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- PDB-6t58: Structure determination of the transactivation domain of p53 in c... -

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Basic information

Entry
Database: PDB / ID: 6t58
TitleStructure determination of the transactivation domain of p53 in complex with S100A4 using annexin A2 as a crystallization chaperone
ComponentsCellular tumor antigen p53,Protein S100-A4,Protein S100-A4,Annexin A2
KeywordsPEPTIDE BINDING PROTEIN / Crystallization chaperon / peptide-protein complex / Ca2+ binding
Function / homology
Function and homology information


positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair ...positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / myelin sheath adaxonal region / RAGE receptor binding / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / vesicle budding from membrane / cornified envelope / plasma membrane protein complex / calcium-dependent phospholipid binding / negative regulation of receptor internalization / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / collagen fibril organization / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / S100 protein binding / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / Dissolution of Fibrin Clot / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / virion binding / positive regulation of programmed necrotic cell death / osteoclast development / mRNA transcription / bone marrow development / circadian behavior / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / histone deacetylase regulator activity / RUNX3 regulates CDKN1A transcription / germ cell nucleus / positive regulation of low-density lipoprotein receptor activity / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / epithelial cell apoptotic process / negative regulation of neuroblast proliferation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / positive regulation of execution phase of apoptosis / positive regulation of receptor recycling / mitochondrial DNA repair / T cell lineage commitment / phosphatidylserine binding / negative regulation of DNA replication / ER overload response / B cell lineage commitment / thymocyte apoptotic process / positive regulation of cardiac muscle cell apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / positive regulation of exocytosis / chemoattractant activity / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / negative regulation of telomere maintenance via telomerase / rRNA transcription / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / mitophagy / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / neuroblast proliferation / transition metal ion binding / general transcription initiation factor binding / cellular response to actinomycin D
Similarity search - Function
S-100 / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...S-100 / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Cellular tumor antigen p53 / Annexin A2 / Protein S100-A4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsEcsedi, P. / Gogl, G. / Nyitray, L.
Funding support Hungary, 1items
OrganizationGrant numberCountry
Hungarian Academy of Sciences Hungary
CitationJournal: Structure / Year: 2020
Title: Structure Determination of the Transactivation Domain of p53 in Complex with S100A4 Using Annexin A2 as a Crystallization Chaperone.
Authors: Ecsedi, P. / Gogl, G. / Hof, H. / Kiss, B. / Harmat, V. / Nyitray, L.
History
DepositionOct 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 19, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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.ptnr2_symmetry / _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_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.ptnr2_symmetry
Revision 1.3Dec 7, 2022Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellular tumor antigen p53,Protein S100-A4,Protein S100-A4,Annexin A2
B: Cellular tumor antigen p53,Protein S100-A4,Protein S100-A4,Annexin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,37522
Polymers126,3652
Non-polymers1,01020
Water0
1
A: Cellular tumor antigen p53,Protein S100-A4,Protein S100-A4,Annexin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,76813
Polymers63,1831
Non-polymers58512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellular tumor antigen p53,Protein S100-A4,Protein S100-A4,Annexin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6079
Polymers63,1831
Non-polymers4258
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.960, 62.770, 106.020
Angle α, β, γ (deg.)90.000, 90.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cellular tumor antigen p53,Protein S100-A4,Protein S100-A4,Annexin A2 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53 / Calvasculin / Metastasin / Placental ...Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53 / Calvasculin / Metastasin / Placental calcium-binding protein / Protein Mts1 / S100 calcium-binding protein A4 / Calvasculin / Metastasin / Placental calcium-binding protein / Protein Mts1 / S100 calcium-binding protein A4 / Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy chain / Chromobindin-8 / Lipocortin II / Placental anticoagulant protein IV / PAP-IV / Protein I / p36


Mass: 63182.734 Da / Num. of mol.: 2 / Mutation: A280E,A280E,A280E,A280E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: TP53, P53, S100A4, CAPL, MTS1, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D
Production host: Escherichia coli (E. coli)
References: UniProt: P04637, UniProt: P26447, UniProt: P07355
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN

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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: 3.33 Å3/Da / Density % sol: 63.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.12 M Alcohols 0.1 M Sodium HEPES; MOPS (acid) pH7.5 20% v/v Ethylene glycol; 10 % w/v PEG 8000 Morpheus D6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→47.98 Å / Num. obs: 23244 / % possible obs: 99.8 % / Redundancy: 6.681 % / Biso Wilson estimate: 58.116 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.157 / Rrim(I) all: 0.17 / Χ2: 0.911 / Net I/σ(I): 10 / Num. measured all: 155290 / Scaling rejects: 28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.1-3.185.3770.9121.749136170116990.7011.0199.9
3.18-3.275.2990.8061.928728164816470.7470.89599.9
3.27-3.365.2030.6252.548377161216100.8230.69599.9
3.36-3.475.0830.5522.838005157515750.8770.616100
3.47-3.585.9990.4143.919143152715240.9070.45299.8
3.58-3.717.0580.3475.210431148114780.9440.37499.8
3.71-3.856.9410.2636.439807141314130.9730.284100
3.85-47.7510.1979.0410766139013890.9830.21199.9
4-4.187.6850.16710.5410006130213020.9890.179100
4.18-4.387.7420.13412.729902127912790.9940.143100
4.38-4.627.6830.13713.019143119111900.9920.14799.9
4.62-4.97.5290.13712.748628114611460.9930.146100
4.9-5.247.4860.14712.38010107110700.990.15799.9
5.24-5.667.4250.16611.047425100110000.9870.17899.9
5.66-6.27.140.16411.565409199160.9840.17799.7
6.2-6.936.3350.13712.4953218438400.9870.14899.6
6.93-86.7690.08919.5250507477460.9950.09699.9
8-9.87.8760.0438.3350016356350.9990.042100
9.8-13.867.7280.03346.8338645035000.9990.03599.4
13.86-47.987.0420.02952.0320072952850.9990.03196.6

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XJL, 3ZWH

1xjl

3zwh


Resolution: 3.1→47.98 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2721 1989 8.57 %
Rwork0.23 21229 -
obs0.2336 23218 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.39 Å2 / Biso mean: 73.1125 Å2 / Biso min: 28.18 Å2
Refinement stepCycle: final / Resolution: 3.1→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6552 0 48 0 6600
Biso mean--69.25 --
Num. residues----835
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.1-3.17730.40851400.34361490
3.1773-3.26320.36561400.33051494
3.2632-3.35920.3481390.2871499
3.3592-3.46760.3071420.27181511
3.4676-3.59150.27391460.25951498
3.5915-3.73530.29891410.23621507
3.7353-3.90520.25171390.21721508
3.9052-4.1110.2311410.19831515
4.111-4.36840.22181410.18651502
4.3684-4.70540.22351430.18581513
4.7054-5.17840.25431480.20031534
5.1784-5.92660.27451420.23491520
5.9266-7.46230.27621460.24721543
7.4623-47.980.26341410.21681595
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)
12.6501-0.08510.59330.3883-0.6421.22350.01210.47320.1185-0.3207-0.0360.1097-0.01710.25920.04191.30950.1219-0.31090.4729-0.0780.6414-79.8853-13.049207.1896
22.02980.70670.00040.355-0.37131.4140.2879-0.2784-0.1125-0.0511-0.18630.3453-0.1601-0.0935-0.13441.26340.027-0.40450.4605-0.04320.6968-87.6532-21.0974223.2555
33.47611.433-1.99922.3347-1.92944.9483-0.01110.19080.2941-0.8698-0.1099-0.0376-0.35780.6480.08481.3570.06930.03380.58680.02540.5362-40.527635.2582230.7998
40.98240.06090.43191.88030.85722.83090.01630.1490.0204-0.329-0.15720.30920.0096-0.27440.14690.5127-0.0184-0.09640.3170.01230.3458-61.289411.1963250.8551
55.90490.05920.17353.6816-3.74084.48320.4677-1.4756-0.40980.739-0.5612-0.87010.20810.32860.07270.961-0.117-0.33730.9020.0790.7142-67.1597-18.9558239.8082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 319 through 476 )B319 - 476
2X-RAY DIFFRACTION2chain 'B' and (resid 477 through 565 )B477 - 565
3X-RAY DIFFRACTION3chain 'A' and (resid 18 through 249 )A18 - 249
4X-RAY DIFFRACTION4chain 'A' and (resid 250 through 565 )A250 - 565
5X-RAY DIFFRACTION5chain 'B' and (resid 255 through 318 )B255 - 318

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