[English] 日本語
Yorodumi
- PDB-8hll: Crystal structure of p53/BCL2 fusion complex (complex 1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hll
TitleCrystal structure of p53/BCL2 fusion complex (complex 1)
Components
  • Apoptosis regulator Bcl-2
  • Cellular tumor antigen p53P53
KeywordsAPOPTOSIS
Function / homology
Function and homology information


negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of melanocyte differentiation ...negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of melanocyte differentiation / myeloid cell apoptotic process / osteoblast proliferation / cochlear nucleus development / mesenchymal cell development / retinal cell programmed cell death / positive regulation of neuron maturation / negative regulation of osteoblast proliferation / gland morphogenesis / renal system process / regulation of cell-matrix adhesion / T cell apoptotic process / stem cell development / negative regulation of calcium ion transport into cytosol / The NLRP1 inflammasome / dendritic cell apoptotic process / melanocyte differentiation / ear development / lymphoid progenitor cell differentiation / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / regulation of nitrogen utilization / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / negative regulation of T cell apoptotic process / negative regulation of dendritic cell apoptotic process / glomerulus development / oocyte development / positive regulation of multicellular organism growth / neuron maturation / metanephros development / regulation of viral genome replication / negative regulation of motor neuron apoptotic process / focal adhesion assembly / endoplasmic reticulum calcium ion homeostasis / negative regulation of ossification / negative regulation of B cell apoptotic process / 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 / response to UV-B / 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 / response to iron ion / negative regulation of miRNA processing / regulation of mitochondrial membrane permeability / 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 / calcium ion transport into cytosol / mRNA transcription / bone marrow development / circadian behavior / negative regulation of mitochondrial depolarization / histone deacetylase regulator activity / motor neuron apoptotic process / RUNX3 regulates CDKN1A transcription / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / channel activity / 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 / axon regeneration / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / epithelial cell apoptotic process / smooth muscle cell migration / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / intrinsic apoptotic signaling pathway in response to oxidative stress / NFE2L2 regulating tumorigenic genes / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / organ growth / branching involved in ureteric bud morphogenesis / digestive tract morphogenesis
Similarity search - Function
Apoptosis regulator, Bcl-2 / 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-2 / 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 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / p53/RUNT-type transcription factor, DNA-binding domain superfamily / 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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / 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 / Apoptosis regulator Bcl-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsWei, H. / Guo, M. / Wang, H. / Chen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
Title: Structures of p53/BCL-2 complex suggest a mechanism for p53 to antagonize BCL-2 activity.
Authors: Wei, H. / Wang, H. / Wang, G. / Qu, L. / Jiang, L. / Dai, S. / Chen, X. / Zhang, Y. / Chen, Z. / Li, Y. / Guo, M. / Chen, Y.
History
DepositionNov 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cellular tumor antigen p53
B: Apoptosis regulator Bcl-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3833
Polymers41,3172
Non-polymers651
Water1086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-3 kcal/mol
Surface area16010 Å2
Unit cell
Length a, b, c (Å)46.870, 70.480, 126.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cellular tumor antigen p53 / P53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 22103.092 Da / Num. of mol.: 1
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
#2: Protein Apoptosis regulator Bcl-2


Mass: 19214.031 Da / Num. of mol.: 1
Mutation: H20S,L95Q,R106L,F124G,R127Y,G128A,R129S,P168V,L175A,T178A,E179T,R183D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2 / Production host: Escherichia coli (E. coli) / References: UniProt: P10415
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: PEG 8K 8%-13%, 0.1M HEPES, 0.8% ethylene glycol / PH range: 7.4-7.9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.62→61.624 Å / Num. obs: 13228 / % possible obs: 99.74 % / Redundancy: 12.9 % / CC1/2: 0.977 / Rmerge(I) obs: 0.2568 / Rpim(I) all: 0.07537 / Rrim(I) all: 0.2679 / Net I/σ(I): 39.74
Reflection shellResolution: 2.62→2.714 Å / Redundancy: 13 % / Rmerge(I) obs: 1.185 / Mean I/σ(I) obs: 2.83 / Num. unique obs: 1299 / CC1/2: 0.867 / CC star: 0.964 / Rpim(I) all: 0.3408 / % possible all: 99.85

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TUP/6QGG

1tup

6qgg


Resolution: 2.62→61.624 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2795 2438 10.03 %
Rwork0.2246 --
obs0.2302 10864 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.62→61.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 1 6 2535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032596
X-RAY DIFFRACTIONf_angle_d0.553535
X-RAY DIFFRACTIONf_dihedral_angle_d7.0221526
X-RAY DIFFRACTIONf_chiral_restr0.041391
X-RAY DIFFRACTIONf_plane_restr0.003461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.67350.34651420.34741276X-RAY DIFFRACTION99
2.6735-2.73160.37661420.33641304X-RAY DIFFRACTION99
2.7316-2.79520.41971400.33131270X-RAY DIFFRACTION100
2.7952-2.86510.47371460.33321272X-RAY DIFFRACTION99
2.8651-2.94250.32651480.30761313X-RAY DIFFRACTION99
2.9425-3.02910.39451420.29581275X-RAY DIFFRACTION99
3.0291-3.12690.43121420.29681268X-RAY DIFFRACTION99
3.1269-3.23860.33381430.26091289X-RAY DIFFRACTION100
3.2386-3.36830.27441480.26031316X-RAY DIFFRACTION100
3.3683-3.52160.32391370.24891294X-RAY DIFFRACTION100
3.5216-3.70720.33551450.22791279X-RAY DIFFRACTION100
3.7072-3.93950.22531470.21871296X-RAY DIFFRACTION100
3.9395-4.24360.25051460.1911307X-RAY DIFFRACTION100
4.2436-4.67050.19681370.16531284X-RAY DIFFRACTION100
4.6705-5.3460.20561450.16251271X-RAY DIFFRACTION100
5.346-6.7340.22291470.19991295X-RAY DIFFRACTION100
6.734-61.60.27231410.19561268X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.21210.259-1.29727.51582.47057.5959-0.20110.9216-0.302-0.86520.5271-0.33640.286-0.0392-0.43170.5293-0.1812-0.0190.6179-0.07050.3147-1.58125.0403-33.5777
25.3256-1.0419-2.84511.75791.65113.0849-0.033-0.8971-0.70141.64870.0497-0.87681.83630.9299-0.13171.14390.2572-0.38060.6258-0.08710.74212.5554-1.1077-13.6103
35.6342-3.612-1.96244.67023.04966.95010.34130.25820.0195-0.34120.0832-1.6667-0.54211.8289-0.4560.2948-0.0107-0.03030.6338-0.24220.6347.92611.4485-28.3768
45.97390.49030.03645.99320.79584.77770.02760.7460.2030.13930.04271.04021.6021-1.5646-0.06030.4389-0.1528-0.03020.7703-0.0620.351-13.23074.7592-22.6926
57.48645.9008-4.01366.1265-5.27215.03651.2203-1.58231.00661.236-0.54481.3789-1.7382-1.0298-0.65540.5773-0.04750.0860.69070.01330.5102-12.78814.6286-9.6925
65.8253.80161.22487.11213.0247.4332-0.44720.0919-0.0978-0.9460.5039-0.0021-1.4155-0.87860.03680.44860.16980.02650.4551-0.00810.3427-8.242916.8706-21.236
70.8765-0.7988-0.03340.76090.38614.34230.09550.2769-0.8050.33990.4515-1.1676-0.21050.7048-0.24230.342-0.1276-0.03230.5987-0.2130.8546.337915.1349-24.4571
82.64721.2839-0.99424.34732.38667.62430.09330.0769-0.36370.62430.2588-0.07381.1883-0.7451-0.19390.46-0.037-0.01990.4684-0.00910.3795-6.43266.7771-20.0167
94.31711.1935-1.31814.65632.35382.06530.1865-0.4892-1.15960.9292-0.1932-0.32592.41410.91730.09931.0990.0362-0.22530.4682-0.06590.641-2.2201-3.0483-18.2391
102.0914-2.0535-3.03257.77391.63954.7851-0.3581-0.1999-0.39981.647-0.14980.6975-0.3461-0.3890.23610.94530.11340.04360.6019-0.06820.4341-0.261739.9219-1.2702
118.10994.8439-4.49762.985-2.03418.5997-0.0288-1.7351-0.41840.7126-0.52081.2987-2.02361.4911-0.08531.15070.0743-0.1770.637-0.09150.78898.37540.77372.0608
129.7921-1.378-2.50829.13120.27822.3671-0.2283-0.4895-0.72361.02550.2760.05561.25910.20380.03380.63190.0425-0.11680.46630.04260.45752.580928.0483-7.0075
133.96621.52271.59748.7667-0.33037.99190.00630.18360.43990.2333-0.1327-0.06-0.69240.52620.13470.4122-0.00480.03640.35250.03390.35353.698138.2997-13.1957
144.69591.47142.62389.23481.48091.59421.0387-1.57520.40082.278-0.35581.5623-0.3559-0.9037-0.08860.39750.04460.37160.7793-0.23110.9384-13.668432.3203-7.6562
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 95 through 112 )
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 140 )
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 155 )
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 176 )
5X-RAY DIFFRACTION5chain 'A' and (resid 177 through 194 )
6X-RAY DIFFRACTION6chain 'A' and (resid 195 through 213 )
7X-RAY DIFFRACTION7chain 'A' and (resid 214 through 229 )
8X-RAY DIFFRACTION8chain 'A' and (resid 230 through 263 )
9X-RAY DIFFRACTION9chain 'A' and (resid 264 through 288 )
10X-RAY DIFFRACTION10chain 'B' and (resid 7 through 25 )
11X-RAY DIFFRACTION11chain 'B' and (resid 26 through 90 )
12X-RAY DIFFRACTION12chain 'B' and (resid 91 through 118 )
13X-RAY DIFFRACTION13chain 'B' and (resid 119 through 184 )
14X-RAY DIFFRACTION14chain 'B' and (resid 185 through 202 )

+
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