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- PDB-3kj1: Mcl-1 in complex with Bim BH3 mutant I2dA -

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Basic information

Entry
Database: PDB / ID: 3kj1
TitleMcl-1 in complex with Bim BH3 mutant I2dA
Components
  • Bcl-2-like protein 11
  • Induced myeloid leukemia cell differentiation protein Mcl-1
KeywordsAPOPTOSIS / bcl-2 / bh3 / protein-peptide complex / Alternative splicing / Cytoplasm / Developmental protein / Differentiation / Isopeptide bond / Membrane / Mitochondrion / Nucleus / Phosphoprotein / Polymorphism / Transmembrane / Ubl conjugation
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / ear development / tube formation / meiosis I / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / mammary gland development / cell fate determination / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of T cell apoptotic process / regulation of organ growth / cellular response to glucocorticoid stimulus / mitochondrial fusion / channel activity / Bcl-2 family protein complex / myeloid cell homeostasis / FOXO-mediated transcription of cell death genes / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / thymocyte apoptotic process / T cell homeostasis / BH3 domain binding / odontogenesis of dentin-containing tooth / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / B cell homeostasis / protein transmembrane transporter activity / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / endomembrane system / positive regulation of cell cycle / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / FLT3 Signaling / response to endoplasmic reticulum stress / cell-matrix adhesion / negative regulation of autophagy / post-embryonic development / release of cytochrome c from mitochondria / thymus development / kidney development / response to cytokine / positive regulation of protein-containing complex assembly / male gonad development / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by BRAF and RAF1 fusions / microtubule binding / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / in utero embryonic development / mitochondrial outer membrane / molecular adaptor activity / positive regulation of apoptotic process / protein heterodimerization activity / apoptotic process / DNA damage response / negative regulation of apoptotic process / protein kinase binding / protein homodimerization activity / mitochondrion / nucleoplasm / membrane / nucleus / 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, 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, Bim N-terminal / Bcl-2-like protein 11 / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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
ACETATE ION / Bcl-2-like protein 11 / Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.945 Å
AuthorsFire, E. / Grant, R.A. / Keating, A.E.
CitationJournal: Protein Sci. / Year: 2010
Title: Mcl-1-Bim complexes accommodate surprising point mutations via minor structural changes.
Authors: Fire, E. / Gulla, S.V. / Grant, R.A. / Keating, A.E.
History
DepositionNov 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1179
Polymers20,6952
Non-polymers4227
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-129 kcal/mol
Surface area8990 Å2
MethodPISA
2
A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Bcl-2-like protein 11
hetero molecules

A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Bcl-2-like protein 11
hetero molecules

A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Bcl-2-like protein 11
hetero molecules

A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,46836
Polymers82,7828
Non-polymers1,68628
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area14620 Å2
ΔGint-636 kcal/mol
Surface area31720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.066, 72.007, 117.845
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-328-

CL

21A-6-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 17937.359 Da / Num. of mol.: 1 / Fragment: (UNP 172-322)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L3, mcl-1, MCL1 / Plasmid: pSV282 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q07820
#2: Protein/peptide Bcl-2-like protein 11 / Bcl2-L-11 / Bcl2-interacting mediator of cell death


Mass: 2758.056 Da / Num. of mol.: 1 / Fragment: BH3 region of BIM (UNP 1-21) / Mutation: I6A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L11, BIM / Plasmid: pSV282 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O43521

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Non-polymers , 4 types, 123 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Imidazole, 0.2 M Zinc Acetate, 16% PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 24, 2008
RadiationMonochromator: VarimaxHR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 16418 / % possible obs: 96.9 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.046 / Χ2: 1.157 / Net I/σ(I): 15.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.95-2.027.60.42612990.68479.5
2.02-2.19.60.27316180.79396.3
2.1-2.210.50.19416360.95198
2.2-2.3110.40.14416601.06298.3
2.31-2.4610.60.10816441.21598.6
2.46-2.6510.60.08316841.20799.1
2.65-2.9110.50.06216581.21699.5
2.91-3.3310.60.04717031.33699.6
3.33-4.210.60.03717201.4999.8
4.2-5010.10.03117961.33299.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.945→28.885 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.3 / σ(F): 1.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.213 831 5.06 %
Rwork0.187 --
obs0.188 16418 51.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.123 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso max: 139.75 Å2 / Biso mean: 42.775 Å2 / Biso min: 14.92 Å2
Baniso -1Baniso -2Baniso -3
1--1.853 Å2-0 Å20 Å2
2---2.429 Å20 Å2
3---4.281 Å2
Refinement stepCycle: LAST / Resolution: 1.945→28.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1424 0 10 116 1550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091454
X-RAY DIFFRACTIONf_angle_d0.9951954
X-RAY DIFFRACTIONf_chiral_restr0.071211
X-RAY DIFFRACTIONf_plane_restr0.004253
X-RAY DIFFRACTIONf_dihedral_angle_d14.976543
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.945-2.0660.2271170.1972230234744
2.066-2.2260.2141450.1722585273051
2.226-2.450.2091410.1762614275552
2.45-2.8040.2341450.1872645279052
2.804-3.5320.2071560.1862684284053
3.532-28.8880.1941270.182829295655
Refinement TLS params.Method: refined / Origin x: 3.2443 Å / Origin y: 20.6557 Å / Origin z: 41.4334 Å
111213212223313233
T0.0947 Å2-0.006 Å20.0108 Å2-0.0354 Å2-0.0034 Å2--0.1081 Å2
L1.5129 °2-0.0212 °20.6064 °2-0.3758 °20.1943 °2--0.9476 °2
S0.0641 Å °-0.034 Å °-0.1712 Å °0.0846 Å °0.005 Å °0.0425 Å °0.1326 Å °0.0161 Å °-0.0745 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA171 - 322
2X-RAY DIFFRACTION1allB1 - 22
3X-RAY DIFFRACTION1allA1 - 5
4X-RAY DIFFRACTION1allA - B1 - 116
5X-RAY DIFFRACTION1allA1428
6X-RAY DIFFRACTION1allA1 - 323

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