6j2j

Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with MERS-CoV-derived peptide MERS-CoV-S3

Method: X-RAY DIFFRACTION Dmax: 108.5 Å Quality: GOOD

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

Ptal-N*01:01

Pteropus alecto

UniProt A0A125R585

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 25–301 Not recorded Beta-2-microglobulin × 1 (P61769) MERS-CoV-S3 × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.2 M sodium acetate trihydrate, 20% w/v polyethylene glycol 3,350 Resolution 2.50 Å R-free 0.267
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 25–301 Not recorded Beta-2-microglobulin × 1 (P61769) MERS-CoV-S3 × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.2 M sodium acetate trihydrate, 20% w/v polyethylene glycol 3,350 Resolution 2.50 Å R-free 0.267

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.

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

View Construct and Data Evidence
UniProt name A0A125R585_PTEAL
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–277; UniProt 25–301 Author chain D; PDBConstruct 1–277; UniProt 25–301

Beta-2-microglobulin

Homo sapiens

UniProt P61769

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 21–119 Not recorded Ptal-N*01:01 × 1 (A0A125R585) MERS-CoV-S3 × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.2 M sodium acetate trihydrate, 20% w/v polyethylene glycol 3,350 Resolution 2.50 Å R-free 0.267
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 21–119 Not recorded Ptal-N*01:01 × 1 (A0A125R585) MERS-CoV-S3 × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.2 M sodium acetate trihydrate, 20% w/v polyethylene glycol 3,350 Resolution 2.50 Å R-free 0.267

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.

1313 other PDB entries and 1997 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name B2MG_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–99; UniProt 21–119 Author chain E; PDBConstruct 1–99; UniProt 21–119

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 6j2j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6j2j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6j2j
Deposition date deposition_date2019-01-01
Structure title titleCrystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with MERS-CoV-derived peptide MERS-CoV-S3
Keywords keywordsImmune system; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.07
Radius of gyration Rg (electron density) rg_electron31.16
Forward intensity I(0) i0134897000.00
Molecular weight molecular_weight88274.0 kDa
Excluded volume excluded_volume108650 ų
Envelope volume envelope_volume143020 ų
Hydration-shell volume shell_volume38810 ų
Envelope diameter envelope_diameter109.6
Shell Rg shell_rg37.76
Envelope Rg envelope_rg30.51
Shape Rg shape_rg31.16
Total Rg total_rg31.73
Total atoms total_atoms6246
Residues n_residues758
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 dmax108.5
Rg (real space) rg_real32.04
Rg uncertainty (real space) rg_real_error0.92
I(0) (real space) i0_real1.3490e+08
I(0) uncertainty (real space) i0_real_error2.1450e+06
Rg (reciprocal space) rg_reciprocal32.05
I(0) (reciprocal space) i0_reciprocal134900000.0000
Solution quality estimate total_estimate0.8135
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.6
Skewness Skewness skewness0.313
Kurtosis Kurtosis kurtosis-0.348
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15180000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.859; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id6j2jA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id6j2jA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6j2jB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6j2jD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id6j2jD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6j2jE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)