2nla

Crystal structure of the Mcl-1:mNoxaB BH3 complex

Method: X-RAY DIFFRACTION Dmax: 50.4 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog

Homo sapiens

UniProt P97287

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 152–189 Fragment:residues 171-208 and residues 209-327 Phorbol-12-myristate-13-acetate-induced protein 1 × 1 (Q9JM54) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;298 K;12% PEG 4K, 4% isopropanol, 5% dioxane, 0.1M tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.80 Å R-free 0.291

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

14 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MCL1_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–38; UniProt 152–189

FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog

Homo sapiens

UniProt Q07820

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 209–327 Fragment:residues 171-208 and residues 209-327 Phorbol-12-myristate-13-acetate-induced protein 1 × 1 (Q9JM54) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;298 K;12% PEG 4K, 4% isopropanol, 5% dioxane, 0.1M tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.80 Å R-free 0.291

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

141 other PDB entries and 285 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MCL1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 39–157; UniProt 209–327

Phorbol-12-myristate-13-acetate-induced protein 1

OrganismNot specified

UniProt Q9JM54

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 68–93 Fragment:BH3 (UNP residues 68-93) FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog × 1 (P97287,Q07820) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;298 K;12% PEG 4K, 4% isopropanol, 5% dioxane, 0.1M tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.80 Å R-free 0.291

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name APR_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–26; UniProt 68–93

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2nla

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2nla
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2nla
Deposition date deposition_date2006-10-19
Structure title titleCrystal structure of the Mcl-1:mNoxaB BH3 complex
Keywords keywordsApoptosis, Bcl-2, Mcl-1, Noxa; APOPTOSIS
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.68
Radius of gyration Rg (electron density) rg_electron15.12
Forward intensity I(0) i07518210.00
Molecular weight molecular_weight19529.0 kDa
Excluded volume excluded_volume24363 ų
Envelope volume envelope_volume27773 ų
Hydration-shell volume shell_volume15135 ų
Envelope diameter envelope_diameter49.7
Shell Rg shell_rg21.43
Envelope Rg envelope_rg15.47
Shape Rg shape_rg15.08
Total Rg total_rg16.38
Total atoms total_atoms1375
Residues n_residues171
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax50.4
Rg (real space) rg_real16.54
Rg uncertainty (real space) rg_real_error0.20
I(0) (real space) i0_real7.5180e+06
I(0) uncertainty (real space) i0_real_error7.9700e+04
Rg (reciprocal space) rg_reciprocal16.56
I(0) (reciprocal space) i0_reciprocal7518000.0000
Solution quality estimate total_estimate0.8951
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.3
Skewness Skewness skewness0.029
Kurtosis Kurtosis kurtosis-0.421
Angular range angular_range— – 0.4750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1786000.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.984

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2nlaa_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.1 — Toxins' membrane translocation domains
Superfamily Superfamily superfamilyf.1.4 — Bcl-2 inhibitors of programmed cell death
Family Family familyf.1.4.1 — Bcl-2 inhibitors of programmed cell death

CATH v4.4 (1 domains)

Domain ID domain_id2nlaA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology437 — Apoptosis Regulator Bcl-x
Homologous superfamily homologous superfamily10 — Blc2-like

8. Citations (1)

9. Files and Curves (10)