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7t6i

Crystal structure of HLA-DP1 in complex with pp65 peptide in reverse orientation

Method: X-RAY DIFFRACTION Dmax: 82.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

HLA class II histocompatibility antigen DP alpha chain

Homo sapiens

UniProt Q95HB9

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 32–211 Not recorded MHC class II antigen × 1 （S6B6U4） pp65 peptide × 1 （P06725） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GLY GLYCINE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；0.1 M Sodium Cacodylate pH 6.5 25% w/v PEG 4000 Resolution 2.30 Å R-free 0.224

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.

Other PDB Difference from Current Entry 7T6I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3L3D Crystal structure of HLA-B*4402 in complex with the F3A mutant of a self-peptide derived from DPA*0201 Deposited 2009-12-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 77–85（9 aa）
Mutation：F3A ACT ACETATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M tri-sodium citrate dihydrate, 12-30% PEG 4000, 0.2M ammonium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.80 Å R-free 0.231
3L3G Crystal structure of HLA-B*4402 in complex with the R5A mutant of a self-peptide derived from DPA*0201 Deposited 2009-12-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 77–85（9 aa）
Mutation：R5A ACT ACETATE ION × 2 GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M tri-sodium citrate dihydrate, 12-30% PEG 4000, 0.2M ammonium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.264
3L3I Crystal structure of HLA-B*4402 in complex with the F7A mutant of a self-peptide derived from DPA*0201 Deposited 2009-12-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 77–85（9 aa）
Mutation：F7A GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M tri-sodium citrate dihydrate, 12-30% PEG 4000, 0.2M ammonium acetate , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.242
3L3J Crystal structure of HLA-B*4402 in complex with the F3A/R5A double mutant of a self-peptide derived from DPA*0201 Deposited 2009-12-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 77–85（9 aa）
Mutation：F3A,R5A ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M tri-sodium citrate dihydrate, 12-30% PEG 4000, 0.2M ammonium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.289
3L3K Crystal structure of HLA-B*4402 in complex with the R5A/F7A double mutant of a self-peptide derived from DPA*0201 Deposited 2009-12-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 77–85（9 aa）
Mutation：R5A,F7A GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M tri-sodium citrate dihydrate, 12-30% PEG 4000, 0.2M ammonium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.275

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

View Construct and Data Evidence
UniProt name Q95HB9_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–180； UniProt 32–211

MHC class II antigen

Homo sapiens

UniProt S6B6U4

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 30–217 Not recorded HLA class II histocompatibility antigen DP alpha chain × 1 （Q95HB9） pp65 peptide × 1 （P06725） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GLY GLYCINE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；0.1 M Sodium Cacodylate pH 6.5 25% w/v PEG 4000 Resolution 2.30 Å R-free 0.224

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 S6B6U4_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–188； UniProt 30–217

pp65 peptide

OrganismNot specified

UniProt P06725

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 142–158 Fragment：residues 142-158 HLA class II histocompatibility antigen DP alpha chain × 1 （Q95HB9） MHC class II antigen × 1 （S6B6U4） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GLY GLYCINE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；0.1 M Sodium Cacodylate pH 6.5 25% w/v PEG 4000 Resolution 2.30 Å R-free 0.224

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.

Other PDB Difference from Current Entry 7T6I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2X4R Crystal structure of MHC CLass I HLA-A2.1 bound to Cytomegalovirus (CMV) pp65 epitope Deposited 2010-02-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 495–503（9 aa） Fragment：EPITOPE, RESIDUES 495-503
Not recorded GOL GLYCEROL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.1 M MES PH 6.5, 20% PEG1500
Resolution 2.30 Å R-free 0.220
2X4R Crystal structure of MHC CLass I HLA-A2.1 bound to Cytomegalovirus (CMV) pp65 epitope Deposited 2010-02-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 495–503（9 aa） Fragment：EPITOPE, RESIDUES 495-503
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.1 M MES PH 6.5, 20% PEG1500
Resolution 2.30 Å R-free 0.220
2X4T Crystal structure of MHC CLass I HLA-A2.1 bound to a Peiodate- cleavable peptide Deposited 2010-02-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 495–503（9 aa） Fragment：EPITOPE, RESIDUES 495-503
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.1 M MES PH 6.5, 22% PEG1500
Resolution 2.30 Å R-free 0.236
2X4T Crystal structure of MHC CLass I HLA-A2.1 bound to a Peiodate- cleavable peptide Deposited 2010-02-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 495–503（9 aa） Fragment：EPITOPE, RESIDUES 495-503
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.1 M MES PH 6.5, 22% PEG1500
Resolution 2.30 Å R-free 0.236
3BW9 Crystal Structure of HLA B*3508 in complex with a HCMV 12-mer peptide from the pp65 protein Deposited 2008-01-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 103–114（12 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；0.2M ammonium acetate, 16% PEG 3350, pH 7.6, vapor diffusion, hanging drop, temperature 277K
Resolution 1.75 Å R-free 0.235
3BWA Crystal Structure of HLA B*3508 in complex with a HCMV 8-mer peptide from the pp65 protein Deposited 2008-01-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 188–195（8 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；0.2M ammonium acetate, 16% PEG 3350, pH 7.6, vapor diffusion, hanging drop, temperature 277K
Resolution 1.30 Å R-free 0.209

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

View Construct and Data Evidence
UniProt name PP65_HCMVA
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–17； UniProt 142–158

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 7t6i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7t6i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7t6i
Deposition date deposition_date2021-12-13
Structure title titleCrystal structure of HLA-DP1 in complex with pp65 peptide in reverse orientation
Keywords keywordsAntigen presentation, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.18 Å
Radius of gyration Rg (electron density) rg_electron23.29 Å
Forward intensity I(0) i032722400.00
Molecular weight molecular_weight43556.0 kDa
Excluded volume excluded_volume54157 ų
Envelope volume envelope_volume65698 ų
Hydration-shell volume shell_volume23887 ų
Envelope diameter envelope_diameter83.4 Å
Shell Rg shell_rg29.82 Å
Envelope Rg envelope_rg23.55 Å
Shape Rg shape_rg23.26 Å
Total Rg total_rg24.18 Å
Total atoms total_atoms3082
Residues n_residues381
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax82.9 Å
Rg (real space) rg_real24.18 Å
Rg uncertainty (real space) rg_real_error0.63 Å
I(0) (real space) i0_real3.2720e+07
I(0) uncertainty (real space) i0_real_error4.9140e+05
Rg (reciprocal space) rg_reciprocal24.18 Å
I(0) (reciprocal space) i0_reciprocal32720000.0000
Solution quality estimate total_estimate0.8755
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.5 Å
Skewness Skewness skewness0.355
Kurtosis Kurtosis kurtosis-0.310
Angular range angular_range— – 0.3300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10290000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.954
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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8. Citations (1)

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9. Files and Curves (10)