3ov6

CD1c in complex with MPM (mannosyl-beta1-phosphomycoketide)

Method: X-RAY DIFFRACTION Dmax: 76.5 Å Quality: EXCELLENT

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

Beta-2-microglobulin, T-cell surface glycoprotein CD1c, T-cell surface glycoprotein CD1b

Homo sapiens

UniProt P29016

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 201–295 Fragment:beta-2-microglobulin Mutation:C-terminal fusion to CD1c ectodomain, N52Q, N57Q, K108G, N128Q, N241Q, W242G, CD1c a3 domain replaced with CD1b a3 domain NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 D12 DODECANE × 1 MK0 1-O-[(S)-hydroxy{[(4S,8S,16S,20S)-4,8,12,16,20-pentamethylheptacosyl]oxy}phosphoryl]-beta-D-mannopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 9.45;291 K;0.1M CHES pH 9.45, 1.05M sodium citrate, 25 mM triglycine, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.50 Å R-free 0.273

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.

27 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CD1B_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 301–395; UniProt 201–295

Beta-2-microglobulin, T-cell surface glycoprotein CD1c, T-cell surface glycoprotein CD1b

Homo sapiens

UniProt P29017

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 19–201 Fragment:beta-2-microglobulin Mutation:C-terminal fusion to CD1c ectodomain, N52Q, N57Q, K108G, N128Q, N241Q, W242G, CD1c a3 domain replaced with CD1b a3 domain NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 D12 DODECANE × 1 MK0 1-O-[(S)-hydroxy{[(4S,8S,16S,20S)-4,8,12,16,20-pentamethylheptacosyl]oxy}phosphoryl]-beta-D-mannopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 9.45;291 K;0.1M CHES pH 9.45, 1.05M sodium citrate, 25 mM triglycine, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.50 Å R-free 0.273

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.

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

View Construct and Data Evidence
UniProt name CD1C_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 118–300; UniProt 19–201

Beta-2-microglobulin, T-cell surface glycoprotein CD1c, T-cell surface glycoprotein CD1b

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 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 21–119 Fragment:beta-2-microglobulin Mutation:C-terminal fusion to CD1c ectodomain, N52Q, N57Q, K108G, N128Q, N241Q, W242G, CD1c a3 domain replaced with CD1b a3 domain NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 D12 DODECANE × 1 MK0 1-O-[(S)-hydroxy{[(4S,8S,16S,20S)-4,8,12,16,20-pentamethylheptacosyl]oxy}phosphoryl]-beta-D-mannopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 9.45;291 K;0.1M CHES pH 9.45, 1.05M sodium citrate, 25 mM triglycine, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.50 Å R-free 0.273

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 1
Chains and sequence ranges Author chain A; PDBConstruct 4–102; UniProt 21–119

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 3ov6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3ov6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3ov6
Deposition date deposition_date2010-09-15
Structure title titleCD1c in complex with MPM (mannosyl-beta1-phosphomycoketide)
Keywords keywordsMHC, Immunoglobulin Domain, Immune System, Antigen Presentation; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.52
Radius of gyration Rg (electron density) rg_electron23.28
Forward intensity I(0) i031742000.00
Molecular weight molecular_weight43677.0 kDa
Excluded volume excluded_volume54792 ų
Envelope volume envelope_volume68066 ų
Hydration-shell volume shell_volume24575 ų
Envelope diameter envelope_diameter77.4
Shell Rg shell_rg30.14
Envelope Rg envelope_rg23.44
Shape Rg shape_rg23.24
Total Rg total_rg24.25
Total atoms total_atoms3088
Residues n_residues376
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 dmax76.5
Rg (real space) rg_real24.48
Rg uncertainty (real space) rg_real_error0.37
I(0) (real space) i0_real3.1740e+07
I(0) uncertainty (real space) i0_real_error4.4130e+05
Rg (reciprocal space) rg_reciprocal24.49
I(0) (reciprocal space) i0_reciprocal31740000.0000
Solution quality estimate total_estimate0.9087
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.9
Skewness Skewness skewness0.304
Kurtosis Kurtosis kurtosis-0.427
Angular range angular_range— – 0.3250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5026000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.982

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd3ov6a1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd3ov6a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.0 — automated matches
Domain ID domain_idd3ov6a3
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd3ov6a4
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3ov6a5
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_id3ov6A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3ov6A02
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_id3ov6A03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)