5eh4

Crystal Structure of the Glycophorin A Transmembrane Dimer in Lipidic Cubic Phase

Method: X-RAY DIFFRACTION Dmax: 71.9 Å Quality: REASONABLE

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

Glycophorin-A

Homo sapiens

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 89–117 Chain B; UniProt 89–117 Fragment:unp residues 89-117 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
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 89–117 Chain D; UniProt 89–117 Fragment:unp residues 89-117 Mutation:M81I Non-standard monomer:Yes (specific site not provided by mmCIF) No other associated polymer 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

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 15 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 Author chain C; PDBConstruct 1–29; UniProt 89–117 Author chain D; 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.

SAXS scattering curve SAXS Profile

SAXS profile for 5eh4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5eh4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5eh4
Deposition date deposition_date2015-10-28
Structure title titleCrystal Structure of the Glycophorin A Transmembrane Dimer in Lipidic Cubic Phase
Keywords keywordsReceptor, lipidic cubic phase, peptides, transmembrane, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.30
Radius of gyration Rg (electron density) rg_electron17.60
Forward intensity I(0) i02737110.00
Molecular weight molecular_weight13521.0 kDa
Excluded volume excluded_volume17946 ų
Envelope volume envelope_volume21727 ų
Hydration-shell volume shell_volume11506 ų
Envelope diameter envelope_diameter70.8
Shell Rg shell_rg21.75
Envelope Rg envelope_rg18.25
Shape Rg shape_rg17.40
Total Rg total_rg19.24
Total atoms total_atoms945
Residues n_residues116
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 dmax71.9
Rg (real space) rg_real19.50
Rg uncertainty (real space) rg_real_error0.72
I(0) (real space) i0_real2.7370e+06
I(0) uncertainty (real space) i0_real_error3.8080e+04
Rg (reciprocal space) rg_reciprocal19.47
I(0) (reciprocal space) i0_reciprocal2737000.0000
Solution quality estimate total_estimate0.6255
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.2
Skewness Skewness skewness0.529
Kurtosis Kurtosis kurtosis-0.040
Angular range angular_range— – 0.4100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha207100.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.623; Stabil: 1.000; Sysdev: 0.226; Positv: 1.000; Valcen: 0.583; Smooth: 0.998

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)