[English] 日本語
Yorodumi
- PDB-7bwn: Crystal Structure of a Designed Protein Heterocatenane -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bwn
TitleCrystal Structure of a Designed Protein Heterocatenane
Components
  • Cellular tumor antigen p53
  • Chimera of Green fluorescent protein and p53dim
KeywordsRECOMBINATION / Heterocatenane
Function / homology
Function and homology information


negative regulation of helicase activity / signal transduction by p53 class mediator / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of cell cycle G2/M phase transition / negative regulation of G1 to G0 transition / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity ...negative regulation of helicase activity / signal transduction by p53 class mediator / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of cell cycle G2/M phase transition / negative regulation of G1 to G0 transition / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity / oligodendrocyte apoptotic process / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / bone marrow development / cellular response to actinomycin D / circadian behavior / positive regulation of programmed necrotic cell death / RUNX3 regulates CDKN1A transcription / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / mRNA transcription / Regulation of TP53 Activity through Association with Co-factors / Urea cycle / ER overload response / hematopoietic stem cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / TP53 Regulates Transcription of Caspase Activators and Caspases / intrinsic apoptotic signaling pathway by p53 class mediator / entrainment of circadian clock by photoperiod / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / PI5P Regulates TP53 Acetylation / positive regulation of release of cytochrome c from mitochondria / hematopoietic progenitor cell differentiation / Association of TriC/CCT with target proteins during biosynthesis / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Transcriptional Regulation by VENTX / TFIID-class transcription factor complex binding / replicative senescence / viral process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Pyroptosis / determination of adult lifespan / positive regulation of RNA polymerase II transcription preinitiation complex assembly / general transcription initiation factor binding / negative regulation of fibroblast proliferation / positive regulation of execution phase of apoptosis / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to glucose starvation / core promoter sequence-specific DNA binding / cis-regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Acetylation / intrinsic apoptotic signaling pathway / mitotic G1 DNA damage checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway / response to gamma radiation / 14-3-3 protein binding / MDM2/MDM4 family protein binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / DNA damage response, signal transduction by p53 class mediator / protein phosphatase 2A binding / transcription initiation-coupled chromatin remodeling / molecular function activator activity / Regulation of PTEN gene transcription / tumor necrosis factor-mediated signaling pathway / bioluminescence / cellular response to ionizing radiation / cellular response to xenobiotic stimulus / TP53 Regulates Metabolic Genes / TP53 Regulates Transcription of DNA Repair Genes / generation of precursor metabolites and energy / cellular response to gamma radiation / Regulation of NF-kappa B signaling / mRNA 3'-UTR binding / protein tetramerization / promoter-specific chromatin binding / Stabilization of p53 / molecular condensate scaffold activity / negative regulation of cell growth / nucleotide-excision repair / G2/M Checkpoints / receptor tyrosine kinase binding / Autodegradation of the E3 ubiquitin ligase COP1 / cellular senescence / PML body / PKR-mediated signaling / positive regulation of miRNA transcription / Oncogene Induced Senescence / DNA-binding transcription repressor activity, RNA polymerase II-specific / Regulation of TP53 Activity through Methylation / G2/M DNA damage checkpoint / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / transcription coactivator binding / positive regulation of reactive oxygen species metabolic process
Similarity search - Function
p53, subunit A / p53-like tetramerisation 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, subunit A / p53-like tetramerisation 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 / Green Fluorescent Protein / Green fluorescent protein / p53-like transcription factor, DNA-binding / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Few Secondary Structures / Irregular / Beta Barrel / Mainly Beta
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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 (eV)
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

-
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 / 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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more