[English] 日本語
Yorodumi
- PDB-8xp5: The Crystal Structure of p53/BCL-xL fusion complex from Biortus. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xp5
TitleThe Crystal Structure of p53/BCL-xL fusion complex from Biortus.
ComponentsBcl-2-like protein 1,Cellular tumor antigen p53
KeywordsPROTEIN BINDING / Apoptosis / Activator
Function / homology
Function and homology information


apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / negative regulation of execution phase of apoptosis ...apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / 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 / regulation of growth / 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 / regulation of mitochondrial membrane permeability / 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 / Bcl-2 family protein complex / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / BH domain binding / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / NFE2L2 regulating tumorigenic genes / mitochondrial DNA repair / T cell lineage commitment / response to cycloheximide / 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 / cellular response to alkaloid / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / STAT5 activation downstream of FLT3 ITD mutants / TP53 Regulates Transcription of Caspase Activators and Caspases / hepatocyte apoptotic process / cardiac septum morphogenesis / entrainment of circadian clock by photoperiod / negative regulation of release of cytochrome c from mitochondria / PI5P Regulates TP53 Acetylation / negative regulation of reproductive process / negative regulation of developmental process / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of release of cytochrome c from mitochondria / necroptotic process / Zygotic genome activation (ZGA) / BH3 domain binding / positive regulation of execution phase of apoptosis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / germ cell development / TFIID-class transcription factor complex binding / rRNA transcription / negative regulation of telomere maintenance via telomerase / apoptotic mitochondrial changes / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / negative regulation of anoikis / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / replicative senescence / response to X-ray / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / 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
Similarity search - Function
Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 ...Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / 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 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / p53-like transcription factor, DNA-binding
Similarity search - Domain/homology
Cellular tumor antigen p53 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Bao, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of p53/BCL-xL fusion complex from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Bao, C.
History
DepositionJan 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bcl-2-like protein 1,Cellular tumor antigen p53
B: Bcl-2-like protein 1,Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5424
Polymers83,4112
Non-polymers1312
Water2,054114
1
A: Bcl-2-like protein 1,Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7712
Polymers41,7061
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20 Å2
ΔGint-4 kcal/mol
Surface area15800 Å2
MethodPISA
2
B: Bcl-2-like protein 1,Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7712
Polymers41,7061
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.976, 68.437, 77.055
Angle α, β, γ (deg.)90.000, 112.356, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Bcl-2-like protein 1,Cellular tumor antigen p53 / Bcl2-L-1 / Apoptosis regulator Bcl-X / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 41705.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Bcl-2-like protein 1/Cellular tumor antigen p53 fusion complex
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX, TP53, P53 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07817, UniProt: P04637
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05M MgCl2, 0.1M MES pH6.5, 5% PEG 4000, 10% 2-Propanol, 30% w/v D-Sorbito

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.55→49.36 Å / Num. obs: 20765 / % possible obs: 88.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 4.1
Reflection shellResolution: 2.55→2.66 Å / Rmerge(I) obs: 0.724 / Num. unique obs: 2602

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→49.36 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.811 / SU B: 21.431 / SU ML: 0.443 / Cross valid method: FREE R-VALUE / ESU R Free: 0.448
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3276 1042 5.024 %
Rwork0.2549 19699 -
all0.259 --
obs-20741 88.591 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.162 Å2
Baniso -1Baniso -2Baniso -3
1-1.193 Å2-0 Å2-4.688 Å2
2---0.789 Å20 Å2
3---2.58 Å2
Refinement stepCycle: LAST / Resolution: 2.55→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4935 0 2 114 5051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125053
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164645
X-RAY DIFFRACTIONr_angle_refined_deg0.8251.6666843
X-RAY DIFFRACTIONr_angle_other_deg0.2741.57810675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3995612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.509543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48110833
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg12.032106
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.2710247
X-RAY DIFFRACTIONr_chiral_restr0.0360.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026052
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021234
X-RAY DIFFRACTIONr_nbd_refined0.2030.21099
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.24442
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22460
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22616
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2161
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1450.224
X-RAY DIFFRACTIONr_nbd_other0.1360.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2070.213
X-RAY DIFFRACTIONr_mcbond_it1.3964.2382478
X-RAY DIFFRACTIONr_mcbond_other1.3954.2382478
X-RAY DIFFRACTIONr_mcangle_it2.5157.5953080
X-RAY DIFFRACTIONr_mcangle_other2.5157.5953081
X-RAY DIFFRACTIONr_scbond_it1.1054.3562575
X-RAY DIFFRACTIONr_scbond_other1.1054.3572576
X-RAY DIFFRACTIONr_scangle_it2.0397.9883763
X-RAY DIFFRACTIONr_scangle_other2.0397.9883764
X-RAY DIFFRACTIONr_lrange_it4.92943.995682
X-RAY DIFFRACTIONr_lrange_other4.92943.9985681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.6160.367760.3521482X-RAY DIFFRACTION91.5932
2.616-2.6880.341690.3331428X-RAY DIFFRACTION91.1693
2.688-2.7650.404740.3291431X-RAY DIFFRACTION91.0466
2.765-2.850.416700.3071352X-RAY DIFFRACTION89.0977
2.85-2.9430.334750.261305X-RAY DIFFRACTION90.4325
2.943-3.0460.343760.2481258X-RAY DIFFRACTION90.2571
3.046-3.1610.412480.2571218X-RAY DIFFRACTION89.2807
3.161-3.2890.264490.251200X-RAY DIFFRACTION89.9856
3.289-3.4350.355770.2471111X-RAY DIFFRACTION89.1892
3.435-3.6010.358420.2511083X-RAY DIFFRACTION88.5827
3.601-3.7950.33570.2441005X-RAY DIFFRACTION88.3527
3.795-4.0240.31570.244963X-RAY DIFFRACTION88.4649
4.024-4.30.348500.224902X-RAY DIFFRACTION87.5
4.3-4.6410.278440.221820X-RAY DIFFRACTION86.4
4.641-5.080.289480.208734X-RAY DIFFRACTION85.8397
5.08-5.6720.271380.232685X-RAY DIFFRACTION84.3641
5.672-6.5350.341380.29584X-RAY DIFFRACTION83.6021
6.535-7.9690.262230.236509X-RAY DIFFRACTION83.5165
7.969-11.1260.337190.205397X-RAY DIFFRACTION81.7289
11.126-49.360.218120.271232X-RAY DIFFRACTION80.2632

+
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