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- PDB-4a0n: Crystal structure of Survivin bound to the phosphorylated N-termi... -

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Basic information

Entry
Database: PDB / ID: 4a0n
TitleCrystal structure of Survivin bound to the phosphorylated N-terminal tail of histone H3
Components
  • BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5
  • HISTONE H3 PEPTIDE
KeywordsCELL CYCLE / MITOSIS / CHROMOSOMAL PASSENGER COMPLEX / CHROMATIN
Function / homology
Function and homology information


chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of exit from mitosis / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / interphase microtubule organizing center / protein-containing complex localization / chromosome passenger complex / cysteine-type endopeptidase inhibitor activity involved in apoptotic process ...chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of exit from mitosis / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / interphase microtubule organizing center / protein-containing complex localization / chromosome passenger complex / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of mitotic cell cycle spindle assembly checkpoint / cobalt ion binding / mitotic spindle assembly checkpoint signaling / intercellular bridge / spindle midzone / nuclear chromosome / 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 / mitotic spindle assembly / chromosome, centromeric region / cysteine-type endopeptidase inhibitor activity / cytoplasmic microtubule / positive regulation of mitotic cell cycle / sensory perception of sound / Chromatin modifying enzymes / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / centriole / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Resolution of Sister Chromatid Cohesion / Assembly of the ORC complex at the origin of replication / mitotic spindle organization / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / spindle microtubule / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / G2/M transition of mitotic cell cycle / HDACs deacetylate histones / chromosome segregation / Transcriptional regulation by small RNAs / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / epigenetic regulation of gene expression / RHO GTPases Activate Formins / tubulin binding / HDMs demethylate histones / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / PKMTs methylate histone lysines / Formation of the beta-catenin:TCF transactivating complex / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / small GTPase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / nucleosomal DNA binding / kinetochore / RMTs methylate histone arginines / HCMV Early Events / microtubule cytoskeleton / structural constituent of chromatin / Separation of Sister Chromatids / nucleosome / Regulation of PD-L1(CD274) transcription / mitotic cell cycle / nucleosome assembly / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / protein-folding chaperone binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / Dengue Virus-Host Interactions / Interleukin-4 and Interleukin-13 signaling / Senescence-Associated Secretory Phenotype (SASP) / midbody / heterochromatin formation / Oxidative Stress Induced Senescence / chromatin organization / Estrogen-dependent gene expression / microtubule binding / microtubule / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / cell division
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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 ...: / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Baculoviral IAP repeat-containing protein 5 / Histone H3.1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.743 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: 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: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5
C: HISTONE H3 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2663
Polymers17,2012
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-1.7 kcal/mol
Surface area8290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.455, 68.234, 89.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: O15392
#2: Protein/peptide HISTONE H3 PEPTIDE


Mass: 785.783 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-7 / Source method: obtained synthetically / Details: PHOSPHORYLATED AT THR 3 / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P68431*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
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: 3.11 Å3/Da / Density % sol: 60.5 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.1 M TRIS PH 8.5, 0.2 M LISO4, 40% PEG 400.

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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: Dec 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.74→54.5 Å / Num. obs: 5652 / % possible obs: 2.7 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 68.15 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.8
Reflection shellResolution: 2.74→2.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.2 / % possible all: 87.7

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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: 2.743→54.366 Å / SU ML: 0.77 / σ(F): 0 / Phase error: 30.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2602 276 4.9 %
Rwork0.218 --
obs0.22 5647 97.72 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.401 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 75.2 Å2
Baniso -1Baniso -2Baniso -3
1--6.3372 Å20 Å20 Å2
2--18.4197 Å20 Å2
3----12.0825 Å2
Refinement stepCycle: LAST / Resolution: 2.743→54.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1019 0 1 0 1020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041043
X-RAY DIFFRACTIONf_angle_d0.7741414
X-RAY DIFFRACTIONf_dihedral_angle_d18.031364
X-RAY DIFFRACTIONf_chiral_restr0.058153
X-RAY DIFFRACTIONf_plane_restr0.003187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7431-3.4560.34971340.2512573X-RAY DIFFRACTION95
3.456-54.37650.23321420.20822798X-RAY DIFFRACTION100
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)
18.73140.2239-1.30134.5007-0.74953.0116-0.15280.2993-0.622-0.37190.3376-0.9839-0.24680.5029-0.01070.6382-0.03330.1270.653-0.2670.744117.989920.3117-16.1635
2-2.0546-0.6716-1.72161.29231.86142.878-0.38460.2689-0.0328-0.0147-0.07870.2670.06970.4531-0.00390.6022-0.02790.00830.9506-0.26480.62733.113915.7161-24.4099
31.26280.67540.23990.38540.12310.0308-0.61610.481-0.581-0.55140.5476-0.6114-1.3615-0.4345-0.11521.1768-0.07060.14451.6398-0.52390.671916.892418.908-27.8166
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 11:88)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 89:141)
3X-RAY DIFFRACTION3CHAIN C

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