6miv

Crystal structure of the mCD1d/xxq (JJ300)/iNKTCR ternary complex

Method: X-RAY DIFFRACTION
▼

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

;T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN,Human nkt tcr alpha chain ;

Homo sapiens

UniProt A0A0B4J1J9

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Heteromer Protein 4 其他Polymer 2 Beta-chain,Tcell receptor chain,T cell receptor beta constant 2 × 1 (A0A5B9,A0N8J3,A2NTY6) Antigen-presenting glycoprotein CD1d1 × 1 (A0A0R4J090) Beta-2-microglobulin × 1 (P01887) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SODIUM ION × 3 GLYCEROL × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 N-[(2S,3S,4R)-1-({4-O-[(4-tert-butylphenyl)methyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name A0A0B4J1J9_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain C; PDBConstruct 2–93; UniProt 22–113

;T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN,Human nkt tcr alpha chain ;

Homo sapiens

UniProt K7N5M3

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Heteromer Protein 4 其他Polymer 2 Beta-chain,Tcell receptor chain,T cell receptor beta constant 2 × 1 (A0A5B9,A0N8J3,A2NTY6) Antigen-presenting glycoprotein CD1d1 × 1 (A0A0R4J090) Beta-2-microglobulin × 1 (P01887) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SODIUM ION × 3 GLYCEROL × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 N-[(2S,3S,4R)-1-({4-O-[(4-tert-butylphenyl)methyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name K7N5M3_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain C; PDBConstruct 115–209; UniProt 116–210

Beta-chain,Tcell receptor chain,T cell receptor beta constant 2

Homo sapiens

UniProt A0A5B9

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Heteromer Protein 4 其他Polymer 2 ;T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN,Human nkt tcr alpha chain ; × 1 (A0A0B4J1J9,K7N5M3) Antigen-presenting glycoprotein CD1d1 × 1 (A0A0R4J090) Beta-2-microglobulin × 1 (P01887) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SODIUM ION × 3 GLYCEROL × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 N-[(2S,3S,4R)-1-({4-O-[(4-tert-butylphenyl)methyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name TRBC2_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 132–241; UniProt 19–128

Beta-chain,Tcell receptor chain,T cell receptor beta constant 2

Homo sapiens

UniProt A0N8J3

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Heteromer Protein 4 其他Polymer 2 ;T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN,Human nkt tcr alpha chain ; × 1 (A0A0B4J1J9,K7N5M3) Antigen-presenting glycoprotein CD1d1 × 1 (A0A0R4J090) Beta-2-microglobulin × 1 (P01887) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SODIUM ION × 3 GLYCEROL × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 N-[(2S,3S,4R)-1-({4-O-[(4-tert-butylphenyl)methyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name A0N8J3_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 100–131; UniProt 96–127

Beta-chain,Tcell receptor chain,T cell receptor beta constant 2

Homo sapiens

UniProt A2NTY6

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Heteromer Protein 4 其他Polymer 2 ;T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN,Human nkt tcr alpha chain ; × 1 (A0A0B4J1J9,K7N5M3) Antigen-presenting glycoprotein CD1d1 × 1 (A0A0R4J090) Beta-2-microglobulin × 1 (P01887) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SODIUM ION × 3 GLYCEROL × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 N-[(2S,3S,4R)-1-({4-O-[(4-tert-butylphenyl)methyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name A2NTY6_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–95; UniProt 29–123

Antigen-presenting glycoprotein CD1d1

Mus musculus

UniProt A0A0R4J090

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Heteromer Protein 4 其他Polymer 2 ;T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN,Human nkt tcr alpha chain ; × 1 (A0A0B4J1J9,K7N5M3) Beta-chain,Tcell receptor chain,T cell receptor beta constant 2 × 1 (A0A5B9,A0N8J3,A2NTY6) Beta-2-microglobulin × 1 (P01887) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SODIUM ION × 3 GLYCEROL × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 N-[(2S,3S,4R)-1-({4-O-[(4-tert-butylphenyl)methyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name A0A0R4J090_MOUSE
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A; PDBConstruct 1–279; UniProt 19–297

Beta-2-microglobulin

Mus musculus

UniProt P01887

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Heteromer Protein 4 其他Polymer 2 ;T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN,Human nkt tcr alpha chain ; × 1 (A0A0B4J1J9,K7N5M3) Beta-chain,Tcell receptor chain,T cell receptor beta constant 2 × 1 (A0A5B9,A0N8J3,A2NTY6) Antigen-presenting glycoprotein CD1d1 × 1 (A0A0R4J090) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SODIUM ION × 3 GLYCEROL × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 N-[(2S,3S,4R)-1-({4-O-[(4-tert-butylphenyl)methyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name B2MG_MOUSE
Isoform —
PDB entities 4
Chains and sequence ranges Author chain B; PDBConstruct 1–99; 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id6miv
Deposition date deposition_date2018-09-20
Structure title titleCrystal structure of the mCD1d/xxq (JJ300)/iNKTCR ternary complex
Keywords keywordsMHC-fold, Ig-fold, glycolipid antigen presentation, T cell receptor, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6miv__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6miv__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6miv__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg(Guinier)39.20 Å
Rg (electron density)39.76 Å
Total Rg39.71 Å
Atom count6515
Residues809
Excluded volume115270 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6miv__assembly_1__model_1 tetrameric (4) Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (11)

▼

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

Domain ID domain_idd6miva1
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_idd6miva2
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_idd6mivb_
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_idd6mivc1
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_idd6mivc2
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_idd6mivd1
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_idd6mivd2
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

CATH v4.4 (6 domains)

Domain ID domain_id6mivA01
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_id6mivA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6mivB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6mivC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6mivD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6mivD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
▶

7. Citations (1)