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- PDB-5c6h: Mcl-1 complexed with Mule -

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Basic information

Entry
Database: PDB / ID: 5c6h
TitleMcl-1 complexed with Mule
Components
  • Induced myeloid leukemia cell differentiation protein Mcl-1
  • Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1
KeywordsAPOPTOSIS/APOPTOSIS REGULATOR / complex. Mcl-1 / Mule / BH3 / APOPTOSIS-APOPTOSIS REGULATOR complex
Function / homology
Function and homology information


negative regulation of mitochondrial fusion / histone ubiquitin ligase activity / positive regulation of mitophagy in response to mitochondrial depolarization / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / HECT-type E3 ubiquitin transferase / cell fate determination / channel activity / mitochondrial fusion / positive regulation of protein targeting to mitochondrion ...negative regulation of mitochondrial fusion / histone ubiquitin ligase activity / positive regulation of mitophagy in response to mitochondrial depolarization / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / HECT-type E3 ubiquitin transferase / cell fate determination / channel activity / mitochondrial fusion / positive regulation of protein targeting to mitochondrion / Bcl-2 family protein complex / Golgi organization / BH3 domain binding / protein monoubiquitination / protein transmembrane transporter activity / 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 / positive regulation of protein ubiquitination / response to cytokine / base-excision repair / circadian regulation of gene expression / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / intrinsic apoptotic signaling pathway in response to DNA damage / Antigen processing: Ubiquitination & Proteasome degradation / regulation of apoptotic process / secretory granule lumen / Interleukin-4 and Interleukin-13 signaling / mitochondrial outer membrane / ficolin-1-rich granule lumen / membrane fusion / cell differentiation / positive regulation of apoptotic process / protein heterodimerization activity / Golgi membrane / DNA damage response / Neutrophil degranulation / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
HUWE1, UBA domain / E3 ubiquitin ligase, domain of unknown function DUF908 / E3 ubiquitin ligase, domain of unknown function DUF913 / Domain of Unknown Function (DUF908) / Domain of Unknown Function (DUF913) / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / WWE domain / WWE domain superfamily / WWE domain ...HUWE1, UBA domain / E3 ubiquitin ligase, domain of unknown function DUF908 / E3 ubiquitin ligase, domain of unknown function DUF913 / Domain of Unknown Function (DUF908) / Domain of Unknown Function (DUF913) / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Apoptosis regulator, Mcl-1 / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Blc2-like / UBA/TS-N domain / Apoptosis Regulator Bcl-x / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / 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. / UBA-like superfamily / Bcl-2-like superfamily / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Induced myeloid leukemia cell differentiation protein Mcl-1 / E3 ubiquitin-protein ligase HUWE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsSong, T. / Wang, Z. / Ji, F. / Chai, G. / Liu, Y. / Li, X. / Li, Z. / Fan, Y. / Zhang, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China21402022 China
National Natural Science Foundation of China21372036 China
CitationJournal: To Be Published
Title: Structure of Mcl-1 complexed with Mule at 2.05 Angstroms resolution
Authors: Song, T. / Wang, Z. / Ji, F. / Chai, G. / Liu, Y. / Li, X. / Li, Z. / Fan, Y. / Zhang, Z.
History
DepositionJun 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1
C: Induced myeloid leukemia cell differentiation protein Mcl-1
D: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1
E: Induced myeloid leukemia cell differentiation protein Mcl-1
F: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1
G: Induced myeloid leukemia cell differentiation protein Mcl-1
H: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1
I: Induced myeloid leukemia cell differentiation protein Mcl-1
J: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1
K: Induced myeloid leukemia cell differentiation protein Mcl-1
L: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1
M: Induced myeloid leukemia cell differentiation protein Mcl-1
N: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1
O: Induced myeloid leukemia cell differentiation protein Mcl-1
P: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1
Q: Induced myeloid leukemia cell differentiation protein Mcl-1
R: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1
S: Induced myeloid leukemia cell differentiation protein Mcl-1
T: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1
U: Induced myeloid leukemia cell differentiation protein Mcl-1
V: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1
W: Induced myeloid leukemia cell differentiation protein Mcl-1
X: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1


Theoretical massNumber of molelcules
Total (without water)250,73624
Polymers250,73624
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39980 Å2
ΔGint-208 kcal/mol
Surface area96530 Å2
2
A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1


Theoretical massNumber of molelcules
Total (without water)20,8952
Polymers20,8952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-17 kcal/mol
Surface area9400 Å2
MethodPISA
3
C: Induced myeloid leukemia cell differentiation protein Mcl-1
D: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1


Theoretical massNumber of molelcules
Total (without water)20,8952
Polymers20,8952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-18 kcal/mol
Surface area9660 Å2
MethodPISA
4
E: Induced myeloid leukemia cell differentiation protein Mcl-1
F: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1


Theoretical massNumber of molelcules
Total (without water)20,8952
Polymers20,8952
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-14 kcal/mol
Surface area9520 Å2
MethodPISA
5
G: Induced myeloid leukemia cell differentiation protein Mcl-1
H: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1


Theoretical massNumber of molelcules
Total (without water)20,8952
Polymers20,8952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-17 kcal/mol
Surface area9380 Å2
MethodPISA
6
I: Induced myeloid leukemia cell differentiation protein Mcl-1
J: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1


Theoretical massNumber of molelcules
Total (without water)20,8952
Polymers20,8952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-17 kcal/mol
Surface area9500 Å2
MethodPISA
7
K: Induced myeloid leukemia cell differentiation protein Mcl-1
L: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1


Theoretical massNumber of molelcules
Total (without water)20,8952
Polymers20,8952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-18 kcal/mol
Surface area9560 Å2
MethodPISA
8
M: Induced myeloid leukemia cell differentiation protein Mcl-1
N: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1


Theoretical massNumber of molelcules
Total (without water)20,8952
Polymers20,8952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-17 kcal/mol
Surface area9650 Å2
MethodPISA
9
O: Induced myeloid leukemia cell differentiation protein Mcl-1
P: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1


Theoretical massNumber of molelcules
Total (without water)20,8952
Polymers20,8952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-19 kcal/mol
Surface area9530 Å2
MethodPISA
10
Q: Induced myeloid leukemia cell differentiation protein Mcl-1
R: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1


Theoretical massNumber of molelcules
Total (without water)20,8952
Polymers20,8952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-18 kcal/mol
Surface area9200 Å2
MethodPISA
11
S: Induced myeloid leukemia cell differentiation protein Mcl-1
T: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1


Theoretical massNumber of molelcules
Total (without water)20,8952
Polymers20,8952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-18 kcal/mol
Surface area9400 Å2
MethodPISA
12
U: Induced myeloid leukemia cell differentiation protein Mcl-1
V: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1


Theoretical massNumber of molelcules
Total (without water)20,8952
Polymers20,8952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-18 kcal/mol
Surface area8820 Å2
MethodPISA
13
W: Induced myeloid leukemia cell differentiation protein Mcl-1
X: Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1


Theoretical massNumber of molelcules
Total (without water)20,8952
Polymers20,8952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-18 kcal/mol
Surface area9260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.790, 114.240, 135.980
Angle α, β, γ (deg.)90.12, 92.32, 90.01
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Induced myeloid leukemia cell differentiation protein Mcl-1 / Bcl-2-like protein 3 / Bcl2-L-3 / Bcl-2-related protein EAT/mcl1 / mcl1/EAT


Mass: 17922.344 Da / Num. of mol.: 12 / Fragment: UNP residues 171-327
Source method: isolated from a genetically manipulated source
Details: Mcl-1, residues 171-327 / Source: (gene. exp.) Homo sapiens (human) / Gene: MCL1, BCL2L3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07820
#2: Protein/peptide
Mule BH3 peptide from E3 ubiquitin-protein ligase HUWE1


Mass: 2972.287 Da / Num. of mol.: 12 / Source method: obtained synthetically / Details: Mule BH3, residues 1969-1994 / Source: (synth.) Homo sapiens (human) / References: UniProt: Q7Z6Z7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG3350, calcium chloride

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.987, 0.988, 1.0
DetectorType: APEX II CCD / Detector: CCD / Date: May 18, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9871
20.9881
311
ReflectionResolution: 2.05→35.451 Å / Num. obs: 114746 / % possible obs: 95.6 % / Redundancy: 5 % / Net I/σ(I): 3.26
Reflection shellResolution: 2.05→2.75 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-20002.6data collection
PHENIX1.8.2_1309model building
Coot0.8.1.1data processing
XDSIA32data reduction
Coot0.8.1.1phasing
HKL-20002.6data extraction
RefinementResolution: 2.05→35.451 Å / SU ML: 0.31 / Cross valid method: NONE / σ(F): 2 / Phase error: 42.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3456 5763 5.02 %
Rwork0.2948 --
obs0.2974 114746 95.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→35.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17309 0 0 172 17481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317572
X-RAY DIFFRACTIONf_angle_d0.65423617
X-RAY DIFFRACTIONf_dihedral_angle_d13.916648
X-RAY DIFFRACTIONf_chiral_restr0.0492609
X-RAY DIFFRACTIONf_plane_restr0.0033053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.07330.41011970.35223450X-RAY DIFFRACTION91
2.0733-2.09770.38151920.33383630X-RAY DIFFRACTION94
2.0977-2.12330.35541920.31263705X-RAY DIFFRACTION96
2.1233-2.15010.35282000.30853525X-RAY DIFFRACTION96
2.1501-2.17840.40731600.30473598X-RAY DIFFRACTION96
2.1784-2.20830.37771760.30483680X-RAY DIFFRACTION96
2.2083-2.23980.39341730.30283727X-RAY DIFFRACTION96
2.2398-2.27320.40121910.3233534X-RAY DIFFRACTION91
2.2732-2.30870.3631970.2943523X-RAY DIFFRACTION96
2.3087-2.34660.34171840.29213617X-RAY DIFFRACTION96
2.3466-2.3870.33891970.28263684X-RAY DIFFRACTION96
2.387-2.43040.3411870.29933778X-RAY DIFFRACTION97
2.4304-2.47720.36741970.30763618X-RAY DIFFRACTION97
2.4772-2.52770.35462040.30523586X-RAY DIFFRACTION97
2.5277-2.58270.36022130.2853692X-RAY DIFFRACTION97
2.5827-2.64270.32391980.28163772X-RAY DIFFRACTION97
2.6427-2.70880.33032060.29393546X-RAY DIFFRACTION96
2.7088-2.7820.34951910.28853664X-RAY DIFFRACTION97
2.782-2.86380.35621840.27963770X-RAY DIFFRACTION97
2.8638-2.95620.3222000.29773675X-RAY DIFFRACTION97
2.9562-3.06180.36311890.30183660X-RAY DIFFRACTION97
3.0618-3.18440.34352020.29563764X-RAY DIFFRACTION97
3.1844-3.32920.34181760.29683589X-RAY DIFFRACTION97
3.3292-3.50450.35362100.30543705X-RAY DIFFRACTION96
3.5045-3.72390.30461750.28143600X-RAY DIFFRACTION96
3.7239-4.01110.32282020.27883717X-RAY DIFFRACTION97
4.0111-4.4140.31651980.26563641X-RAY DIFFRACTION97
4.414-5.05120.32061750.26753643X-RAY DIFFRACTION96
5.0512-6.3580.32152160.29853628X-RAY DIFFRACTION95
6.358-35.45670.30981810.29133262X-RAY DIFFRACTION87

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