6qzd

HLA-DR1 with SGP Influenza Matrix Peptide

Method: X-RAY DIFFRACTION Dmax: 91.3 Å Quality: GOOD

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

HLA class II histocompatibility antigen, DR alpha chain

Homo sapiens

UniProt P01903

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 AAA; UniProt 28–207 Not recorded HLA class II histocompatibility antigen, DRB1-1 beta chain × 1 (P04229) Matrix protein 1 × 1 (P05777) PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;291 K;0.1 M Tris 0.2 M NH4 SO4 25% PEG 4000 Resolution 2.66 Å R-free 0.254
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain DDD; UniProt 28–207 Not recorded HLA class II histocompatibility antigen, DRB1-1 beta chain × 1 (P04229) Matrix protein 1 × 1 (P05777) PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;291 K;0.1 M Tris 0.2 M NH4 SO4 25% PEG 4000 Resolution 2.66 Å R-free 0.254

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.

139 other PDB entries and 218 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DRA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain AAA; PDBConstruct 1–180; UniProt 28–207 Author chain DDD; PDBConstruct 1–180; UniProt 28–207

HLA class II histocompatibility antigen, DRB1-1 beta chain

Homo sapiens

UniProt P04229

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 BBB; UniProt 30–219 Not recorded HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) Matrix protein 1 × 1 (P05777) PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;291 K;0.1 M Tris 0.2 M NH4 SO4 25% PEG 4000 Resolution 2.66 Å R-free 0.254
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain EEE; UniProt 30–219 Not recorded HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) Matrix protein 1 × 1 (P05777) PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;291 K;0.1 M Tris 0.2 M NH4 SO4 25% PEG 4000 Resolution 2.66 Å R-free 0.254

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.

48 other PDB entries and 82 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 2B11_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain BBB; PDBConstruct 2–191; UniProt 30–219 Author chain EEE; PDBConstruct 2–191; UniProt 30–219

Matrix protein 1

OrganismNot specified

UniProt P05777

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 CCC; UniProt 17–30 Not recorded HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) HLA class II histocompatibility antigen, DRB1-1 beta chain × 1 (P04229) PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;291 K;0.1 M Tris 0.2 M NH4 SO4 25% PEG 4000 Resolution 2.66 Å R-free 0.254
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain FFF; UniProt 17–30 Not recorded HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) HLA class II histocompatibility antigen, DRB1-1 beta chain × 1 (P04229) PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;291 K;0.1 M Tris 0.2 M NH4 SO4 25% PEG 4000 Resolution 2.66 Å R-free 0.254

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.

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name M1_I33A0
Isoform
PDB entities 3
Chains and sequence ranges Author chain CCC; PDBConstruct 1–14; UniProt 17–30 Author chain FFF; PDBConstruct 1–14; UniProt 17–30

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 6qzd

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6qzd
Deposition date deposition_date2019-03-11
Structure title titleHLA-DR1 with SGP Influenza Matrix Peptide
Keywords keywordsHLA-DR1, Influenza, CD4, T-Cell, Helper T-cell, Matrix, 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_guinier29.21
Radius of gyration Rg (electron density) rg_electron28.26
Forward intensity I(0) i0129493000.00
Molecular weight molecular_weight89361.0 kDa
Excluded volume excluded_volume111540 ų
Envelope volume envelope_volume144060 ų
Hydration-shell volume shell_volume41358 ų
Envelope diameter envelope_diameter95.9
Shell Rg shell_rg36.51
Envelope Rg envelope_rg28.02
Shape Rg shape_rg28.23
Total Rg total_rg29.13
Total atoms total_atoms6311
Residues n_residues770
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 dmax91.3
Rg (real space) rg_real29.06
Rg uncertainty (real space) rg_real_error0.54
I(0) (real space) i0_real1.2950e+08
I(0) uncertainty (real space) i0_real_error1.9120e+06
Rg (reciprocal space) rg_reciprocal29.13
I(0) (reciprocal space) i0_reciprocal129500000.0000
Solution quality estimate total_estimate0.8905
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.9
Skewness Skewness skewness0.184
Kurtosis Kurtosis kurtosis-0.316
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23480000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.933

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

8. Citations (1)

9. Files and Curves (10)