5nig

Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340 (arginine 327 to citrulline)

Method: X-RAY DIFFRACTION Dmax: 87.6 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 A; UniProt 26–206 Not recorded HLA class II histocompatibility antigen, DRB1-4 beta chain × 1 (P13760) Alpha-enolase × 1 (P06733) MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3 URE UREA × 1 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;0.1 M MES pH 6.5 10% (vol/vol) MPD 15% (vol/vol) PEG 3350 Resolution 1.35 Å R-free 0.181

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 219 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 A; PDBConstruct 1–181; UniProt 26–206

HLA class II histocompatibility antigen, DRB1-4 beta chain

Homo sapiens

UniProt P13760

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 30–219 Not recorded HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) Alpha-enolase × 1 (P06733) MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3 URE UREA × 1 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;0.1 M MES pH 6.5 10% (vol/vol) MPD 15% (vol/vol) PEG 3350 Resolution 1.35 Å R-free 0.181

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.

32 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 2B14_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–190; UniProt 30–219

Alpha-enolase

OrganismNot specified

UniProt P06733

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 326–340 Fragment:UNP Residues 326-340 Non-standard monomer:Yes (specific site not provided by mmCIF) HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) HLA class II histocompatibility antigen, DRB1-4 beta chain × 1 (P13760) MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3 URE UREA × 1 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;0.1 M MES pH 6.5 10% (vol/vol) MPD 15% (vol/vol) PEG 3350 Resolution 1.35 Å R-free 0.181

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.

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ENOA_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–15; UniProt 326–340

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 5nig

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5nig
Deposition date deposition_date2017-03-24
Structure title titleCrystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340 (arginine 327 to citrulline)
Keywords keywordsHLA-DR, enolase, arthritis, citrulline, 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_guinier25.20
Radius of gyration Rg (electron density) rg_electron24.34
Forward intensity I(0) i035418800.00
Molecular weight molecular_weight46058.0 kDa
Excluded volume excluded_volume57611 ų
Envelope volume envelope_volume69698 ų
Hydration-shell volume shell_volume24452 ų
Envelope diameter envelope_diameter92.9
Shell Rg shell_rg30.68
Envelope Rg envelope_rg24.70
Shape Rg shape_rg24.30
Total Rg total_rg25.21
Total atoms total_atoms3255
Residues n_residues391
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 dmax87.6
Rg (real space) rg_real25.26
Rg uncertainty (real space) rg_real_error0.78
I(0) (real space) i0_real3.5420e+07
I(0) uncertainty (real space) i0_real_error4.3980e+05
Rg (reciprocal space) rg_reciprocal25.25
I(0) (reciprocal space) i0_reciprocal35420000.0000
Solution quality estimate total_estimate0.8622
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.2
Skewness Skewness skewness0.420
Kurtosis Kurtosis kurtosis-0.276
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8304000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.800; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.853; Smooth: 0.958

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5nigA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id5nigA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nigB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id5nigB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)