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- PDB-4a0j: Crystal structure of Survivin bound to the phosphorylated N-termi... -

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Basic information

Entry
Database: PDB / ID: 4a0j
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


survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of exit from mitosis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / interphase microtubule organizing center / chromosome passenger complex ...survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of exit from mitosis / positive regulation of mitotic cell cycle spindle assembly checkpoint / 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 / nuclear chromosome / cobalt ion binding / mitotic spindle assembly checkpoint signaling / cytoplasmic microtubule / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / mitotic cytokinesis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / SUMOylation of DNA replication proteins / chromosome, centromeric region / mitotic spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Chromatin modifying enzymes / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / telomere organization / centriole / tubulin binding / Interleukin-7 signaling / positive regulation of mitotic cell cycle / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / : / negative regulation of peptidase activity / 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 / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / spindle microtubule / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RHO GTPases Activate Formins / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / sensory perception of sound / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / kinetochore / Meiotic recombination / small GTPase binding / PKMTs methylate histone lysines / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / spindle / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / G2/M transition of mitotic cell cycle / Separation of Sister Chromatids / microtubule cytoskeleton / structural constituent of chromatin / nucleosome / nucleosome assembly / mitotic cell cycle / chromatin organization / protein-folding chaperone binding / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / midbody / Senescence-Associated Secretory Phenotype (SASP) / microtubule binding / gene expression / Interleukin-4 and Interleukin-13 signaling / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / microtubule / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / cell division / negative regulation of DNA-templated transcription / protein phosphorylation / positive regulation of cell population proliferation / negative regulation of apoptotic process / apoptotic process
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 / 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: 2.803 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 23, 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
B: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5
C: HISTONE H3 PEPTIDE
D: HISTONE H3 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5326
Polymers34,4014
Non-polymers1312
Water1448
1
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
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-0.9 kcal/mol
Surface area9380 Å2
MethodPISA
2
B: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5
D: HISTONE H3 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2663
Polymers17,2012
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-3.1 kcal/mol
Surface area9160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.365, 70.896, 81.465
Angle α, β, γ (deg.)90.00, 129.03, 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 20:85 )
211CHAIN B AND (RESSEQ 20:85 )

NCS oper: (Code: given
Matrix: (0.1281, 0.09229, 0.9875), (0.07803, -0.993512, 0.082734), (0.988692, 0.06646, -0.13443)
Vector: 0.423, -46.938, 3.6575)

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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 HISTONE H3 PEPTIDE


Mass: 785.783 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: PHOSPHORYLATED AT THR3 / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P68431*PLUS
#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.: 8 / 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: 3.8 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growpH: 6 / Details: 0.1 M MES PH 6.0, 18% PEG 4000.

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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: 2.8→63.2 Å / Num. obs: 12491 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 78.83 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.1
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.1 / % possible all: 96.1

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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: 2.803→56.937 Å / SU ML: 0.43 / σ(F): 0 / Phase error: 29.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2684 625 5 %
Rwork0.1977 --
obs0.2011 12477 99.47 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.461 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso mean: 94 Å2
Baniso -1Baniso -2Baniso -3
1-2.3147 Å20 Å216.0833 Å2
2---12.3648 Å20 Å2
3---10.0501 Å2
Refinement stepCycle: LAST / Resolution: 2.803→56.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2213 0 2 8 2223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062265
X-RAY DIFFRACTIONf_angle_d1.0243057
X-RAY DIFFRACTIONf_dihedral_angle_d18.508837
X-RAY DIFFRACTIONf_chiral_restr0.065324
X-RAY DIFFRACTIONf_plane_restr0.004402
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A486X-RAY DIFFRACTIONPOSITIONAL
12B486X-RAY DIFFRACTIONPOSITIONAL0.029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8034-3.08550.39451530.33792906X-RAY DIFFRACTION98
3.0855-3.53190.30611560.22872955X-RAY DIFFRACTION100
3.5319-4.44950.25221560.17982965X-RAY DIFFRACTION100
4.4495-56.94890.24551600.17663026X-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)
11.579-2.0936-0.33315.0135-2.37733.79520.02660.46570.7272-0.3041-0.224-1.24750.1070.90550.30730.4958-0.0724-0.04870.78140.18630.726312.2462-33.406217.0974
22.6836-0.2244-1.56311.53160.28210.9285-0.23910.92-0.6846-0.7227-0.17170.23760.0469-0.2673-0.52490.4033-0.0451-0.08920.35160.02710.31086.2992-47.580921.7801
32.84290.4951-0.13253.1711-0.28180.0263-0.04170.1621-0.11230.53830.3030.5624-0.1073-0.1911-0.04020.6388-0.0905-0.00220.58640.13940.55511.0747-37.496624.2394
40.26970.3379-0.3330.0691-0.14060.65750.1398-0.10060.4491-0.38430.1635-0.0366-0.3059-0.009-0.14050.7262-0.00470.08690.45180.00790.73242.1454-25.394439.481
52.657-1.28490.46052.0958-1.05691.9092-0.53350.12312.51630.2231-0.1525-1.6534-1.50550.3442-0.2870.0157-0.2802-0.09350.25660.13111.190620.94-5.65191.9158
60.2842-0.2580.00220.25080.04490.20430.0933-0.0644-0.0312-0.07560.05630.0979-0.0944-0.18970.30650.4731-0.1562-0.27420.87380.87310.6676.503-16.7432.8589
70.37860.0357-0.1521-0.1273-0.0656-0.1014-0.05050.4417-0.1436-0.55140.07750.20920.1571-0.0497-0.01510.47940.0720.07770.42540.05610.882137.9748-20.7159-1.2908
83.3541-2.88852.04757.76752.39314.5376-0.24710.16710.25760.81270.2914-0.3524-0.0363-0.50390.0741.2514-0.15440.13650.60910.07710.7507-0.7652-39.72736.815
90.73190.70180.10280.71130.18160.19290.17370.18030.0158-0.0818-0.005-0.7209-0.0822-0.0118-0.24240.4199-0.04960.20140.95350.29231.578632.2301-5.6436-5.6244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 5:21)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 22:40)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 41:97)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 98:140)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 5:88)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 89:97)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 98:141)
8X-RAY DIFFRACTION8CHAIN C
9X-RAY DIFFRACTION9CHAIN D

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