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- PDB-9c5s: Disulfide-linked, antiparallel p53-derived peptide dimer (CV1) -

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Basic information

Entry
Database: PDB / ID: 9c5s
TitleDisulfide-linked, antiparallel p53-derived peptide dimer (CV1)
ComponentsCellular tumor antigen p53
KeywordsUNKNOWN FUNCTION / Antiparallel dimer / p53
Function / homology
Function and homology information


Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / 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 ...Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / 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 / 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 / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / circadian behavior / bone marrow development / histone deacetylase regulator activity / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / 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 / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / T cell lineage commitment / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / negative regulation of DNA replication / 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 / cardiac septum morphogenesis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of release of cytochrome c from mitochondria / necroptotic process / Zygotic genome activation (ZGA) / positive regulation of execution phase of apoptosis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / rRNA transcription / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / replicative senescence / response to X-ray / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / mitophagy / cellular response to UV-C / positive regulation of RNA polymerase II transcription preinitiation complex assembly / hematopoietic stem cell differentiation / neuroblast proliferation / negative regulation of reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chromosome organization / T cell proliferation involved in immune response / Pyroptosis / embryonic organ development / glial cell proliferation / viral process / cis-regulatory region sequence-specific DNA binding / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / hematopoietic progenitor cell differentiation / type II interferon-mediated signaling pathway / somitogenesis / cellular response to actinomycin D / core promoter sequence-specific DNA binding / cellular response to glucose starvation / negative regulation of stem cell proliferation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / gastrulation / MDM2/MDM4 family protein binding / response to salt stress / cardiac muscle cell apoptotic process / mitotic G1 DNA damage checkpoint signaling / tumor necrosis factor-mediated signaling pathway / 14-3-3 protein binding / Regulation of TP53 Activity through Acetylation
Similarity search - Function
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 ...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
Similarity search - Domain/homology
Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.01 Å
AuthorsVithanage, N. / Kreitler, D.K. / DiGiorno, M.C. / Victorio, C.G. / Sawyer, N. / Outlaw, V.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Res Sq / Year: 2024
Title: Structural Characterization of Disulfide-Linked p53-Derived Peptide Dimers.
Authors: DiGiorno, M.C. / Vithanage, N. / Victorio, C.G. / Kreitler, D.F. / Outlaw, V.K. / Sawyer, N.
History
DepositionJun 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellular tumor antigen p53
B: Cellular tumor antigen p53
C: Cellular tumor antigen p53
D: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8085
Polymers6,7124
Non-polymers961
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-63 kcal/mol
Surface area3320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.243, 45.243, 62.699
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein/peptide
Cellular tumor antigen p53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 1677.991 Da / Num. of mol.: 4 / Mutation: p53-derived / Source method: obtained synthetically
Details: This molecule is a synthetic peptide derived from residues 17-30 of the p53 protein. It is acetylated at the N-terminus and amidated at the C-terminus.
Source: (synth.) Homo sapiens (human) / References: UniProt: P04637
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 20% v/v glycerol, 10% w/v PEG4000, 100 mM imidazole/MES monohydrate buffer, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92011 Å / Relative weight: 1
ReflectionResolution: 1.01→33.23 Å / Num. obs: 35044 / % possible obs: 88.6 % / Redundancy: 10.6 % / Biso Wilson estimate: 14.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Net I/σ(I): 15
Reflection shellResolution: 1.01→1.068 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.553 / Num. unique obs: 1752 / CC1/2: 0.524 / % possible all: 28.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.01→33.23 Å / SU ML: 0.1037 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.9692
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2015 1699 4.85 %
Rwork0.1904 33342 -
obs0.1909 35041 88.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.87 Å2
Refinement stepCycle: LAST / Resolution: 1.01→33.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms472 0 5 71 548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044484
X-RAY DIFFRACTIONf_angle_d0.8244658
X-RAY DIFFRACTIONf_chiral_restr0.054172
X-RAY DIFFRACTIONf_plane_restr0.004984
X-RAY DIFFRACTIONf_dihedral_angle_d8.566164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.01-1.040.3494170.376305X-RAY DIFFRACTION10.01
1.04-1.070.28631000.31951698X-RAY DIFFRACTION55.14
1.07-1.110.28891350.27883029X-RAY DIFFRACTION97.5
1.11-1.160.24831210.26693142X-RAY DIFFRACTION100
1.16-1.210.21071500.23223117X-RAY DIFFRACTION99.97
1.21-1.270.26821420.21823118X-RAY DIFFRACTION100
1.27-1.350.22661790.20563097X-RAY DIFFRACTION100
1.35-1.460.22181540.19923155X-RAY DIFFRACTION99.97
1.46-1.60.1751730.18953109X-RAY DIFFRACTION100
1.6-1.830.1861590.18063151X-RAY DIFFRACTION100
1.83-2.310.1621860.17723169X-RAY DIFFRACTION100
2.31-33.230.21391830.18153252X-RAY DIFFRACTION98.23
Refinement TLS params.Method: refined / Origin x: -13.911 Å / Origin y: 10.57 Å / Origin z: 4.425 Å
111213212223313233
T0.126795389039 Å2-0.0268009730784 Å2-0.00843600895083 Å2-0.101230355949 Å2-0.00389821042246 Å2--0.103016014259 Å2
L3.24313455436 °21.27315579524 °22.60762407649 °2-3.08974919546 °21.72461217933 °2--4.54394151365 °2
S0.0307888780188 Å °0.0147582035078 Å °-0.16560641241 Å °-0.026233619184 Å °0.104845157707 Å °-0.131982514352 Å °0.325824015357 Å °0.0287843624297 Å °-0.068269696598 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:118 ) ) OR ( CHAIN B AND ( RESID 0:14 OR RESID 15:15 OR RESID 201:225 OR RESID 101:101 ) ) OR ( CHAIN C AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:111 ) ) OR ( CHAIN D AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:117 ) )A0 - 14
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:118 ) ) OR ( CHAIN B AND ( RESID 0:14 OR RESID 15:15 OR RESID 201:225 OR RESID 101:101 ) ) OR ( CHAIN C AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:111 ) ) OR ( CHAIN D AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:117 ) )A15
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:118 ) ) OR ( CHAIN B AND ( RESID 0:14 OR RESID 15:15 OR RESID 201:225 OR RESID 101:101 ) ) OR ( CHAIN C AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:111 ) ) OR ( CHAIN D AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:117 ) )A101 - 118
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:118 ) ) OR ( CHAIN B AND ( RESID 0:14 OR RESID 15:15 OR RESID 201:225 OR RESID 101:101 ) ) OR ( CHAIN C AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:111 ) ) OR ( CHAIN D AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:117 ) )B0 - 14
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:118 ) ) OR ( CHAIN B AND ( RESID 0:14 OR RESID 15:15 OR RESID 201:225 OR RESID 101:101 ) ) OR ( CHAIN C AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:111 ) ) OR ( CHAIN D AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:117 ) )B15
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:118 ) ) OR ( CHAIN B AND ( RESID 0:14 OR RESID 15:15 OR RESID 201:225 OR RESID 101:101 ) ) OR ( CHAIN C AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:111 ) ) OR ( CHAIN D AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:117 ) )B201 - 225
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:118 ) ) OR ( CHAIN B AND ( RESID 0:14 OR RESID 15:15 OR RESID 201:225 OR RESID 101:101 ) ) OR ( CHAIN C AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:111 ) ) OR ( CHAIN D AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:117 ) )B101
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:118 ) ) OR ( CHAIN B AND ( RESID 0:14 OR RESID 15:15 OR RESID 201:225 OR RESID 101:101 ) ) OR ( CHAIN C AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:111 ) ) OR ( CHAIN D AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:117 ) )C0 - 14
9X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:118 ) ) OR ( CHAIN B AND ( RESID 0:14 OR RESID 15:15 OR RESID 201:225 OR RESID 101:101 ) ) OR ( CHAIN C AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:111 ) ) OR ( CHAIN D AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:117 ) )C15
10X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:118 ) ) OR ( CHAIN B AND ( RESID 0:14 OR RESID 15:15 OR RESID 201:225 OR RESID 101:101 ) ) OR ( CHAIN C AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:111 ) ) OR ( CHAIN D AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:117 ) )C101 - 111
11X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:118 ) ) OR ( CHAIN B AND ( RESID 0:14 OR RESID 15:15 OR RESID 201:225 OR RESID 101:101 ) ) OR ( CHAIN C AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:111 ) ) OR ( CHAIN D AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:117 ) )D0 - 14
12X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:118 ) ) OR ( CHAIN B AND ( RESID 0:14 OR RESID 15:15 OR RESID 201:225 OR RESID 101:101 ) ) OR ( CHAIN C AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:111 ) ) OR ( CHAIN D AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:117 ) )D15
13X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:118 ) ) OR ( CHAIN B AND ( RESID 0:14 OR RESID 15:15 OR RESID 201:225 OR RESID 101:101 ) ) OR ( CHAIN C AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:111 ) ) OR ( CHAIN D AND ( RESID 0:14 OR RESID 15:15 OR RESID 101:117 ) )D101 - 117

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