2cly

Subcomplex of the stator of bovine mitochondrial ATP synthase

Method: X-RAY DIFFRACTION Dmax: 181.3 Å Quality: REASONABLE

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

ATP SYNTHASE B CHAIN, MITOCHONDRIAL

BOS TAURUS

UniProt P13619

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–214 Fragment:STATOR SUBCOMPLEX ATP SYNTHASE D CHAIN, MITOCHONDRIAL × 1 (P13620) ATP SYNTHASE COUPLING FACTOR 6, MITOCHONDRIAL × 1 (P02721) X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;100 MM TRIS, 150 MM NACL, 17% PEG 5K MME, 7.5% GLYCEROL, 1% PICOLINE, pH 8.00 Resolution 2.80 Å R-free 0.295
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 1–214 Fragment:STATOR SUBCOMPLEX ATP SYNTHASE D CHAIN, MITOCHONDRIAL × 1 (P13620) ATP SYNTHASE COUPLING FACTOR 6, MITOCHONDRIAL × 1 (P02721) X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;100 MM TRIS, 150 MM NACL, 17% PEG 5K MME, 7.5% GLYCEROL, 1% PICOLINE, pH 8.00 Resolution 2.80 Å R-free 0.295

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.

31 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AT5F1_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–214; UniProt 1–214 Author chain D; PDBConstruct 1–214; UniProt 1–214

ATP SYNTHASE D CHAIN, MITOCHONDRIAL

BOS TAURUS

UniProt P13620

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 1–160 Fragment:STATOR SUBCOMPLEX ATP SYNTHASE B CHAIN, MITOCHONDRIAL × 1 (P13619) ATP SYNTHASE COUPLING FACTOR 6, MITOCHONDRIAL × 1 (P02721) X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;100 MM TRIS, 150 MM NACL, 17% PEG 5K MME, 7.5% GLYCEROL, 1% PICOLINE, pH 8.00 Resolution 2.80 Å R-free 0.295
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 1–160 Fragment:STATOR SUBCOMPLEX ATP SYNTHASE B CHAIN, MITOCHONDRIAL × 1 (P13619) ATP SYNTHASE COUPLING FACTOR 6, MITOCHONDRIAL × 1 (P02721) X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;100 MM TRIS, 150 MM NACL, 17% PEG 5K MME, 7.5% GLYCEROL, 1% PICOLINE, pH 8.00 Resolution 2.80 Å R-free 0.295

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.

29 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ATP5H_BOVIN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–160; UniProt 1–160 Author chain E; PDBConstruct 1–160; UniProt 1–160

ATP SYNTHASE COUPLING FACTOR 6, MITOCHONDRIAL

BOS TAURUS

UniProt P02721

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 32–108 Fragment:STATOR SUBCOMPLEX ATP SYNTHASE B CHAIN, MITOCHONDRIAL × 1 (P13619) ATP SYNTHASE D CHAIN, MITOCHONDRIAL × 1 (P13620) X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;100 MM TRIS, 150 MM NACL, 17% PEG 5K MME, 7.5% GLYCEROL, 1% PICOLINE, pH 8.00 Resolution 2.80 Å R-free 0.295
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 32–108 Fragment:STATOR SUBCOMPLEX ATP SYNTHASE B CHAIN, MITOCHONDRIAL × 1 (P13619) ATP SYNTHASE D CHAIN, MITOCHONDRIAL × 1 (P13620) X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;100 MM TRIS, 150 MM NACL, 17% PEG 5K MME, 7.5% GLYCEROL, 1% PICOLINE, pH 8.00 Resolution 2.80 Å R-free 0.295

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.

30 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ATP5J_BOVIN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–77; UniProt 32–108 Author chain F; PDBConstruct 1–77; UniProt 32–108

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 2cly

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2cly
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id2cly
Deposition date deposition_date2006-05-03
Structure title titleSubcomplex of the stator of bovine mitochondrial ATP synthase
Keywords keywords;MITOCHONDRIA, MITOCHONDRION, ION TRANSPORT, CF(0), STATOR, TRANSPORT, ACETYLATION, ATP SYNTHASE, HYDROGEN ION TRANSPORT, TRANSIT PEPTIDE, PERIPHERAL STALK, HYDROLASE ;; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier43.08
Radius of gyration Rg (electron density) rg_electron43.95
Forward intensity I(0) i073852900.00
Molecular weight molecular_weight68700.0 kDa
Excluded volume excluded_volume86153 ų
Envelope volume envelope_volume138790 ų
Hydration-shell volume shell_volume30702 ų
Envelope diameter envelope_diameter184.3
Shell Rg shell_rg38.83
Envelope Rg envelope_rg46.37
Shape Rg shape_rg43.89
Total Rg total_rg43.78
Total atoms total_atoms4839
Residues n_residues583
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 dmax181.3
Rg (real space) rg_real43.79
Rg uncertainty (real space) rg_real_error3.42
I(0) (real space) i0_real7.3850e+07
I(0) uncertainty (real space) i0_real_error1.6750e+06
Rg (reciprocal space) rg_reciprocal43.08
I(0) (reciprocal space) i0_reciprocal73790000.0000
Solution quality estimate total_estimate0.6446
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary39.2
Skewness Skewness skewness0.682
Kurtosis Kurtosis kurtosis0.043
Angular range angular_range— – 0.1850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4385000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.371; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.262; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd2clya1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.52 — ATP synthase B chain-like
Superfamily Superfamily superfamilyf.52.1 — ATP synthase B chain-like
Family Family familyf.52.1.1 — ATP synthase B chain-like
Domain ID domain_idd2clyb1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.53 — ATP synthase D chain-like
Superfamily Superfamily superfamilyf.53.1 — ATP synthase D chain-like
Family Family familyf.53.1.1 — ATP synthase D chain-like
Domain ID domain_idd2clyc_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.45 — Mitochondrial ATP synthase coupling factor 6
Superfamily Superfamily superfamilyf.45.1 — Mitochondrial ATP synthase coupling factor 6
Family Family familyf.45.1.1 — Mitochondrial ATP synthase coupling factor 6
Domain ID domain_idd2clyd_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.52 — ATP synthase B chain-like
Superfamily Superfamily superfamilyf.52.1 — ATP synthase B chain-like
Family Family familyf.52.1.1 — ATP synthase B chain-like
Domain ID domain_idd2clye_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.53 — ATP synthase D chain-like
Superfamily Superfamily superfamilyf.53.1 — ATP synthase D chain-like
Family Family familyf.53.1.1 — ATP synthase D chain-like
Domain ID domain_idd2clyf_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.45 — Mitochondrial ATP synthase coupling factor 6
Superfamily Superfamily superfamilyf.45.1 — Mitochondrial ATP synthase coupling factor 6
Family Family familyf.45.1.1 — Mitochondrial ATP synthase coupling factor 6

CATH v4.4 (6 domains)

Domain ID domain_id2clyA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily2210
Domain ID domain_id2clyB00
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily70
Domain ID domain_id2clyC01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily200
Domain ID domain_id2clyD00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily2210
Domain ID domain_id2clyE00
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily70
Domain ID domain_id2clyF01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily200

8. Citations (2)

9. Files and Curves (10)