[English] 日本語
Yorodumi
- PDB-4a1w: Crystal structure of alpha-beta foldamer 4c in complex with Bcl-xL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4a1w
TitleCrystal structure of alpha-beta foldamer 4c in complex with Bcl-xL
Components
  • ALPHA-BETA-FOLDAMER 2C
  • BCL-2-LIKE PROTEIN 1
KeywordsAPOPTOSIS/INHIBITOR / APOPTOSIS-INHIBITOR COMPLEX / MIMICRY
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / meiosis I / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of fibroblast apoptotic process / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Activation of BIM and translocation to mitochondria / dendritic cell apoptotic process / dendritic cell proliferation / apoptotic process in bone marrow cell ...BIM-BCL-xl complex / BIM-BCL-2 complex / meiosis I / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of fibroblast apoptotic process / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Activation of BIM and translocation to mitochondria / dendritic cell apoptotic process / dendritic cell proliferation / apoptotic process in bone marrow cell / The NLRP1 inflammasome / positive regulation of mononuclear cell proliferation / SARS-CoV-1-mediated effects on programmed cell death / negative regulation of dendritic cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / fertilization / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of growth / regulation of mitochondrial membrane permeability / germ cell development / apoptotic mitochondrial changes / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / cellular response to glucocorticoid stimulus / hepatocyte apoptotic process / response to cycloheximide / NRAGE signals death through JNK / STAT5 activation downstream of FLT3 ITD mutants / cellular response to alkaloid / negative regulation of release of cytochrome c from mitochondria / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / negative regulation of intrinsic apoptotic signaling pathway / FOXO-mediated transcription of cell death genes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / ectopic germ cell programmed cell death / negative regulation of anoikis / BH3 domain binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / epithelial cell proliferation / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of protein localization to plasma membrane / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / response to cytokine / FLT3 Signaling / endomembrane system / release of cytochrome c from mitochondria / negative regulation of autophagy / response to endoplasmic reticulum stress / regulation of mitochondrial membrane potential / cellular response to amino acid stimulus / regulation of cytokinesis / male gonad development / positive regulation of protein-containing complex assembly / cellular response to gamma radiation / intrinsic apoptotic signaling pathway in response to DNA damage / endocytosis / in utero embryonic development / RAS processing / neuron apoptotic process / Signaling by BRAF and RAF1 fusions / synaptic vesicle membrane / nuclear membrane / channel activity / Interleukin-4 and Interleukin-13 signaling / spermatogenesis / regulation of apoptotic process / negative regulation of neuron apoptotic process / defense response to virus / microtubule binding / mitochondrial outer membrane / mitochondrial inner membrane / positive regulation of apoptotic process / mitochondrial matrix / centrosome / apoptotic process / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / mitochondrion / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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
ALPHA-BETA-FOLDAMER 2C / Bcl-2-like protein 11 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.497 Å
AuthorsBoersma, M.D. / Haase, H.S. / Kaufman, K.J. / Horne, W.S. / Lee, E.F. / Clarke, O.B. / Smith, B.J. / Colman, P.M. / Gellman, S.H. / Fairlie, W.D.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Evaluation of Diverse Alpha/Beta-Backbone Patterns for Functional Alpha-Helix Mimicry: Analogues of the Bim Bh3 Domain.
Authors: Boersma, M.D. / Haase, H.S. / Peterson-Kaufman, K.J. / Lee, E.F. / Clarke, O.B. / Colman, P.M. / Smith, B.J. / Horne, W.S. / Fairlie, W.D. / Gellman, S.H.
History
DepositionSep 20, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Jun 20, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_unobs_or_zero_occ_atoms / struct_conn
Revision 2.0Apr 24, 2019Group: Data collection / Polymer sequence
Category: diffrn_source / entity_poly / pdbx_seq_map_depositor_info
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BCL-2-LIKE PROTEIN 1
B: BCL-2-LIKE PROTEIN 1
C: BCL-2-LIKE PROTEIN 1
D: BCL-2-LIKE PROTEIN 1
P: ALPHA-BETA-FOLDAMER 2C
Q: ALPHA-BETA-FOLDAMER 2C
R: ALPHA-BETA-FOLDAMER 2C
S: ALPHA-BETA-FOLDAMER 2C


Theoretical massNumber of molelcules
Total (without water)80,9828
Polymers80,9828
Non-polymers00
Water4,612256
1
A: BCL-2-LIKE PROTEIN 1
D: BCL-2-LIKE PROTEIN 1
P: ALPHA-BETA-FOLDAMER 2C
S: ALPHA-BETA-FOLDAMER 2C


Theoretical massNumber of molelcules
Total (without water)40,4914
Polymers40,4914
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-43.2 kcal/mol
Surface area14960 Å2
MethodPISA
2
B: BCL-2-LIKE PROTEIN 1
C: BCL-2-LIKE PROTEIN 1
Q: ALPHA-BETA-FOLDAMER 2C
R: ALPHA-BETA-FOLDAMER 2C


Theoretical massNumber of molelcules
Total (without water)40,4914
Polymers40,4914
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-41.4 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.213, 106.290, 100.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-2001-

HOH

-
Components

#1: Protein
BCL-2-LIKE PROTEIN 1 / BCL2-L-1 / APOPTOSIS REGULATOR BCL-X


Mass: 17917.959 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07817
#2: Protein/peptide
ALPHA-BETA-FOLDAMER 2C


Type: Peptide-like / Class: Inhibitor / Mass: 2327.661 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) / References: ALPHA-BETA-FOLDAMER 2C, UniProt: O43521*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsAMIDE (NH2): TERMINAL AMIDE 3-AMINO-4-(P-TOLYL)BUTANOIC ACID (BTY): BETA PEPTIDE 3-AMINO-4- ...AMIDE (NH2): TERMINAL AMIDE 3-AMINO-4-(P-TOLYL)BUTANOIC ACID (BTY): BETA PEPTIDE 3-AMINO-4-METHYLHEXANOIC ACID (BIL): BETA PEPTIDE 3-AMINO-4-PHENYLBUTANOIC ACID (BFE): BETA PEPTIDE 3-AMINO-4-(1H-INDOL-3-YL)BUTANOIC ACID (W3B): BETA PEPTIDE 3-AMINOPROPANOIC ACID (BGL): BETA PEPTIDE
Sequence detailsDELETION OF AMINO ACID RESIDUES 27-82 AND 210-233.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.98 %
Description: MOLECULAR REPLACEMENT WAS PERFORMED USING THE STRUCTURE OF BCL-XL FROM THE PDB ENTRY 3FDL, WITH THE PEPTIDE REMOVED, AS A SEARCH MODEL
Crystal growpH: 7.5
Details: 25% (W/V) PEG 3350, 0.2 M LITHIUM SULFATE, 0.1 M HEPES PH 7.5.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 30333 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 6.55 % / Biso Wilson estimate: 37.36 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 14.99
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 5.55 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.17 / % possible all: 96.3

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FDL

3fdl


Resolution: 2.497→64.027 Å / SU ML: 0.85 / σ(F): 1.99 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2639 1522 5 %
Rwork0.1972 --
obs0.2004 30333 99.37 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.098 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-17.992 Å20 Å20 Å2
2---9.6346 Å20 Å2
3----8.3575 Å2
Refinement stepCycle: LAST / Resolution: 2.497→64.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5207 0 0 256 5463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085386
X-RAY DIFFRACTIONf_angle_d1.1557291
X-RAY DIFFRACTIONf_dihedral_angle_d18.1031972
X-RAY DIFFRACTIONf_chiral_restr0.082745
X-RAY DIFFRACTIONf_plane_restr0.004938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4967-2.57730.35381310.27852453X-RAY DIFFRACTION94
2.5773-2.66940.34471370.25852591X-RAY DIFFRACTION100
2.6694-2.77630.29581380.25372590X-RAY DIFFRACTION100
2.7763-2.90260.33131360.22952583X-RAY DIFFRACTION100
2.9026-3.05570.33531400.20762626X-RAY DIFFRACTION100
3.0557-3.24710.27661360.20232592X-RAY DIFFRACTION100
3.2471-3.49780.29261380.2122631X-RAY DIFFRACTION100
3.4978-3.84980.23691380.18772616X-RAY DIFFRACTION100
3.8498-4.40670.22331400.15512653X-RAY DIFFRACTION100
4.4067-5.55150.23071410.15822681X-RAY DIFFRACTION100
5.5515-64.04790.22561470.20052795X-RAY DIFFRACTION99

+
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