP repeat-containing protein 5

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–127 Chain B； UniProt 2–127	Not recorded	Histone-H3-peptide conjugated to molecular tweezer × 2 ZN ZINC ION × 2 CA CALCIUM ION × 3 A1JXR Molecular tweezer (BIRC5) × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.1M imidazole pH 8.0, 0.05M Ca-acetate, 35% v/v 2-ethoxyethanol	Resolution 2.00 Å R-free 0.263

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9TPH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1E31 SURVIVIN DIMER H. SAPIENS Deposited 2000-06-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–142（142 aa） Chain B 1–142（142 aa）	Not recorded	ZN ZINC ION × 2 CO COBALT (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；3 % PEG MME 2K, 2 MM HEXAMINE COBALT, 100 MM HEPES PH 7.1	Resolution 2.71 Å R-free 0.270
1F3H X-RAY CRYSTAL STRUCTURE OF THE HUMAN ANTI-APOPTOTIC PROTEIN SURVIVIN Deposited 2000-06-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–142（142 aa） Chain B 1–142（142 aa）	Mutation：L54M Mutation：L54M	ZN ZINC ION × 2 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 8000, LITHIUMSULPHATE, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.58 Å R-free 0.287
1XOX SOLUTION STRUCTURE OF HUMAN SURVIVIN Deposited 2004-10-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–117（117 aa） Fragment：residues 1-117 Chain B 1–117（117 aa） Fragment：residues 1-117	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 50 mM phosphate；Pressure ambient	Resolution not provided
2QFA Crystal structure of a Survivin-Borealin-INCENP core complex Deposited 2007-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–142（142 aa）	Not recorded	ZN ZINC ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；50mM MES pH6, 10% PEG3350, VAPOR DIFFUSION, temperature 293K	Resolution 1.40 Å R-free 0.202
2RAW Crystal structure of the Borealin-Survivin complex Deposited 2007-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–142（142 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.5 ul protein and 0.5 ul well solution (0.1 M Na HEPES, pH 7.5; 0.2 M CaCl2; 28% (w/v) PEG 400), VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.40 Å R-free 0.298
2RAX Crystal structure of Borealin (20-78) bound to Survivin (1-120) Deposited 2007-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–120（120 aa） Fragment：residues 1-120	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.5 ul protein plus 0.5 uL well solution consisting of 0.1 M HEPES, pH 7.5; 10% (w/v) PEG 8000; 8 % (v/v) ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.30 Å R-free 0.284
2RAX Crystal structure of Borealin (20-78) bound to Survivin (1-120) Deposited 2007-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–120（120 aa） Fragment：residues 1-120	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.5 ul protein plus 0.5 uL well solution consisting of 0.1 M HEPES, pH 7.5; 10% (w/v) PEG 8000; 8 % (v/v) ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.30 Å R-free 0.284
2RAX Crystal structure of Borealin (20-78) bound to Survivin (1-120) Deposited 2007-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 1–120（120 aa） Fragment：residues 1-120	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.5 ul protein plus 0.5 uL well solution consisting of 0.1 M HEPES, pH 7.5; 10% (w/v) PEG 8000; 8 % (v/v) ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.30 Å R-free 0.284
3UEC Crystal structure of human Survivin bound to histone H3 phosphorylated on threonine-3. Deposited 2011-10-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–142（142 aa）	Mutation：E129K	ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 4 PG4 TETRAETHYLENE GLYCOL × 2 1PE PENTAETHYLENE GLYCOL × 2 ACT ACETATE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；12% peg 8000; O.1 M MOPS 7.5; 0.1 M Magnesium acetate tetrahydrate , VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.18 Å R-free 0.215
3UED Crystal structure of human Survivin bound to histone H3 phosphorylated on threonine-3 (C2 space group). Deposited 2011-10-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–142（142 aa） Chain C 1–142（142 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；15% PEG 3350, 0.16 M sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.70 Å R-free 0.241
3UEE Crystal structure of human Survivin K62A mutant bound to N-terminal histone H3 Deposited 2011-10-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–142（142 aa） Chain C 1–142（142 aa）	Mutation：K62A, E129K Mutation：K62A, E129K	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；12% PEG 3350, 0.12 M succinic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.61 Å R-free 0.237
3UEF Crystal structure of human Survivin bound to histone H3 (C2 space group). Deposited 2011-10-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–142（142 aa） Chain C 1–142（142 aa）	Not recorded	ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；12% PEG 3350, 0.2 M potassium/sodium tartate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.45 Å R-free 0.214
3UEG Crystal structure of human Survivin K62A mutant Deposited 2011-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–142（142 aa） Chain B 1–142（142 aa）	Mutation：E129K, K62A Mutation：E129K, K62A	ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M HEPES-Na, 20% PEG 3350, 0.18 M AMMONIUM SULFATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.80 Å R-free 0.239
3UEH Crystal structure of human Survivin H80A mutant Deposited 2011-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–142（142 aa） Chain B 1–142（142 aa）	Mutation：E129K, K62A Mutation：E129K, K62A	ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；20% PEG 3350, 0.2 M SODIUM FORMATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.60 Å R-free 0.224
3UEI Crystal structure of human Survivin E65A mutant Deposited 2011-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–142（142 aa） Chain B 1–142（142 aa）	Mutation：E129K, K62A Mutation：E129K, K62A	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；5% Tacsimate, 0.1 M HEPES-Na, 12% PEG monomethyl eter, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.70 Å R-free 0.228
3UIG crystal structure of human Survivin in complex with T3 phosphorylated H3(1-15) peptide Deposited 2011-11-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–142（142 aa） Fragment：unp residues 1-142 Chain B 1–142（142 aa） Fragment：unp residues 1-142	Mutation：K139E Mutation：K139E	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M DL-malic acid, pH 7.0, 12% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.250
3UIH crystal structure of human Survivin in complex with Smac/DIABLO(1-15) peptide Deposited 2011-11-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–142（142 aa） Fragment：unp residues 1-142 Chain B 1–142（142 aa） Fragment：unp residues 1-142	Mutation：K139E Mutation：K139E	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.2 M potassium thiocyanate, 10% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.245
3UII crystal structure of human Survivin in complex with H3(1-10) peptide Deposited 2011-11-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–142（142 aa） Fragment：unp residues 1-142 Chain B 1–142（142 aa） Fragment：unp residues 1-142	Mutation：K139E Mutation：K139E	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M ammonium citrate tribasic, pH 7.0, 12% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.273
3UIJ Crystal structure of human Survivin K62Y/H80W mutant in complex with Smac/DIABLO(1-15) peptide Deposited 2011-11-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–142（142 aa） Fragment：unp residues 1-142 Chain B 1–142（142 aa） Fragment：unp residues 1-142	Mutation：K62Y, H80W, K139E Mutation：K62Y, H80W, K139E	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.2 M sodium bromide, 12% PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.71 Å R-free 0.242
3UIK crystal structure of human Survivin mutant K62Y/H80W in complex with H3(1-10) peptide Deposited 2011-11-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–142（142 aa） Fragment：unp residues 1-142 Chain B 1–142（142 aa） Fragment：unp residues 1-142	Mutation：K62Y, H80W, K139E Mutation：K62Y, H80W, K139E	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.2 M succinic acid, pH 7.0, 12% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.281
4A0I Crystal structure of Survivin bound to the N-terminal tail of hSgo1 Deposited 2011-09-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–142（142 aa） Chain B 1–142（142 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；100MM TRIS PH 8, 200MM NACL, 20% PEG 6000	Resolution 2.60 Å R-free 0.252
4A0J Crystal structure of Survivin bound to the phosphorylated N-terminal tail of histone H3 Deposited 2011-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–142（142 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.1 M MES PH 6.0, 18% PEG 4000.	Resolution 2.80 Å R-free 0.268
4A0J Crystal structure of Survivin bound to the phosphorylated N-terminal tail of histone H3 Deposited 2011-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–142（142 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.1 M MES PH 6.0, 18% PEG 4000.	Resolution 2.80 Å R-free 0.268
4A0N Crystal structure of Survivin bound to the phosphorylated N-terminal tail of histone H3 Deposited 2011-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–142（142 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1 M TRIS PH 8.5, 0.2 M LISO4, 40% PEG 400.	Resolution 2.74 Å R-free 0.260
6SHO SAD structure of Human Survivin recovered by continuous rotation data collection and multivariate analysis of Friedel pairs Deposited 2019-08-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–142（142 aa） Chain B 1–142（142 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；0.2 M NaCitrate pH 6.5, 0.1 M BisTris Propane and 20% PEG3500	Resolution 3.20 Å R-free 0.259
6YIE Structure of a Borealin-INCENP-Survivin complex Deposited 2020-04-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–142（142 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；5 % (w/v) PEG 3,350, 50 mM MES pH 6.0	Resolution 3.49 Å R-free 0.324
6YIE Structure of a Borealin-INCENP-Survivin complex Deposited 2020-04-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–142（142 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；5 % (w/v) PEG 3,350, 50 mM MES pH 6.0	Resolution 3.49 Å R-free 0.324
6YIF Structure of Chromosomal Passenger Complex (CPC) bound to phosphorylated Histone 3 peptide at 1.8 A. Deposited 2020-04-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–142（142 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；20 % (w/v) PEG 4,000, 200 mM Lithium sulphate, 50 mM MES pH 6.5	Resolution 1.81 Å R-free 0.223
6YIH Structure of Chromosomal Passenger Complex (CPC) bound to phosphorylated Histone 3 peptide at 2.6 A. Deposited 2020-04-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–142（142 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；20 % (w/v) PEG 4,000, 100 mM HEPES pH 7.0, 150 mM ammonium sulphate	Resolution 2.55 Å R-free 0.259
7LBK Crystal structure of human Survivin bound to histone H3 T3phK4me3 peptide Deposited 2021-01-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–142（142 aa） Chain B 1–142（142 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；The crystal was obtained by mixing 1 uL of protein at 10 mg/mL with 1 uL of mother liquor composed of 0.16 M potassium/sodium tartrate, 14% PEG 3350.	Resolution 2.70 Å R-free 0.253
7LBO Crystal structure of human Survivin bound to histone H3 T3phK4me1 peptide Deposited 2021-01-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–142（142 aa） Chain B 1–142（142 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；1 uL of protein at 10 mg/mL was mixed with 1 uL of buffer composed of 0.16 M potassium/sodium tartrate, 12% PEG 3350	Resolution 2.50 Å R-free 0.261
7LBP Crystal structure of human Survivin bound to histone H3T3phK4ac peptide Deposited 2021-01-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–142（142 aa） Chain C 1–142（142 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；1 uL of protein at 10mg/mL was mixed with 1 uL of buffer composed of 0.16 M potassium/sodium tartrate, 12% PEG 3350	Resolution 2.60 Å R-free 0.247
7LBQ Crystal structure of human Survivin bound to histone H3 T3phK4me2 peptide Deposited 2021-01-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–142（142 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；1 uL of protein was mixed with 1uL of buffer composed of 2.25 mM spermine, 9 mM MgCl2, 0.9 mM spermidine, 1.8 mM cobalt (III)hexamine chloride, 0.05 sodium cacodylate pH 7.0, 5% PEG 400	Resolution 2.69 Å R-free 0.268
8RUP Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome Deposited 2024-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric	Chain K 1–142（142 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM TRIS-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, 0.3% n-octyl-beta-D-glucoside cryo-EM vitrification conditions Cryogen ETHANE；3 s blotting time, -10 force, no wait time.	Resolution 2.42 Å
9SI3 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome Deposited 2025-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain M 1–142（142 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.83 Å
9SI9 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Class0) Deposited 2025-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain M 1–142（142 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.86 Å
9SJ5 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Class1) Deposited 2025-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain M 1–142（142 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.85 Å
9SLJ Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Double Occupancy) Deposited 2025-09-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric	Chain M 1–142（142 aa） Chain P 1–142（142 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9TPI Survivin 1-122 in complex with a molecular tweezer-Histone-H3-peptide conjugate Deposited 2025-12-18	Different construct Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–122（121 aa） Chain B 2–122（121 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3 A1JXR Molecular tweezer (BIRC5) × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.1M imidazole pH 8.0, 0.05M Ca-acetate, 35% v/v 2-ethoxyethanol	Resolution 1.80 Å R-free 0.235

35 other PDB entries and 39 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BIRC5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–126； UniProt 2–127 Author chain B； PDBConstruct 1–126； UniProt 2–127

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9tph
Deposition date deposition_date	2025-12-18
最后修订 last_revision	2026-04-15
Structure title title	Survivin 1-127 in complex with a molecular tweezer-Histone-H3-peptide conjugate
Keywords keywords	;protein-protein interactions, supramolecular ligands, molecular tweezers, peptide binding, BIR domain, zinc finger, chromosomal passenger complex, cell cycle, mitosis, apoptosis ;; CELL CYCLE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	22.72 Å
Radius of gyration Rg (electron density) rg_electron	22.56 Å
Forward intensity I(0) i0	32156100.00
Molecular weight molecular_weight	29251.0 kDa
Excluded volume excluded_volume	28372 Å³
Envelope volume envelope_volume	49502 Å³
Hydration-shell volume shell_volume	19537 Å³
Envelope diameter envelope_diameter	82.5 Å
Shell Rg shell_rg	28.15 Å
Envelope Rg envelope_rg	23.07 Å
Shape Rg shape_rg	22.68 Å
Total Rg total_rg	22.95 Å
Total atoms total_atoms	2193
Residues n_residues	248
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	81.1 Å
Rg (real space) rg_real	22.90 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	3.2160e+07
I(0) uncertainty (real space) i0_real_error	4.4390e+05
Rg (reciprocal space) rg_reciprocal	22.86 Å
I(0) (reciprocal space) i0_reciprocal	32160000.0000
Solution quality estimate total_estimate	0.6432
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.1 Å
Skewness Skewness skewness	0.602
Kurtosis Kurtosis kurtosis	-0.028
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8733000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.654; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.778; Smooth: 0.891

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Baculoviral IAP repeat-containing protein 5
Molecular weight formula_weight	14597.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2282

GAPTLPPAWQPFLKDHRISTFKNWPFLEGCACTPERMAEAGFIHCPTENEPDLAQCFFCFKELEGWEPDDDPIEEHKKHSSGCAFLSVKKQFEELTLGEFLKLDRERAKNKIAKETNNKKKEFEET

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Histone-H3-peptide conjugated to molecular tweezer
Molecular weight formula_weight	653.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

ARTKXX

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	Molecular tweezer (BIRC5)
Molecular weight formula_weight	821.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	71

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8. Citations (1)

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Unit-cell length a length_a	101.549 Å
Unit-cell length b length_b	64.091 Å
Unit-cell length c length_c	75.872 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	141.42 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	49.970 Å
R factor r_factor	0.2163
R_work r_work	0.2139
R_free r_free	0.2629

fit	/app/data/saxs_computation/tp/9tph/9tph.fit
pddf	/app/data/pr_computation/tp/9tph/9tph.pr.out
profile	/app/data/saxs_computation/tp/9tph/9tph.dat

Survivin 1-127 in complex with a molecular tweezer-Histone-H3-peptide conjugate

1. Protein Identity and Related Structures Protein Identity & Related Structures

Baculoviral IAP repeat-containing protein 5

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)