SAXSdb — 2kpe

▼

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

Glycophorin-A

Homo sapiens

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 89–117 Chain B； UniProt 89–117	Fragment：transmembrane segment (UNP residues 89-117)	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 5.5；313 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition：3 mM [U-100% 13C; U-100% 15N] GpA, 3 mM GpA, 180 mM [U-2H] DPC, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

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 2KPE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AFO DIMERIC TRANSMEMBRANE DOMAIN OF HUMAN GLYCOPHORIN A, NMR, 20 STRUCTURES Deposited 1997-03-11	Different construct Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 81–120（40 aa） Fragment：TRANSMEMBRANE PEPTIDE Chain B 81–120（40 aa） Fragment：TRANSMEMBRANE PEPTIDE	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；313 K	Resolution not provided
2KPF Spatial structure of the dimeric transmembrane domain of glycophorin A in bicelles soluton Deposited 2009-10-13	Different construct Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 80–117（38 aa） Fragment：transmembrane domain (UNP residues 80-117) Chain B 80–117（38 aa） Fragment：transmembrane domain (UNP residues 80-117)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；313 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 1mM unlabeled Glycophorin A, 1mM 13-C/15-N labeled Glycophorin A, 16mM DMPC d-54, 64 mM DHPC d-22, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
5EH4 Crystal Structure of the Glycophorin A Transmembrane Dimer in Lipidic Cubic Phase Deposited 2015-10-28	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 89–117（29 aa） Fragment：unp residues 89-117 Chain B 89–117（29 aa） Fragment：unp residues 89-117	Mutation：M81I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M81I Non-standard monomer：Yes (specific site not provided by mmCIF)	OLB (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；20% (w/v)PEG 8000, 0.1 M sodium HEPES pH 7.5 10 mM TRIS-HCl pH 8, 40 mM NaCl	Resolution 2.81 Å R-free 0.260
5EH4 Crystal Structure of the Glycophorin A Transmembrane Dimer in Lipidic Cubic Phase Deposited 2015-10-28	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 89–117（29 aa） Fragment：unp residues 89-117 Chain D 89–117（29 aa） Fragment：unp residues 89-117	Mutation：M81I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M81I Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；20% (w/v)PEG 8000, 0.1 M sodium HEPES pH 7.5 10 mM TRIS-HCl pH 8, 40 mM NaCl	Resolution 2.81 Å R-free 0.260
5EH6 Crystal Structure of the Glycophorin A Transmembrane Monomer in Lipidic Cubic Phase Deposited 2015-10-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 89–117（29 aa） Fragment：unp resideus 89-117	Mutation：M100I Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7.5；293 K；0.1 M HEPES, 20% PEG8000, 10 mM Tris, 40 mM NaCl	Resolution 1.92 Å R-free 0.238
7UZ3 Band 3-Glycophorin A complex, outward facing Deposited 2022-05-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–150（150 aa） Chain D 1–150（150 aa）	Not recorded	CLR CHOLESTEROL × 4 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, 130mM KCl, 20mM HEPES pH 7.4, 1mM ATP, 1mM MgCl2, 1mM PMSF. Peak fractions were concentrated to 8mg/mL, and 0.01% (w/v) of glycyrrhizic acid was added immediately prior to vitrification. cryo-EM vitrification conditions Cryogen ETHANE；4-6 seconds, wait time 30 seconds.	Resolution 2.35 Å
7V07 Band 3-I-TM local refinement from erythrocyte ankyrin-1 complex consensus reconstruction Deposited 2022-05-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–150（150 aa） Chain D 1–150（150 aa）	Not recorded	CLR CHOLESTEROL × 4 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 2.80 Å
7V0K Consensus refinement of human erythrocyte ankyrin-1 complex (Composite map) Deposited 2022-05-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain D 1–150（150 aa） Chain N 1–150（150 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
7V19 Local refinement of Band 3-II transmembrane domains, class 1 of erythrocyte ankyrin-1 complex Deposited 2022-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–150（150 aa） Chain D 1–150（150 aa）	Not recorded	CLR CHOLESTEROL × 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 3.30 Å
8CRQ Local refinement of Band 3-I transmembrane domains, class 1 of erythrocyte ankyrin-1 complex Deposited 2022-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–150（150 aa） Chain D 1–150（150 aa）	Not recorded	CLR CHOLESTEROL × 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 3.20 Å
8CRR Local refinement of Band 3-III transmembrane domains, class 1 of erythrocyte ankyrin-1 complex Deposited 2022-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–150（150 aa） Chain D 1–150（150 aa）	Not recorded	CLR CHOLESTEROL × 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 3.00 Å
8CRT Local refinement of Rh trimer, glycophorin B and Band3-III transmembrane region, class 1a of erythrocyte ankyrin-1 complex Deposited 2022-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–150（150 aa） Chain D 1–150（150 aa）	Not recorded	CLR CHOLESTEROL × 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 3.00 Å
8CS9 Composite reconstruction of Class 1 of the erythrocyte ankyrin-1 complex Deposited 2022-05-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain R 1–150（150 aa） Chain S 1–150（150 aa） Chain T 1–150（150 aa） Chain a 1–150（150 aa） Chain b 1–150（150 aa） Chain c 1–150（150 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 construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain R 1–150（150 aa） Chain S 1–150（150 aa） Chain T 1–150（150 aa） Chain a 1–150（150 aa） Chain b 1–150（150 aa） Chain c 1–150（150 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
8CT3 Local refinement of band3-I transmembrane region from class 2 of erythrocyte ankyrin-1 complex Deposited 2022-05-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–150（150 aa） Chain D 1–150（150 aa）	Not recorded	CLR CHOLESTEROL × 4 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 3.30 Å
8CTE Class 2 of erythrocyte ankyrin-1 complex (Composite map) Deposited 2022-05-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain D 1–150（150 aa） Chain N 1–150（150 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

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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–29； UniProt 89–117 Author chain B； PDBConstruct 1–29； UniProt 89–117

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2kpe
Deposition date deposition_date	2009-10-13
Structure title title	Refined structure of Glycophorin A transmembrane segment dimer in DPC micelles
Keywords keywords	;Glycophorin A, transmembrane dimer, micelles, Blood group antigen, Cell membrane, Glycoprotein, Host-virus interaction, Membrane, Sialic acid, Transmembrane, MEMBRANE PROTEIN ;; MEMBRANE PROTEIN
Experimental Method method	SOLUTION NMR

▼

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

Radius of gyration Rg (Guinier) rg_guinier	14.21 Å
Radius of gyration Rg (electron density) rg_electron	14.34 Å
Forward intensity I(0) i0	153803000.00
Molecular weight molecular_weight	125680.0 kDa
Excluded volume excluded_volume	166420 Å³
Envelope volume envelope_volume	17931 Å³
Hydration-shell volume shell_volume	9650 Å³
Envelope diameter envelope_diameter	54.9 Å
Shell Rg shell_rg	21.06 Å
Envelope Rg envelope_rg	17.63 Å
Shape Rg shape_rg	14.35 Å
Total Rg total_rg	14.49 Å
Total atoms total_atoms	18720
Residues n_residues	1160
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

▼

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

Maximum dimension Dmax dmax	50.7 Å
Rg (real space) rg_real	14.48 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	1.5380e+08
I(0) uncertainty (real space) i0_real_error	2.0320e+06
Rg (reciprocal space) rg_reciprocal	14.46 Å
I(0) (reciprocal space) i0_reciprocal	153800000.0000
Solution quality estimate total_estimate	0.7672
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	12.8 Å
Skewness Skewness skewness	0.439
Kurtosis Kurtosis kurtosis	-0.526
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12640.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.590; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.250; Smooth: 0.950

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▶

8. Citations (1)

▶

Description description	Glycophorin-A
Molecular weight formula_weight	3160.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	18720

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/kp/2kpe/2kpe.fit
pddf	/app/data/pr_computation/kp/2kpe/2kpe.pr.out
profile	/app/data/saxs_computation/kp/2kpe/2kpe.dat

Refined structure of Glycophorin A transmembrane segment dimer in DPC micelles

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

Glycophorin-A

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)