- PDB-2nla: Crystal structure of the Mcl-1:mNoxaB BH3 complex -
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Basic information
Entry
Database: PDB / ID: 2nla
Title
Crystal structure of the Mcl-1:mNoxaB BH3 complex
Components
FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
Phorbol-12-myristate-13-acetate-induced protein 1
Keywords
APOPTOSIS / Bcl-2 / Mcl-1 / Noxa
Function / homology
Function and homology information
Activation of NOXA and translocation to mitochondria / positive regulation of establishment of protein localization to mitochondrion / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of DNA damage response, signal transduction by p53 class mediator / BH domain binding / positive regulation of fibroblast apoptotic process / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / channel activity ...Activation of NOXA and translocation to mitochondria / positive regulation of establishment of protein localization to mitochondrion / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of DNA damage response, signal transduction by p53 class mediator / BH domain binding / positive regulation of fibroblast apoptotic process / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / channel activity / fibroblast apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / T cell homeostasis / BH3 domain binding / negative regulation of mitochondrial membrane potential / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of anoikis / response to X-ray / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to UV / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / response to cytokine / activation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / Signaling by ALK fusions and activated point mutants / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / mitochondrial outer membrane / cell differentiation / protein dimerization activity / positive regulation of apoptotic process / protein heterodimerization activity / apoptotic process / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function
Phorbol-12-myristate-13-acetate-induced protein 1 / Phorbol-12-myristate-13-acetate-induced / 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 ...Phorbol-12-myristate-13-acetate-induced protein 1 / Phorbol-12-myristate-13-acetate-induced / 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
Induced myeloid leukemia cell differentiation protein Mcl-1 homolog / Induced myeloid leukemia cell differentiation protein Mcl-1 / Phorbol-12-myristate-13-acetate-induced protein 1 Similarity search - Component
A: FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog B: Phorbol-12-myristate-13-acetate-induced protein 1
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→73.92 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.873 / SU B: 55.937 / SU ML: 0.472 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: CHAIN D REFERS TO THE NOXA PEPTIDE WHICH IS COVALENTLY LINKED TO MCL-1 THROUGH CYS 286 OF MCL-1 AND CYS 75 OF NOXA. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.291
230
4.7 %
RANDOM
Rwork
0.207
-
-
-
obs
0.211
4699
99.86 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 80.22 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.36 Å2
0.68 Å2
0 Å2
2-
-
1.36 Å2
0 Å2
3-
-
-
-2.04 Å2
Refinement step
Cycle: LAST / Resolution: 2.8→73.92 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1375
0
0
31
1406
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.022
1395
X-RAY DIFFRACTION
r_angle_refined_deg
1.341
1.951
1874
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.571
5
169
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.213
22.958
71
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
19.407
15
264
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.516
15
17
X-RAY DIFFRACTION
r_chiral_restr
0.088
0.2
208
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
1044
X-RAY DIFFRACTION
r_nbd_refined
0.242
0.2
717
X-RAY DIFFRACTION
r_nbtor_refined
0.303
0.2
947
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.204
0.2
68
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.208
0.2
47
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.226
0.2
9
X-RAY DIFFRACTION
r_mcbond_it
0.425
1.5
875
X-RAY DIFFRACTION
r_mcangle_it
0.705
2
1353
X-RAY DIFFRACTION
r_scbond_it
0.949
3
590
X-RAY DIFFRACTION
r_scangle_it
1.561
4.5
521
LS refinement shell
Resolution: 2.798→2.871 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.428
18
-
Rwork
0.413
344
-
obs
-
362
98.91 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
7.3458
-0.5017
-0.6155
5.7216
0.085
10.5334
-0.0137
-0.4616
0.776
-0.1552
0.1268
-0.0328
-0.9296
-0.6959
-0.1132
-0.3586
0.061
0.031
-0.3017
-0.0586
-0.323
-26.6062
3.2318
-7.1963
2
20.4622
-9.6652
3.5592
20.4276
0.3025
7.7655
0.5758
1.2816
-0.6782
-1.8879
-0.0637
1.5006
-0.1188
0.0764
-0.5121
-0.1677
-0.0108
0.0187
-0.1562
-0.1316
-0.4211
-18.7253
20.7181
4.2364
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION / Selection: ALL
ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
1
A
A
175 - 321
5 - 151
2
2
B
B
73 - 93
6 - 26
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