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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


Regulation of TP53 Expression / positive regulation of programmed necrotic cell death / negative regulation of pentose-phosphate shunt / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / signal transduction by p53 class mediator / regulation of fibroblast apoptotic process / : / Transcriptional activation of cell cycle inhibitor p21 / intrinsic apoptotic signaling pathway in response to hypoxia / negative regulation of glucose catabolic process to lactate via pyruvate ...Regulation of TP53 Expression / positive regulation of programmed necrotic cell death / negative regulation of pentose-phosphate shunt / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / signal transduction by p53 class mediator / regulation of fibroblast apoptotic process / : / Transcriptional activation of cell cycle inhibitor p21 / intrinsic apoptotic signaling pathway in response to hypoxia / negative regulation of glucose catabolic process to lactate via pyruvate / Activation of NOXA and translocation to mitochondria / oxidative stress-induced premature senescence / regulation of transcription from RNA polymerase II promoter in response to DNA damage / oligodendrocyte apoptotic process / negative regulation of helicase activity / positive regulation of thymocyte apoptotic process / negative regulation of mitophagy / regulation of tissue remodeling / bone marrow development / positive regulation of cell aging / circadian behavior / mRNA transcription / positive regulation of mitochondrial membrane permeability / regulation of mitochondrial membrane permeability involved in apoptotic process / positive regulation of transcription from RNA polymerase II promoter in response to stress / histone deacetylase regulator activity / RUNX3 regulates CDKN1A transcription / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / regulation of DNA damage response, signal transduction by p53 class mediator / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of neuroblast proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / cardiac septum morphogenesis / positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress / regulation of cell cycle G2/M phase transition / positive regulation of execution phase of apoptosis / regulation of cellular senescence / negative regulation of DNA replication / chromatin assembly / TFIID-class transcription factor complex binding / T cell lineage commitment / DNA damage response, signal transduction by p53 class mediator / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / positive regulation of histone deacetylation / Association of TriC/CCT with target proteins during biosynthesis / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / positive regulation of cardiac muscle cell apoptotic process / B cell lineage commitment / positive regulation of transcription from RNA polymerase II promoter in response to hypoxia / rRNA transcription / ER overload response / hematopoietic stem cell differentiation / TP53 Regulates Transcription of Caspase Activators and Caspases / T cell proliferation involved in immune response / entrainment of circadian clock by photoperiod / cellular response to UV-C / PI5P Regulates TP53 Acetylation / intrinsic apoptotic signaling pathway by p53 class mediator / regulation of cell cycle => GO:0051726 / cellular response to actinomycin D / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / response to salt stress / necroptotic process / gastrulation / MDM2/MDM4 family protein binding / cis-regulatory region sequence-specific DNA binding / positive regulation of release of cytochrome c from mitochondria / SUMOylation of transcription factors / somitogenesis / cellular response to glucose starvation / histone acetyltransferase binding / regulation of transcription initiation from RNA polymerase II promoter / DNA-binding transcription activator activity / Transcriptional Regulation by VENTX / negative regulation of reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / negative regulation of fibroblast proliferation / positive regulation of production of miRNAs involved in gene silencing by miRNA / embryonic organ development / cell aging / cellular protein localization / intrinsic apoptotic signaling pathway / core promoter sequence-specific DNA binding / hematopoietic progenitor cell differentiation / determination of adult lifespan / negative regulation of telomerase activity / regulation of cell cycle => GO:0051726 / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / negative regulation of production of miRNAs involved in gene silencing by miRNA / mitotic G1 DNA damage checkpoint signaling / replication fork / positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / cerebellum development
Similarity search - Function
Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / P53 transactivation motif / p53 transactivation domain / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53-like tetramerisation domain superfamily / P53 DNA-binding domain / p53 tumour suppressor family ...Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / P53 transactivation motif / p53 transactivation domain / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53-like tetramerisation domain superfamily / P53 DNA-binding domain / p53 tumour suppressor family / p53, DNA-binding domain / 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

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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
γ
α
β
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:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 280
211chain CC1 - 280
311chain EE1 - 280
411chain FF1 - 280
511chain HH1 - 280
611chain JJ1 - 280
711chain MM1 - 280
811chain OO1 - 280
112(chain B and resid 326 through 353)B326 - 353
212(chain D and resid 326 through 353)D326 - 353
312(chain G and resid 326 through 353)G326 - 353
412(chain I and resid 326 through 353)I326 - 353
512chain KK326 - 353
612(chain L and resid 326 through 353)L326 - 353
712chain NN326 - 353
812(chain P and resid 326 through 353)P326 - 353

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
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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