5gsr

Mouse MHC class I H-2Kd with a MERS-CoV-derived peptide I5A

Method: X-RAY DIFFRACTION Dmax: 104.6 Å Quality: GOOD

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

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 D; UniProt 20–119 Not recorded H-2 class I histocompatibility antigen, K-D alpha chain × 1 (P01902) 9-mer peptide from Spike protein × 1 (A0A0U2W1D8) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.2 M Magnesium chloride hexahydrate, 0.1 M Sodium HEPES 7.5, 30 % v/v 2-Propanol Resolution 2.20 Å R-free 0.231
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 20–119 Not recorded H-2 class I histocompatibility antigen, K-D alpha chain × 1 (P01902) 9-mer peptide from Spike protein × 1 (A0A0U2W1D8) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.2 M Magnesium chloride hexahydrate, 0.1 M Sodium HEPES 7.5, 30 % v/v 2-Propanol Resolution 2.20 Å R-free 0.231

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 1
Chains and sequence ranges Author chain B; PDBConstruct 1–100; UniProt 20–119 Author chain D; PDBConstruct 1–100; UniProt 20–119

H-2 class I histocompatibility antigen, K-D alpha chain

Mus musculus

UniProt P01902

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 C; UniProt 22–295 Fragment:UNP RESIDUES 22-295 Beta-2-microglobulin × 1 (P61769) 9-mer peptide from Spike protein × 1 (A0A0U2W1D8) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.2 M Magnesium chloride hexahydrate, 0.1 M Sodium HEPES 7.5, 30 % v/v 2-Propanol Resolution 2.20 Å R-free 0.231
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 22–295 Fragment:UNP RESIDUES 22-295 Beta-2-microglobulin × 1 (P61769) 9-mer peptide from Spike protein × 1 (A0A0U2W1D8) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.2 M Magnesium chloride hexahydrate, 0.1 M Sodium HEPES 7.5, 30 % v/v 2-Propanol Resolution 2.20 Å R-free 0.231

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.

13 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HA1D_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 1–274; UniProt 22–295 Author chain C; PDBConstruct 1–274; UniProt 22–295

9-mer peptide from Spike protein

OrganismNot specified

UniProt A0A0U2W1D8

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 Q; UniProt 292–300 Fragment:UNP RESIDUES 292-300 Mutation:I5A Beta-2-microglobulin × 1 (P61769) H-2 class I histocompatibility antigen, K-D alpha chain × 1 (P01902) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.2 M Magnesium chloride hexahydrate, 0.1 M Sodium HEPES 7.5, 30 % v/v 2-Propanol Resolution 2.20 Å R-free 0.231
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain P; UniProt 292–300 Fragment:UNP RESIDUES 292-300 Mutation:I5A Beta-2-microglobulin × 1 (P61769) H-2 class I histocompatibility antigen, K-D alpha chain × 1 (P01902) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;0.2 M Magnesium chloride hexahydrate, 0.1 M Sodium HEPES 7.5, 30 % v/v 2-Propanol Resolution 2.20 Å R-free 0.231

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A0U2W1D8_9BETC
Isoform
PDB entities 3
Chains and sequence ranges Author chain P; PDBConstruct 1–9; UniProt 292–300 Author chain Q; PDBConstruct 1–9; UniProt 292–300

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 5gsr

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5gsr
Deposition date deposition_date2016-08-17
Structure title titleMouse MHC class I H-2Kd with a MERS-CoV-derived peptide I5A
Keywords keywordsmouse, H-2Kd, MERS-CoV, T-cell, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.94
Radius of gyration Rg (electron density) rg_electron31.29
Forward intensity I(0) i0131520000.00
Molecular weight molecular_weight89476.0 kDa
Excluded volume excluded_volume111110 ų
Envelope volume envelope_volume146150 ų
Hydration-shell volume shell_volume39192 ų
Envelope diameter envelope_diameter107.5
Shell Rg shell_rg38.05
Envelope Rg envelope_rg31.13
Shape Rg shape_rg31.26
Total Rg total_rg31.96
Total atoms total_atoms6336
Residues n_residues766
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 dmax104.6
Rg (real space) rg_real31.92
Rg uncertainty (real space) rg_real_error0.75
I(0) (real space) i0_real1.3150e+08
I(0) uncertainty (real space) i0_real_error2.0200e+06
Rg (reciprocal space) rg_reciprocal31.94
I(0) (reciprocal space) i0_reciprocal131500000.0000
Solution quality estimate total_estimate0.8952
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.6
Skewness Skewness skewness0.316
Kurtosis Kurtosis kurtosis-0.402
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18250000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.932

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_id5gsrA01
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_id5gsrA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5gsrB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5gsrC01
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_id5gsrC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5gsrD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)