[English] 日本語
Yorodumi
- PDB-4g35: Mcl-1 in complex with a biphenyl cross-linked Noxa peptide. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4g35
TitleMcl-1 in complex with a biphenyl cross-linked Noxa peptide.
Components
  • Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
  • Noxa BH3 peptide (cysteine-mediated cross-linked)
KeywordsApoptosis/Inhibitor / APOPTOSIS / BH3 domain / Bcl-2 family / Apoptosis-Inhibitor complex
Function / homology
Function and homology information


BH domain binding / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy ...BH domain binding / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / channel activity / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / response to cytokine / intrinsic apoptotic signaling pathway in response to DNA damage / regulation of apoptotic process / mitochondrial outer membrane / cell differentiation / protein dimerization activity / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Apoptosis regulator, Mcl-1 / Blc2-like / Apoptosis Regulator Bcl-x / 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 (B-Cell lymphoma); contains BH1, BH2 regions ...Apoptosis regulator, Mcl-1 / Blc2-like / Apoptosis Regulator Bcl-x / 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 (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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Noxa BH3 peptide (cysteine-mediated cross-linked) / 4,4'-bis(bromomethyl)biphenyl / Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDrake, E. / Edwardraja, S. / Lin, Q. / Gulick, A.M.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Rational design of proteolytically stable, cell-permeable peptide-based selective Mcl-1 inhibitors.
Authors: Muppidi, A. / Doi, K. / Edwardraja, S. / Drake, E.J. / Gulick, A.M. / Wang, H.G. / Lin, Q.
History
DepositionJul 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Derived calculations

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
B: Noxa BH3 peptide (cysteine-mediated cross-linked)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1593
Polymers20,8192
Non-polymers3401
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-14 kcal/mol
Surface area8170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.040, 47.970, 68.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Induced myeloid leukemia cell differentiation protein Mcl-1 homolog / Bcl-2-related protein EAT/mcl1


Mass: 18634.074 Da / Num. of mol.: 1 / Fragment: residues 152-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mcl1 / Production host: Escherichia coli (E. coli) / References: UniProt: P97287
#2: Protein/peptide Noxa BH3 peptide (cysteine-mediated cross-linked)


Type: Polypeptide / Class: Anticancer / Mass: 2184.657 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic Construct
References: Noxa BH3 peptide (cysteine-mediated cross-linked)
#3: Chemical ChemComp-4BP / 4,4'-bis(bromomethyl)biphenyl


Type: Polypeptide / Class: Anticancer / Mass: 340.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12Br2
References: Noxa BH3 peptide (cysteine-mediated cross-linked)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1.73 Å3/Da / Density % sol: 28.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% Peg 8000, 225 mM CaCl2, 2% Ethylene Glycol,50 mM Epps (pH 8.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 7, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2→39.31 Å / Num. all: 9850 / Num. obs: 9801 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 6.1 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.31 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.194 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23879 468 4.8 %RANDOM
Rwork0.19171 ---
all0.1972 9357 --
obs0.19389 9295 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0 Å20 Å2
2---1.36 Å20 Å2
3---1.54 Å2
Refinement stepCycle: LAST / Resolution: 2→39.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1202 0 14 39 1255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211237
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.9591663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0015142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48622.06363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30315217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1341516
X-RAY DIFFRACTIONr_chiral_restr0.1360.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02933
X-RAY DIFFRACTIONr_mcbond_it1.2181.5731
X-RAY DIFFRACTIONr_mcangle_it2.36221169
X-RAY DIFFRACTIONr_scbond_it3.7913506
X-RAY DIFFRACTIONr_scangle_it6.2584.5494
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 39 -
Rwork0.202 652 -
obs--99 %

+
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://pdbjlvh1.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