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- PDB-7bwn: Crystal Structure of a Designed Protein Heterocatenane -

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Basic information

Entry
Database: PDB / ID: 7bwn
TitleCrystal Structure of a Designed Protein Heterocatenane
Components
  • Cellular tumor antigen p53P53
  • Chimera of Green fluorescent protein and p53dim
KeywordsRECOMBINATION / Heterocatenane
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 / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / germ cell nucleus / 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 / 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 / mitochondrial DNA repair / T cell lineage commitment / 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 / 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 / positive regulation of release of cytochrome c from mitochondria / rRNA transcription / 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 / general transcription initiation factor binding / cellular response to actinomycin D / Transcriptional Regulation by VENTX / response to X-ray / DNA damage response, signal transduction by p53 class mediator / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / chromosome organization / gastrulation / cellular response to UV-C / response to inorganic substance / hematopoietic stem cell differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of reactive oxygen species metabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / MDM2/MDM4 family protein binding / glial cell proliferation / embryonic organ development / cellular response to glucose starvation / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / type II interferon-mediated signaling pathway / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / cardiac muscle cell apoptotic process / response to salt stress / transcription initiation-coupled chromatin remodeling / mitotic G1 DNA damage checkpoint signaling / 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 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Green fluorescent protein / Cellular tumor antigen p53 / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.396 Å
AuthorsLiu, Y.J. / Duan, Z.L. / Fang, J. / Zhang, F. / Xiao, J.Y. / Zhang, W.B.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21925102 China
National Natural Science Foundation of China (NSFC)21991132 China
National Natural Science Foundation of China (NSFC)21674003 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Cellular Synthesis and X-ray Crystal Structure of a Designed Protein Heterocatenane.
Authors: Liu, Y. / Duan, Z. / Fang, J. / Zhang, F. / Xiao, J. / Zhang, W.B.
History
DepositionApr 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Sep 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Chimera of Green fluorescent protein and p53dim
L: Cellular tumor antigen p53
A: Chimera of Green fluorescent protein and p53dim
B: Cellular tumor antigen p53
C: Chimera of Green fluorescent protein and p53dim
D: Cellular tumor antigen p53
E: Chimera of Green fluorescent protein and p53dim
G: Cellular tumor antigen p53
H: Chimera of Green fluorescent protein and p53dim
I: Cellular tumor antigen p53
J: Chimera of Green fluorescent protein and p53dim
K: Cellular tumor antigen p53
M: Chimera of Green fluorescent protein and p53dim
N: Cellular tumor antigen p53
O: Chimera of Green fluorescent protein and p53dim
P: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)297,09316
Polymers297,09316
Non-polymers00
Water10,178565
1
F: Chimera of Green fluorescent protein and p53dim
L: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)37,1372
Polymers37,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-9 kcal/mol
Surface area15430 Å2
MethodPISA
2
A: Chimera of Green fluorescent protein and p53dim
B: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)37,1372
Polymers37,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-10 kcal/mol
Surface area15450 Å2
MethodPISA
3
C: Chimera of Green fluorescent protein and p53dim
D: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)37,1372
Polymers37,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-10 kcal/mol
Surface area16080 Å2
MethodPISA
4
E: Chimera of Green fluorescent protein and p53dim
G: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)37,1372
Polymers37,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-9 kcal/mol
Surface area15560 Å2
MethodPISA
5
H: Chimera of Green fluorescent protein and p53dim
I: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)37,1372
Polymers37,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-9 kcal/mol
Surface area15600 Å2
MethodPISA
6
J: Chimera of Green fluorescent protein and p53dim
K: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)37,1372
Polymers37,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-7 kcal/mol
Surface area15010 Å2
MethodPISA
7
M: Chimera of Green fluorescent protein and p53dim
N: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)37,1372
Polymers37,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-7 kcal/mol
Surface area15070 Å2
MethodPISA
8
O: Chimera of Green fluorescent protein and p53dim
P: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)37,1372
Polymers37,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-10 kcal/mol
Surface area15720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.897, 108.897, 684.966
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-355-

HOH

21E-316-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
31chain E
41chain F
51chain H
61chain J
71chain M
81chain O
12(chain B and resid 326 through 353)
22(chain D and resid 326 through 353)
32(chain G and resid 326 through 353)
42(chain I and resid 326 through 353)
52chain K
62(chain L and resid 326 through 353)
72chain N
82(chain P and resid 326 through 353)

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETSERSERchain AAC1 - 2801 - 280
21METMETSERSERchain CCE1 - 2801 - 280
31METMETSERSERchain EEG1 - 2801 - 280
41METMETSERSERchain FFA1 - 2801 - 280
51METMETSERSERchain HHI1 - 2801 - 280
61METMETSERSERchain JJK1 - 2801 - 280
71METMETSERSERchain MMM1 - 2801 - 280
81METMETSERSERchain OOO1 - 2801 - 280
12GLUGLUALAALA(chain B and resid 326 through 353)BD326 - 35311 - 38
22GLUGLUALAALA(chain D and resid 326 through 353)DF326 - 35311 - 38
32GLUGLUALAALA(chain G and resid 326 through 353)GH326 - 35311 - 38
42GLUGLUALAALA(chain I and resid 326 through 353)IJ326 - 35311 - 38
52GLUGLUALAALAchain KKL326 - 35311 - 38
62GLUGLUALAALA(chain L and resid 326 through 353)LB326 - 35311 - 38
72GLUGLUALAALAchain NNN326 - 35311 - 38
82GLUGLUALAALA(chain P and resid 326 through 353)PP326 - 35311 - 38

NCS ensembles :
ID
1
2

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Components

#1: Protein
Chimera of Green fluorescent protein and p53dim


Mass: 31618.549 Da / Num. of mol.: 8 / Mutation: R2S,S30R,A72S,Q80R,A206V,M340E,L344K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059PIQ0, UniProt: P42212*PLUS
#2: Protein/peptide
Cellular tumor antigen p53 / P53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 5518.018 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Production host: Escherichia coli (E. coli) / References: UniProt: P04637
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 565 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: Bis-Tris, (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97892 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.396→50 Å / Num. obs: 114682 / % possible obs: 97.8 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 15.3
Reflection shellResolution: 2.396→2.482 Å / Num. unique obs: 10477 / Rpim(I) all: 0.22

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B61, 4D1M

5b61

4d1m


Resolution: 2.396→49.145 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.44
RfactorNum. reflection% reflection
Rfree0.2386 2007 1.75 %
Rwork0.187 --
obs0.1879 114682 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.68 Å2 / Biso mean: 39.0098 Å2 / Biso min: 17.46 Å2
Refinement stepCycle: final / Resolution: 2.396→49.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20031 0 0 565 20596
Biso mean---36.94 -
Num. residues----2497
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A11058X-RAY DIFFRACTION13.144TORSIONAL
12C11058X-RAY DIFFRACTION13.144TORSIONAL
13E11058X-RAY DIFFRACTION13.144TORSIONAL
14F11058X-RAY DIFFRACTION13.144TORSIONAL
15H11058X-RAY DIFFRACTION13.144TORSIONAL
16J11058X-RAY DIFFRACTION13.144TORSIONAL
17M11058X-RAY DIFFRACTION13.144TORSIONAL
18O11058X-RAY DIFFRACTION13.144TORSIONAL
21B1218X-RAY DIFFRACTION13.144TORSIONAL
22D1218X-RAY DIFFRACTION13.144TORSIONAL
23G1218X-RAY DIFFRACTION13.144TORSIONAL
24I1218X-RAY DIFFRACTION13.144TORSIONAL
25K1218X-RAY DIFFRACTION13.144TORSIONAL
26L1218X-RAY DIFFRACTION13.144TORSIONAL
27N1218X-RAY DIFFRACTION13.144TORSIONAL
28P1218X-RAY DIFFRACTION13.144TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.396-2.45580.25551230.2048727087
2.4558-2.52220.27971340.2263749889
2.5222-2.59640.31661450.2189771892
2.5964-2.68020.33521380.2315775693
2.6802-2.7760.30491450.2281797795
2.776-2.88720.28351430.2228811997
2.8872-3.01860.28851470.2181821098
3.0186-3.17770.22171510.2054819898
3.1777-3.37670.23831460.1997824799
3.3767-3.63740.2331460.1897833899
3.6374-4.00330.22971520.17468319100
4.0033-4.58220.19791450.14698345100
4.5822-5.77160.21361450.15418378100
5.7716-49.1450.2081470.1851830299

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