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- PDB-4a0i: Crystal structure of Survivin bound to the N-terminal tail of hSgo1 -

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Basic information

Entry
Database: PDB / ID: 4a0i
TitleCrystal structure of Survivin bound to the N-terminal tail of hSgo1
Components
  • BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5
  • SHUGOSHIN-LIKE 1
KeywordsCELL CYCLE / MITOSIS / CELL DIVISION / CHROMOSOMAL PASSENGER COMPLEX / CHROMATIN / CENTROMERE
Function / homology
Function and homology information


mitotic sister chromatid cohesion, centromeric / survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / centriole-centriole cohesion / positive regulation of exit from mitosis / positive regulation of mitotic cytokinesis / positive regulation of mitotic cell cycle spindle assembly checkpoint / meiotic chromosome segregation / mitotic spindle midzone assembly ...mitotic sister chromatid cohesion, centromeric / survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / centriole-centriole cohesion / positive regulation of exit from mitosis / positive regulation of mitotic cytokinesis / positive regulation of mitotic cell cycle spindle assembly checkpoint / meiotic chromosome segregation / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / attachment of spindle microtubules to kinetochore / interphase microtubule organizing center / condensed chromosome, centromeric region / 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 / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / centriole / positive regulation of mitotic cell cycle / tubulin binding / chromosome segregation / RHO GTPases Activate Formins / spindle microtubule / sensory perception of sound / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / kinetochore / spindle / small GTPase binding / kinase binding / spindle pole / Separation of Sister Chromatids / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / mitotic cell cycle / Neddylation / midbody / protein-folding chaperone binding / microtubule binding / Interleukin-4 and Interleukin-13 signaling / microtubule / protein heterodimerization activity / cell division / protein phosphorylation / negative regulation of DNA-templated transcription / centrosome / apoptotic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Shugoshin, C-terminal / Shugoshin, N-terminal coiled-coil domain / Shugoshin / Shugoshin C terminus / Shugoshin N-terminal coiled-coil region / 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. ...Shugoshin, C-terminal / Shugoshin, N-terminal coiled-coil domain / Shugoshin / Shugoshin C terminus / Shugoshin N-terminal coiled-coil region / 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 / Shugoshin 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.605 Å
AuthorsJeyaprakash, A.A. / Basquin, C. / Jayachandran, U. / Conti, E.
CitationJournal: Structure / Year: 2011
Title: Structural Basis for the Recognition of Phosphorylated Histone H3 by the Survivin Subunit of the Chromosomal Passenger Complex.
Authors: Jeyaprakash, A.A. / Basquin, C. / Jayachandran, U. / Conti, E.
History
DepositionSep 9, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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
C: SHUGOSHIN-LIKE 1
D: SHUGOSHIN-LIKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1766
Polymers34,0454
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-9.4 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.650, 70.514, 82.382
Angle α, β, γ (deg.)90.00, 131.80, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 20:90 )
211CHAIN B AND (RESSEQ 20:90 )

NCS oper: (Code: given
Matrix: (0.04116, 0.07393, 0.9964), (0.09385, -0.9931, 0.06981), (0.9947, 0.09064, -0.04781)
Vector: 0.9699, -45.9, 2.698)

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Components

#1: Protein BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5 / SURVIVIN / APOPTOSIS INHIBITOR 4 / APOPTOSIS INHIBITOR SURVIVIN


Mass: 16414.736 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: O15392
#2: Protein/peptide SHUGOSHIN-LIKE 1 / HSGO1 / SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-85


Mass: 607.723 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-6 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q5FBB7
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 3.65 Å3/Da / Density % sol: 66.3 % / Description: NONE
Crystal growpH: 8 / Details: 100MM TRIS PH 8, 200MM NACL, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.6→42.4 Å / Num. obs: 14834 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 71.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.5
Reflection shellResolution: 2.6→2.75 Å / Redundancy: 5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.4 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QFA

2qfa


Resolution: 2.605→41.066 Å / SU ML: 0.85 / σ(F): 0 / Phase error: 30.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2522 740 5 %
Rwork0.2042 --
obs0.2065 14801 98.78 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.972 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 95 Å2
Baniso -1Baniso -2Baniso -3
1--4.3508 Å20 Å214.9666 Å2
2---22.7621 Å20 Å2
3---27.1129 Å2
Refinement stepCycle: LAST / Resolution: 2.605→41.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 0 2 0 2166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082216
X-RAY DIFFRACTIONf_angle_d1.1062996
X-RAY DIFFRACTIONf_dihedral_angle_d15.163804
X-RAY DIFFRACTIONf_chiral_restr0.074320
X-RAY DIFFRACTIONf_plane_restr0.005400
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A532X-RAY DIFFRACTIONPOSITIONAL
12B532X-RAY DIFFRACTIONPOSITIONAL0.037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6052-2.80630.35071390.34872689X-RAY DIFFRACTION95
2.8063-3.08870.34821460.26662835X-RAY DIFFRACTION100
3.0887-3.53540.30531500.22392830X-RAY DIFFRACTION100
3.5354-4.45330.22371540.1842834X-RAY DIFFRACTION100
4.4533-41.07070.22431510.18452873X-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)
19.6556-3.1809-1.15074.8088-4.06785.4972-1.22510.6710.5838-0.0063-0.4261-2.50021.04691.25961.43030.78170.0319-0.03540.86460.23720.926411.1131-32.939616.3437
25.6869-0.7666-0.30057.6319-2.01286.4490.1376-0.1981-0.03831.3151-0.04390.523-0.5464-0.1081-0.14010.833-0.09860.09230.5040.08220.48261.7244-42.043225.1969
38.47087.2128-7.11766.1259-5.98255.8974-0.76750.5626-1.4982-0.44860.23230.57540.8808-1.26530.48940.6373-0.20010.06050.95790.12741.154-1.7189-29.968212.2018
40.58231.5427-2.53490.208-1.84133.0891-0.3715-0.0795-0.0691-0.2218-0.1574-0.25080.6618-0.66550.52940.78970.10540.02150.6670.0410.5989-0.3216-24.402537.0654
58.70730.17462.34487.2972-1.09714.6637-0.54580.08092.00480.3813-0.0413-1.6364-0.81060.28250.48280.5103-0.0399-0.16960.66550.03121.335220.9069-4.61411.5258
62.43080.95720.2087-0.2465-0.3450.12970.06230.67690.3759-0.1781-0.00240.0598-0.02120.0277-0.11930.52170.042-0.03850.70130.09410.9932.3408-19.0702-1.1685
75.01281.8359-3.45644.84873.05016.85660.7398-1.02030.00292.85890.24480.0608-0.1995-0.6209-0.92441.6636-0.2370.01780.91950.21270.5419-2.587-39.559534.481
84.1134-0.98010.29370.2286-0.0710.0177-0.61380.4969-0.1402-0.185-0.1465-0.17910.2497-0.3040.01550.1572-0.3480.56791.55650.94542.338431.7648-4.6221-4.7118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 5:21)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 22:80)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 81:97)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 98:140)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 5:88)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 89:141)
7X-RAY DIFFRACTION7CHAIN C
8X-RAY DIFFRACTION8CHAIN D

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