[English] 日本語
Yorodumi
- PDB-7y99: Crystal Structure Analysis of cp2 bound BCLxl -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7y99
TitleCrystal Structure Analysis of cp2 bound BCLxl
Components
  • Bcl-2-like protein 1
  • CP2 peptide
KeywordsAPOPTOSIS / Complex
Function / homology
Function and homology information


The NLRP1 inflammasome / apoptotic process in bone marrow cell / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / synaptic vesicle recycling via endosome / positive regulation of synaptic vesicle exocytosis / positive regulation of synaptic vesicle clustering / RAS processing / BH domain binding / fertilization / regulation of growth ...The NLRP1 inflammasome / apoptotic process in bone marrow cell / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / synaptic vesicle recycling via endosome / positive regulation of synaptic vesicle exocytosis / positive regulation of synaptic vesicle clustering / RAS processing / BH domain binding / fertilization / regulation of growth / positive regulation of synaptic vesicle endocytosis / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / germ cell development / hepatocyte apoptotic process / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cellular response to alkaloid / regulation of mitochondrial membrane permeability / response to cycloheximide / Bcl-2 family protein complex / negative regulation of release of cytochrome c from mitochondria / clathrin binding / negative regulation of intrinsic apoptotic signaling pathway / ovarian follicle development / positive regulation of ATP biosynthetic process / negative regulation of anoikis / extrinsic apoptotic signaling pathway in absence of ligand / BH3 domain binding / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of protein localization to plasma membrane / regulation of synaptic vesicle endocytosis / neuron apoptotic process / response to ischemia / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of long-term synaptic depression / response to cytokine / male gonad development / clathrin-coated pit / in utero embryonic development / MDM2/MDM4 family protein binding / regulation of mitochondrial membrane potential / cellular response to amino acid stimulus / regulation of cytokinesis / mitochondrion organization / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to gamma radiation / response to radiation / response to virus / cell population proliferation / mitochondrial membrane / synaptic vesicle membrane / negative regulation of neuron apoptotic process / synaptic vesicle / presynapse / nuclear membrane / channel activity / GTPase binding / spermatogenesis / defense response to virus / regulation of apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / positive regulation of apoptotic process / mitochondrial matrix / centrosome / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / protein-containing complex binding / endoplasmic reticulum / mitochondrion / membrane / identical protein binding / cytosol / cytoplasm
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 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. ...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 / 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
Similarity search - Domain/homology
Chem-IQ8 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLi, F.W. / Liu, C. / Wu, C.L. / Wu, D.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2024
Title: Cyclic peptides discriminate BCL-2 and its clinical mutants from BCL-X L by engaging a single-residue discrepancy.
Authors: Li, F. / Liu, J. / Liu, C. / Liu, Z. / Peng, X. / Huang, Y. / Chen, X. / Sun, X. / Wang, S. / Chen, W. / Xiong, D. / Diao, X. / Wang, S. / Zhuang, J. / Wu, C. / Wu, D.
History
DepositionJun 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Structure summary / Category: entity / Item: _entity.details
Revision 1.2Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bcl-2-like protein 1
B: CP2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9113
Polymers17,6202
Non-polymers2911
Water1,49583
1
A: Bcl-2-like protein 1
B: CP2 peptide
hetero molecules

A: Bcl-2-like protein 1
B: CP2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8226
Polymers35,2394
Non-polymers5832
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area7220 Å2
ΔGint-36 kcal/mol
Surface area14620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.433, 100.478, 51.326
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Bcl-2-like protein 1 / Bcl2-L-1 / Apoptosis regulator Bcl-X


Mass: 16190.101 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bcl2l1, Bcl2l, Bclx / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q64373
#2: Protein/peptide CP2 peptide


Mass: 1429.575 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Molecule 2 is a cyclic peptide, IQ8 is a special linker connected with A and C.
Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-IQ8 / N-(2-acetamidoethyl)-4-(4,5-dihydro-1,3-thiazol-2-yl)benzamide


Mass: 291.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17N3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: Ammonium acetate, BIS-TRIS, MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 21, 2021 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 14253 / % possible obs: 99.9 % / Redundancy: 12.6 % / CC1/2: 0.975 / CC star: 0.994 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.045 / Rrim(I) all: 0.159 / Χ2: 0.961 / Net I/σ(I): 7.9 / Num. measured all: 179227
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.9-1.9312.80.4926670.9560.9890.1410.5120.99399.9
1.93-1.9712.90.4097100.9660.9910.1180.4260.931100
1.97-2.0112.80.386860.9710.9930.1090.3950.957100
2.01-2.0512.60.3217150.9760.9940.0930.3340.94100
2.05-2.0912.60.2917190.980.9950.0850.3031.041100
2.09-2.14120.2586930.980.9950.0760.2690.956100
2.14-2.1911.20.2386930.9790.9950.0740.251.013100
2.19-2.25130.2187150.9860.9960.0630.2281.053100
2.25-2.3213.20.2077020.9860.9960.0590.2160.971100
2.32-2.39130.1947060.9840.9960.0560.2020.953100
2.39-2.4813.10.1817080.9840.9960.0520.1890.957100
2.48-2.5812.80.1697120.9880.9970.0490.1760.921100
2.58-2.712.60.167020.9890.9970.0470.1670.92699.7
2.7-2.8411.50.1517230.9870.9970.0460.1580.97299.9
2.84-3.0213.30.1457150.9890.9970.0410.1510.924100
3.02-3.2513.20.1417160.9920.9980.040.1470.909100
3.25-3.5812.90.1377280.9880.9970.0390.1420.909100
3.58-4.0911.70.1377210.9880.9970.0410.1430.97899.7
4.09-5.1612.70.1327390.990.9980.0390.1380.93699.9
5.16-5011.50.1447830.9540.9880.0450.1521.00299.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.49 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.756 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19217 697 5 %RANDOM
Rwork0.17446 ---
obs0.17538 13311 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.556 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å2-0 Å2-0 Å2
2---0.11 Å2-0 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.9→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1247 0 0 83 1330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131281
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181144
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.6531734
X-RAY DIFFRACTIONr_angle_other_deg1.5551.6012620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3635148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.57922.07877
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58315199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.579159
X-RAY DIFFRACTIONr_chiral_restr0.0910.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021468
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02338
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.381.895599
X-RAY DIFFRACTIONr_mcbond_other2.2441.89598
X-RAY DIFFRACTIONr_mcangle_it3.3342.817746
X-RAY DIFFRACTIONr_mcangle_other3.3322.82747
X-RAY DIFFRACTIONr_scbond_it3.4322.322681
X-RAY DIFFRACTIONr_scbond_other3.3912.321681
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3163.332989
X-RAY DIFFRACTIONr_long_range_B_refined7.36135.0715140
X-RAY DIFFRACTIONr_long_range_B_other7.32934.9465100
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 38 -
Rwork0.206 831 -
obs--86.04 %

+
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