3lv3

Crystal structure of HLA-B*2705 complexed with a peptide derived from the human voltage-dependent calcium channel alpha1 subunit (residues 513-521)

Method: X-RAY DIFFRACTION Dmax: 76.7 Å Quality: EXCELLENT

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

HLA class I histocompatibility antigen, B-27 alpha chain

Homo sapiens

UniProt P03989

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 25–300 Fragment:EXTRACELLULAR DOMAIN, UNP residues 25-300 Beta-2-microglobulin × 1 (P61769) 9-meric peptide from Voltage-dependent L-type calcium channel subunit alpha-1D × 1 (Q01668) GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;291 K;20%(w/v) PEG 8000, 150mM NaCl, 20mM Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 1.94 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.

32 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1B27_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–276; UniProt 25–300

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 HLA class I histocompatibility antigen, B-27 alpha chain × 1 (P03989) 9-meric peptide from Voltage-dependent L-type calcium channel subunit alpha-1D × 1 (Q01668) GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;291 K;20%(w/v) PEG 8000, 150mM NaCl, 20mM Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 1.94 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.

1313 other PDB entries and 1998 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 2–100; UniProt 21–119

9-meric peptide from Voltage-dependent L-type calcium channel subunit alpha-1D

OrganismNot specified

UniProt Q01668

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 502–510 Fragment:UNP residues 502-510 HLA class I histocompatibility antigen, B-27 alpha chain × 1 (P03989) Beta-2-microglobulin × 1 (P61769) GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;291 K;20%(w/v) PEG 8000, 150mM NaCl, 20mM Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 1.94 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.

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

View Construct and Data Evidence
UniProt name CAC1D_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 502–510

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 3lv3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3lv3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3lv3
Deposition date deposition_date2010-02-19
Structure title titleCrystal structure of HLA-B*2705 complexed with a peptide derived from the human voltage-dependent calcium channel alpha1 subunit (residues 513-521)
Keywords keywords;IMMUNE SYSTEM, MHC (MAJOR HISTOCOMPATIBILITY COMPLEX), HLA-B*2705, Disulfide bond, Glycoprotein, Immune response, Membrane, MHC I, Transmembrane, Amyloid, Amyloidosis, Disease mutation, Glycation, Immunoglobulin domain, Secreted, Calcium channel, Voltage-gated channel ;; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.13
Radius of gyration Rg (electron density) rg_electron23.00
Forward intensity I(0) i037868500.00
Molecular weight molecular_weight45386.0 kDa
Excluded volume excluded_volume55877 ų
Envelope volume envelope_volume69197 ų
Hydration-shell volume shell_volume25160 ų
Envelope diameter envelope_diameter81.6
Shell Rg shell_rg29.88
Envelope Rg envelope_rg23.13
Shape Rg shape_rg22.99
Total Rg total_rg23.84
Total atoms total_atoms3205
Residues n_residues385
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 dmax76.7
Rg (real space) rg_real24.06
Rg uncertainty (real space) rg_real_error0.40
I(0) (real space) i0_real3.7870e+07
I(0) uncertainty (real space) i0_real_error5.1570e+05
Rg (reciprocal space) rg_reciprocal24.08
I(0) (reciprocal space) i0_reciprocal37870000.0000
Solution quality estimate total_estimate0.9068
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.0
Skewness Skewness skewness0.256
Kurtosis Kurtosis kurtosis-0.459
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11670000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.999

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3lv3b1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd3lv3b2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id3lv3A01
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_id3lv3A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3lv3B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)