8cte

Class 2 of erythrocyte ankyrin-1 complex (Composite map)

Method: ELECTRON MICROSCOPY Dmax: 212.1 Å Quality: GOOD

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

Ankyrin-1

OrganismNot specified

UniProt P16157

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 × 14 PDB declaration: tetradecameric(14) Consistent with protein copy count Chain A; UniProt 1–1881 Not recorded Band 3 anion transport protein × 3 (P02730) Protein 4.2 × 1 (P16452) Blood group Rh(CE) polypeptide × 1 (P18577) Ammonium transporter Rh type A × 2 (Q02094) Glycophorin-A × 2 (P02724) Aquaporin-1 × 4 (P29972) CLR CHOLESTEROL × 10 AJP Digitonin × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL, and 0.01% w/v glycyrrhizic acid was added immediately prior to vitrification. cryo-EM vitrification conditions:Cryogen ETHANE;4-6 seconds, wait time 30 seconds Resolution 2.90 Å

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.

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

View Construct and Data Evidence
UniProt name ANK1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–1881; UniProt 1–1881

Band 3 anion transport protein

OrganismNot specified

UniProt P02730

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 × 14 PDB declaration: tetradecameric(14) Consistent with protein copy count Chain P; UniProt 1–911 Chain T; UniProt 1–911 Chain W; UniProt 1–911 Not recorded Ankyrin-1 × 1 (P16157) Protein 4.2 × 1 (P16452) Blood group Rh(CE) polypeptide × 1 (P18577) Ammonium transporter Rh type A × 2 (Q02094) Glycophorin-A × 2 (P02724) Aquaporin-1 × 4 (P29972) CLR CHOLESTEROL × 10 AJP Digitonin × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL, and 0.01% w/v glycyrrhizic acid was added immediately prior to vitrification. cryo-EM vitrification conditions:Cryogen ETHANE;4-6 seconds, wait time 30 seconds Resolution 2.90 Å

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.

53 other PDB entries and 56 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name B3AT_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain P; PDBConstruct 1–911; UniProt 1–911 Author chain T; PDBConstruct 1–911; UniProt 1–911 Author chain W; PDBConstruct 1–911; UniProt 1–911

Protein 4.2

OrganismNot specified

UniProt P16452

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 × 14 PDB declaration: tetradecameric(14) Consistent with protein copy count Chain X; UniProt 1–691 Not recorded Ankyrin-1 × 1 (P16157) Band 3 anion transport protein × 3 (P02730) Blood group Rh(CE) polypeptide × 1 (P18577) Ammonium transporter Rh type A × 2 (Q02094) Glycophorin-A × 2 (P02724) Aquaporin-1 × 4 (P29972) CLR CHOLESTEROL × 10 AJP Digitonin × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL, and 0.01% w/v glycyrrhizic acid was added immediately prior to vitrification. cryo-EM vitrification conditions:Cryogen ETHANE;4-6 seconds, wait time 30 seconds Resolution 2.90 Å

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.

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EPB42_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain X; PDBConstruct 1–691; UniProt 1–691

Blood group Rh(CE) polypeptide

OrganismNot specified

UniProt P18577

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 × 14 PDB declaration: tetradecameric(14) Consistent with protein copy count Chain K; UniProt 1–417 Not recorded Ankyrin-1 × 1 (P16157) Band 3 anion transport protein × 3 (P02730) Protein 4.2 × 1 (P16452) Ammonium transporter Rh type A × 2 (Q02094) Glycophorin-A × 2 (P02724) Aquaporin-1 × 4 (P29972) CLR CHOLESTEROL × 10 AJP Digitonin × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL, and 0.01% w/v glycyrrhizic acid was added immediately prior to vitrification. cryo-EM vitrification conditions:Cryogen ETHANE;4-6 seconds, wait time 30 seconds Resolution 2.90 Å

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.

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RHCE_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain K; PDBConstruct 1–417; UniProt 1–417

Ammonium transporter Rh type A

OrganismNot specified

UniProt Q02094

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 × 14 PDB declaration: tetradecameric(14) Consistent with protein copy count Chain L; UniProt 1–409 Chain Q; UniProt 1–409 Not recorded Ankyrin-1 × 1 (P16157) Band 3 anion transport protein × 3 (P02730) Protein 4.2 × 1 (P16452) Blood group Rh(CE) polypeptide × 1 (P18577) Glycophorin-A × 2 (P02724) Aquaporin-1 × 4 (P29972) CLR CHOLESTEROL × 10 AJP Digitonin × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL, and 0.01% w/v glycyrrhizic acid was added immediately prior to vitrification. cryo-EM vitrification conditions:Cryogen ETHANE;4-6 seconds, wait time 30 seconds Resolution 2.90 Å

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.

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RHAG_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain L; PDBConstruct 1–409; UniProt 1–409 Author chain Q; PDBConstruct 1–409; UniProt 1–409

Glycophorin-A

OrganismNot specified

UniProt P02724

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 × 14 PDB declaration: tetradecameric(14) Consistent with protein copy count Chain D; UniProt 1–150 Chain N; UniProt 1–150 Not recorded Ankyrin-1 × 1 (P16157) Band 3 anion transport protein × 3 (P02730) Protein 4.2 × 1 (P16452) Blood group Rh(CE) polypeptide × 1 (P18577) Ammonium transporter Rh type A × 2 (Q02094) Aquaporin-1 × 4 (P29972) CLR CHOLESTEROL × 10 AJP Digitonin × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL, and 0.01% w/v glycyrrhizic acid was added immediately prior to vitrification. cryo-EM vitrification conditions:Cryogen ETHANE;4-6 seconds, wait time 30 seconds Resolution 2.90 Å

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.

15 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GLPA_HUMAN
Isoform
PDB entities 6
Chains and sequence ranges Author chain D; PDBConstruct 1–150; UniProt 1–150 Author chain N; PDBConstruct 1–150; UniProt 1–150

Aquaporin-1

OrganismNot specified

UniProt P29972

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 × 14 PDB declaration: tetradecameric(14) Consistent with protein copy count Chain M; UniProt 1–269 Chain O; UniProt 1–269 Chain R; UniProt 1–269 Chain S; UniProt 1–269 Non-standard monomer:Yes (specific site not provided by mmCIF) Ankyrin-1 × 1 (P16157) Band 3 anion transport protein × 3 (P02730) Protein 4.2 × 1 (P16452) Blood group Rh(CE) polypeptide × 1 (P18577) Ammonium transporter Rh type A × 2 (Q02094) Glycophorin-A × 2 (P02724) CLR CHOLESTEROL × 10 AJP Digitonin × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL, and 0.01% w/v glycyrrhizic acid was added immediately prior to vitrification. cryo-EM vitrification conditions:Cryogen ETHANE;4-6 seconds, wait time 30 seconds Resolution 2.90 Å

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.

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AQP1_HUMAN
Isoform
PDB entities 7
Chains and sequence ranges Author chain M; PDBConstruct 1–269; UniProt 1–269 Author chain O; PDBConstruct 1–269; UniProt 1–269 Author chain R; PDBConstruct 1–269; UniProt 1–269 Author chain S; PDBConstruct 1–269; UniProt 1–269

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 8cte

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8cte
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8cte
Deposition date deposition_date2022-05-14
Structure title titleClass 2 of erythrocyte ankyrin-1 complex (Composite map)
Keywords keywordsMembrane Protein, Anion Exchange, Erythrocyte, Glycoprotein, TRANSPORT PROTEIN-STRUCTURAL PROTEIN complex; TRANSPORT PROTEIN/STRUCTURAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier63.29
Radius of gyration Rg (electron density) rg_electron62.91
Forward intensity I(0) i03649950000.00
Molecular weight molecular_weight549740.0 kDa
Excluded volume excluded_volume704170 ų
Envelope volume envelope_volume989850 ų
Hydration-shell volume shell_volume129310 ų
Envelope diameter envelope_diameter205.4
Shell Rg shell_rg66.52
Envelope Rg envelope_rg60.80
Shape Rg shape_rg62.91
Total Rg total_rg63.00
Total atoms total_atoms38776
Residues n_residues4980
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 dmax212.1
Rg (real space) rg_real62.99
Rg uncertainty (real space) rg_real_error2.11
I(0) (real space) i0_real3.6500e+09
I(0) uncertainty (real space) i0_real_error7.2730e+07
Rg (reciprocal space) rg_reciprocal63.51
I(0) (reciprocal space) i0_reciprocal3653000000.0000
Solution quality estimate total_estimate0.8746
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary84.8
Skewness Skewness skewness0.110
Kurtosis Kurtosis kurtosis-0.509
Angular range angular_range— – 0.1250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha233800000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.842

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (11)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id8cteK01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3430 — Ammonium transporter fold
Homologous superfamily homologous superfamily10 — Ammonium transporter AmtB like domains
Domain ID domain_id8cteL01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3430 — Ammonium transporter fold
Homologous superfamily homologous superfamily10 — Ammonium transporter AmtB like domains
Domain ID domain_id8cteQ01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3430 — Ammonium transporter fold
Homologous superfamily homologous superfamily10 — Ammonium transporter AmtB like domains
Domain ID domain_id8cteT01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology930 — Mannitol-specific EII; Chain A
Homologous superfamily homologous superfamily10 — Mannitol-specific EII; Chain A
Domain ID domain_id8cteX01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id8cteX02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology260 — Coagulation Factor XIII; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Transglutaminase-like
Domain ID domain_id8cteX03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id8cteX04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)