SAXSdb — 7v0q

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

Protein 4.2

OrganismNot specified

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain X； UniProt 1–691	Not recorded	No other associated polymer	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 2.50 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.

Other PDB	Difference from Current Entry 7V0Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7TVZ Cryo-EM structure of human band 3-protein 4.2 complex in diagonal conformation Deposited 2022-02-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–691（691 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 LMT DODECYL-BETA-D-MALTOSIDE × 5 CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7TW0 Cryo-EM structure of human band 3-protein 4.2 complex in vertical conformation Deposited 2022-02-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–691（691 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
7TW1 Cryo-EM structure of human band 3-protein 4.2 complex (B2P2vertical) Deposited 2022-02-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–691（691 aa） Chain F 1–691（691 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
7TW3 Cryo-EM structure of human ankyrin complex (B2P1A1) from red blood cell Deposited 2022-02-06	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–691（691 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
7TW5 Cryo-EM structure of human ankyrin complex (B2P1A2) from red blood cell Deposited 2022-02-06	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–691（691 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.70 Å
7TW6 Cryo-EM structure of human ankyrin complex (B4P1A1) from red blood cell Deposited 2022-02-06	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 1–691（691 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.60 Å
7UZS Protein 4.2 (local refinement from consensus reconstruction of ankyrin complex classes) Deposited 2022-05-09	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–691（691 aa）	Not recorded	No recorded non-water small molecule	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 2.20 Å
7V0K Consensus refinement of human erythrocyte ankyrin-1 complex (Composite map) Deposited 2022-05-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain X 1–691（691 aa）	Not recorded	CLR CHOLESTEROL × 6 AJP Digitonin × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 PLC DIUNDECYL PHOSPHATIDYL CHOLINE × 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 2.40 Å
8CS9 Composite reconstruction of Class 1 of the erythrocyte ankyrin-1 complex Deposited 2022-05-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain X 1–691（691 aa）	Not recorded	CLR CHOLESTEROL × 8 AJP Digitonin × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 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 × 6	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 2.74 Å
8CSL Sub-tomogram averaging of erythrocyte ankyrin-1 complex Deposited 2022-05-12	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain X 1–691（691 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；130 mM KCl, 10 mM HEPES, pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 25.00 Å
8CSW Local refinement of protein 4.2 in Class 2 of erythrocyte ankyrin-1 complex Deposited 2022-05-13	Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–691（691 aa）	Not recorded	No recorded non-water small molecule	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 2.50 Å
8CTE Class 2 of erythrocyte ankyrin-1 complex (Composite map) Deposited 2022-05-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain X 1–691（691 aa）	Not recorded	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

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	1
Chains and sequence ranges	Author chain X； PDBConstruct 1–691； UniProt 1–691

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7v0q
Deposition date deposition_date	2022-05-10
Structure title title	Local refinement of protein 4.2, class 1 of erythrocyte ankyrin-1 complex
Keywords keywords	Membrane Protein, ankyrin complex, Erythrocyte, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	30.02 Å
Radius of gyration Rg (electron density) rg_electron	29.89 Å
Forward intensity I(0) i0	85814300.00
Molecular weight molecular_weight	73475.0 kDa
Excluded volume excluded_volume	92235 Å³
Envelope volume envelope_volume	114480 Å³
Hydration-shell volume shell_volume	33644 Å³
Envelope diameter envelope_diameter	116.8 Å
Shell Rg shell_rg	35.13 Å
Envelope Rg envelope_rg	30.35 Å
Shape Rg shape_rg	29.87 Å
Total Rg total_rg	30.44 Å
Total atoms total_atoms	5174
Residues n_residues	658
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	109.5 Å
Rg (real space) rg_real	30.21 Å
Rg uncertainty (real space) rg_real_error	1.09 Å
I(0) (real space) i0_real	8.5810e+07
I(0) uncertainty (real space) i0_real_error	1.4440e+06
Rg (reciprocal space) rg_reciprocal	30.13 Å
I(0) (reciprocal space) i0_reciprocal	85810000.0000
Solution quality estimate total_estimate	0.6321
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	107.5 Å
Skewness Skewness skewness	0.590
Kurtosis Kurtosis kurtosis	0.158
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	25030000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.668; Stabil: 1.000; Sysdev: 0.135; Positv: 1.000; Valcen: 0.850; Smooth: 0.952

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7v0qX01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7v0qX02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	260 — Coagulation Factor XIII; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Transglutaminase-like

Domain ID domain_id	7v0qX03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7v0qX04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.50 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	126197

Description description	Protein 4.2
Molecular weight formula_weight	77096.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	X
Atom count atom_count	5301

Local refinement of protein 4.2, class 1 of erythrocyte ankyrin-1 complex

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

Protein 4.2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	127

fit	/app/data/saxs_computation/v0/7v0q/7v0q.fit
pddf	/app/data/pr_computation/v0/7v0q/7v0q.pr.out
profile	/app/data/saxs_computation/v0/7v0q/7v0q.dat