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Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-sulfatide
4APQ
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Immune System
    Structure Weight: 99118.75
    Molecule: ANTIGEN-PRESENTING GLYCOPROTEIN CD1D1
    Polymer: 1 Type: protein Length: 302
    Chains: A
    Fragment: EXTRACELLULAR DOMAIN, RESIDUES 19-297
    Organism: Mus musculus
    Gene Names: Cd1d1 Cd1.1
    UniProtKB: Protein Feature View | Search PDB | P11609  
    Molecule: BETA-2-MICROGLOBULIN
    Polymer: 2 Type: protein Length: 99
    Chains: B
    Organism: Mus musculus
    Gene Name: B2m
    UniProtKB: Protein Feature View | Search PDB | P01887  
    Molecule: MOUSE NKT TCR VALPHA14, HUMAN NKT TCR VALPHA14
    Polymer: 3 Type: protein Length: 207
    Chains: C
    Fragment: MOUSE VARIABLE DOMAIN, RESIDUES 1-121, HUMAN CONSTANT DOMAIN, RESIDUES 122-212
    Organism: Mus musculus
    Gene Names: TRAC TCRA
    UniProtKB: Protein Feature View | Search PDB | P01848  
    Molecule: MOUSE NKT TCR AUTOREACTIVE-VBETA6, HUMAN NKT TCR AUTOREACTIVE-VBETA6
    Polymer: 4 Type: protein Length: 243
    Chains: D
    Fragment: MOUSE VARIABLE DOMAIN, RESIDUES 1-121, HUMAN CONSTANT DOMAIN, RESIDUES 122-247
    Organism: Mus musculus
     
  •   Structure Validation Hide

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  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Mus musculus   Taxonomy   Common Name: House mouse Expression System: Trichoplusia ni  
    Polymer: 2
    Scientific Name: Mus musculus   Taxonomy   Common Name: House mouse Expression System: Trichoplusia ni  
    Polymer: 3
    Scientific Name: Mus musculus   Taxonomy   Common Name: House mouse Expression System: Escherichia coli  
    Polymer: 4
    Scientific Name: Mus musculus   Taxonomy   Common Name: House mouse Expression System: Escherichia coli  
    Polymer: 5
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 6
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 7
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    1BII  THE CRYSTAL STRUCTURE OF H-2DD MHC CLASS I IN COMPLEX WITH THE HIV-1 DERIVED PEPTIDE P18-110 
    1BQH  MURINE CD8AA ECTODOMAIN FRAGMENT IN COMPLEX WITH H-2KB /VSV8 
    1BZ9  CRYSTAL STRUCTURE OF MURINE CLASS I MHC H2-DB COMPLEXED WITH A SYNTHETIC PEPTIDE P1027 
    1CD1  CD1(MOUSE) ANTIGEN PRESENTING MOLECULE 
    1DDH  MHC CLASS I H-2DD HEAVY CHAIN COMPLEXED WITH BETA- 2MICROGLOBULIN AND AN IMMUNODOMINANT PEPTIDE P18-I10 FROMTHE HUMAN IMMUNODEFICIENCY VIRUS ENVELOPE GLYCOPROTEIN 120 
    1FFN  CRYSTAL STRUCTURE OF MURINE CLASS I H-2DB COMPLEXED WITHPEPTIDE GP33(C9M) 
    1FFO  CRYSTAL STRUCTURE OF MURINE CLASS I H-2DB COMPLEXED WITHSYNTHETIC PEPTIDE GP33 (C9M/K1A) 
    1FFP  CRYSTAL STRUCTURE OF MURINE CLASS I H-2DB COMPLEXED WITHPEPTIDE GP33 (C9M/K1S) 
    1FG2  CRYSTAL STRUCTURE OF THE LCMV PEPTIDIC EPITOPE GP33 INCOMPLEX WITH THE MURINE CLASS I MHC MOLECULE H-2DB 
    1FO0  MURINE ALLOREACTIVE SCFV TCR-PEPTIDE-MHC CLASS I MOLECULECOMPLEX 
    1FZJ  MHC CLASS I NATURAL MUTANT H-2KBM1 HEAVY CHAIN COMPLEXEDWITH BETA-2 MICROGLOBULIN AND VESICULAR STOMATITIS VIRUSNUCLEOPROTEIN 
    1FZK  MHC CLASS I NATURAL MUTANT H-2KBM1 HEAVY CHAIN COMPLEXEDWITH BETA-2 MICROGLOBULIN AND SENDAI VIRUS NUCLEOPROTEIN 
    1FZM  MHC CLASS I NATURAL MUTANT H-2KBM8 HEAVY CHAIN COMPLEXEDWITH BETA-2 MICROGLOBULIN AND VESICULAR STOMATITIS VIRUSNUCLEOPROTEIN 
    1FZO  MHC CLASS I NATURAL MUTANT H-2KBM8 HEAVY CHAIN COMPLEXEDWITH BETA-2 MICROGLOBULIN AND SENDAI VIRUS NUCLEOPROTEIN 
    1G6R  A FUNCTIONAL HOT SPOT FOR ANTIGEN RECOGNITION IN ASUPERAGONIST TCR/MHC COMPLEX 
    1G7P  CRYSTAL STRUCTURE OF MHC CLASS I H-2KB HEAVY CHAINCOMPLEXED WITH BETA-2 MICROGLOBULIN AND YEAST ALPHA -GLUCOSIDASE 
    1G7Q  CRYSTAL STRUCTURE OF MHC CLASS I H-2KB HEAVY CHAINCOMPLEXED WITH BETA-2 MICROGLOBULIN AND MUC1 VNTR PEPTIDESAPDTRPA 
    1HOC  MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX CONSISTING OF H-2D==B==, B2-MICROGLOBULIN, AND A 9-RESIDUE PEPTIDE 
    1INQ  STRUCTURE OF MINOR HISTOCOMPATIBILITY ANTIGEN PEPTIDE, H13A,COMPLEXED TO H2-DB 
    1JPF  CRYSTAL STRUCTURE OF THE LCMV PEPTIDIC EPITOPE GP276 INCOMPLEX WITH THE MURINE CLASS I MHC MOLECULE H-2DB 
    1JPG  CRYSTAL STRUCTURE OF THE LCMV PEPTIDIC EPITOPE NP396 INCOMPLEX WITH THE MURINE CLASS I MHC MOLECULE H-2DB 
    1JUF  STRUCTURE OF MINOR HISTOCOMPATIBILITY ANTIGEN PEPTIDE, H13B,COMPLEXED TO H2-DB 
    1K8D  CRYSTAL STRUCTURE OF THE NON-CLASSICAL MHC CLASS IB QA-2COMPLEXED WITH A SELF PEPTIDE 
    1KBG  MHC CLASS I H-2KB PRESENTED GLYCOPEPTIDE RGY8-6H- GAL2 
    1KJ2  MURINE ALLOREACTIVE SCFV TCR-PEPTIDE-MHC CLASS I MOLECULECOMPLEX 
    1KJ3  MHC CLASS I H-2KB MOLECULE COMPLEXED WITH PKB1 PEPTIDE 
    1KPU  HIGH RESOLUTION CRYSTAL STRUCTURE OF THE MHC CLASS ICOMPLEX H-2KB/VSV8 
    1KPV  HIGH RESOLUTION CRYSTAL STRUCTURE OF THE MHC CLASS ICOMPLEX H-2KB/SEV9 
    1L6Q  MOUSE MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I PROTEIN H2-KD 
    1LD9  THE THREE-DIMENSIONAL STRUCTURE OF AN H-2LD PEPTIDE COMPLEX EXPLAINS THE UNIQUE INTERACTION OF LD WITH BETA2M AND PEPTIDE 
    1LDP  CRYSTAL STRUCTURE OF MURINE MHC CLASS I H-2LD WITH A MIXTURE OF BOUND PEPTIDES 
    1LEG  CRYSTAL STRUCTURE OF H-2KB BOUND TO THE DEV8 PEPTIDE 
    1LEK  CRYSTAL STRUCTURE OF H-2KBM3 BOUND TO DEV8 
    1LK2  1.35A CRYSTAL STRUCTURE OF H-2KB COMPLEXED WITH THEGNYSFYAL PEPTIDE 
    1MHC  MODEL OF MHC CLASS I H2-M3 WITH NONAPEPTIDE FROM RAT ND1 REFINED AT 2.3 ANGSTROMS RESOLUTION 
    1MWA  2C/H-2KBM3/DEV8 ALLOGENEIC COMPLEX 
    1N3N  CRYSTAL STRUCTURE OF A MYCOBACTERIAL HSP60 EPITOPE WITH THEMURINE CLASS I MHC MOLECULE H-2DB 
    1N59  CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJORHISTOCOMPATIBILITY COMPLEX OF H-2KB, B2-MICROGLOBULIN , ANDA 9-RESIDUE IMMUNODOMINANT PEPTIDE EPITOPE GP33 DERIVEDFROM LCMV 
    1N5A  CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJORHISTOCOMPATIBILITY COMPLEX OF H-2DB, B2-MICROGLOBULIN , ANDA 9-RESIDUE IMMUNODOMINANT PEPTIDE EPITOPE GP33 DERIVEDFROM LCMV 
    1NAM  MURINE ALLOREACTIVE SCFV TCR-PEPTIDE-MHC CLASS I MOLECULECOMPLEX 
    1NAN  MCH CLASS I H-2KB MOLECULE COMPLEXED WITH PBM1 PEPTIDE 
    1NEZ  THE CRYSTAL STRUCTURE OF A TL/CD8AA COMPLEX AT 2. 1ARESOLUTION:IMPLICATIONS FOR MEMORY T CELL GENERATION, CO-RECEPTOR PREFERENCE AND AFFINITY 
    1OSZ  MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA- 2MICROGLOBULIN AND AN (L4V) MUTANT OF THE VESICULARSTOMATITIS VIRUS NUCLEOPROTEIN 
    1P1Z  X-RAY CRYSTAL STRUCTURE OF THE LECTIN-LIKE NATURAL KILLERCELL RECEPTOR LY-49C BOUND TO ITS MHC CLASS I LIGAND H-2KB 
    1P4L  CRYSTAL STRUCTURE OF NK RECEPTOR LY49C MUTANT WITH ITS MHCCLASS I LIGAND H-2KB 
    1PQZ  MURINE CYTOMEGULOVIRUS IMMUNOMODULATORY PROTEIN M144 
    1QO3  COMPLEX BETWEEN NK CELL RECEPTOR LY49A AND ITS MHC CLASS I LIGAND H-2DD 
    1RJY  MHC CLASS I NATURAL MUTANT H-2KBM8 HEAVY CHAIN COMPLEXEDWITH BETA-2 MICROGLOBULIN AND HERPES SIMPLEX VIRUSGLYCOPROTEIN B PEPTIDE 
    1RJZ  MHC CLASS I NATURAL MUTANT H-2KBM8 HEAVY CHAIN COMPLEXEDWITH BETA-2 MICROGLOBULIN AND HERPIES SIMPLEX VIRUS MUTANTGLYCOPROTEIN B PEPTIDE 
    1RK0  MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA- 2MICROGLOBULIN AND HERPES SIMPLEX VIRUS GLYCOPROTEIN BPEPTIDE 
    1RK1  MHC CLASS I NATURAL H-2KB HEAVY CHAIN COMPLEXED WITH BETA-2MICROGLOBULIN AND HERPES SIMPLEX VIRUS MUTANT GLYCOPROTEINB PEPTIDE 
    1S7Q  CRYSTAL STRUCTURES OF THE MURINE CLASS I MAJORHISTOCOMPATIBILITY COMPLEX H-2KB IN COMPLEX WITH LCMV-DERIVED GP33 INDEX PEPTIDE AND THREE OF ITS ESCAPE VARIANTS 
    1S7R  CRYSTAL STRUCTURES OF THE MURINE CLASS I MAJORHISTOCOMPATIBILITY COMPLEX H-2KB IN COMPLEX WITH LCMV-DERIVED GP33 INDEX PEPTIDE AND THREE OF ITS ESCAPE VARIANTS 
    1S7S  CRYSTAL STRUCTURES OF THE MURINE CLASS I MAJORHISTOCOMPATIBILITY COMPLEX H-2KB IN COMPLEX WITH LCMV-DERIVED GP33 INDEX PEPTIDE AND THREE OF ITS ESCAPE VARIANTS 
    1S7T  CRYSTAL STRUCTURES OF THE MURINE CLASS I MAJORHISTOCOMPATIBILITY COMPLEX H-2KB IN COMPLEX WITH LCMV-DERIVED GP33 INDEX PEPTIDE AND THREE OF ITS ESCAPE VARIANTS 
    1S7U  CRYSTAL STRUCTURES OF THE MURINE CLASS I MAJORHISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX WITH LCMV-DERIVED GP33 INDEX PEPTIDE AND THREE OF ITS ESCAPE VARIANTS 
    1S7V  CRYSTAL STRUCTURES OF THE MURINE CLASS I MAJORHISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX WITH LCMV-DERIVED GP33 INDEX PEPTIDE AND THREE OF ITS ESCAPE VARIANTS 
    1S7W  CRYSTAL STRUCTURES OF THE MURINE CLASS I MAJORHISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX WITH LCMV-DERIVED GP33 INDEX PEPTIDE AND THREE OF ITS ESCAPE VARIANTS 
    1S7X  CRYSTAL STRUCTURES OF THE MURINE CLASS I MAJORHISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX WITH LCMV-DERIVED GP33 INDEX PEPTIDE AND THREE OF ITS ESCAPE VARIANTS 
    1T0M  CONFORMATIONAL SWITCH IN POLYMORPHIC H-2K MOLECULESCONTAINING AN HSV PEPTIDE 
    1T0N  CONFORMATIONAL SWITCH IN POLYMORPHIC H-2K MOLECULESCONTAINING AN HSV PEPTIDE 
    1U58  CRYSTAL STRUCTURE OF THE MURINE CYTOMEGALOVIRUS MHC- IHOMOLOG M144 
    1VAC  MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA- 2 MICROGLOBULIN AND CHICKEN OVALBUMIN 
    1VAD  MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA- 2 MICROGLOBULIN AND YEAST ALPHA-GLUCOSIDASE 
    1WBX  CRYSTAL STRUCTURES OF MURINE MHC CLASS I H-2 DB AND KB MOLECULES IN COMPLEX WITH CTL EPITOPES FROM INFLUENZA A VIRUS: IMPLICATIONS FOR TCR REPERTOIRE SELECTION AND IMMUNODOMINANCE 
    1WBY  CRYSTAL STRUCTURES OF MURINE MHC CLASS I H-2 DB AND KB MOLECULES IN COMPLEX WITH CTL EPITOPES FROM INFLUENZA A VIRUS: IMPLICATIONS FOR TCR REPERTOIRE SELECTION AND IMMUNODOMINANCE 
    1WBZ  CRYSTAL STRUCTURES OF MURINE MHC CLASS I H-2 DB AND KB MOLECULES IN COMPLEX WITH CTL EPITOPES FROM INFLUENZA A VIRUS: IMPLICATIONS FOR TCR REPERTOIRE SELECTION AND IMMUNODOMINANCE 
    1YN6  CRYSTAL STRUCTURE OF A MOUSE MHC CLASS I PROTEIN, H2 -DB, INCOMPLEX WITH A PEPTIDE FROM THE INFLUENZA A ACID POLYMERASE 
    1YN7  CRYSTAL STRUCTURE OF A MOUSE MHC CLASS I PROTEIN, H2 -DB, INCOMPLEX WITH A MUTATED PEPTIDE (R7A) OF THE INFLUENZA AACID POLYMERASE 
    1Z5L  STRUCTURE OF A HIGHLY POTENT SHORT-CHAIN GALACTOSYLCERAMIDE AGONIST BOUND TO CD1D 
    1ZHB  CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJORHISTOCOMPATIBILITY COMPLEX OF H-2DB, B2-MICROGLOBULIN , ANDA 9-RESIDUE PEPTIDE DERIVED FROM RAT DOPAMINE BETA-MONOOXIGENASE 
    1ZHN  CRYSTAL STRUCTURE OF MOUSE CD1D BOUND TO THE SELF LIGANDPHOSPHATIDYLCHOLINE 
    1ZT1  CRYSTAL STRUCTURE OF CLASS I MHC H-2KK IN COMPLEX WITH ANOCTAPEPTIDE 
    1ZT7  CRYSTAL STRUCTURE OF CLASS I MHC H-2KK IN COMPLEX WITH ANONAPEPTIDE 
    2AKR  STRUCTURAL BASIS OF SULFATIDE PRESENTATION BY MOUSE CD1D 
    2CKB  STRUCTURE OF THE 2C/KB/DEV8 COMPLEX 
    2CLV  MHC CLASS I NATURAL MUTANT H-2KBM8 HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND PBM8 PEPTIDE 
    2CLZ  MHC CLASS I NATURAL MUTANT H-2KBM8 HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND PBM1 PEPTIDE 
    2FIK  STRUCTURE OF A MICROBIAL GLYCOSPHINGOLIPID BOUND TO MOUSECD1D 
    2FWO  MHC CLASS I H-2KD HEAVY CHAIN IN COMPLEX WITH BETA -2MICROGLOBULIN AND PEPTIDE DERIVED FROM INFLUENZANUCLEOPROTEIN 
    2MHA  CLASS I HISTOCOMPATIBILITY ANTIGEN H-2K(B) COMPLEX WITH OCTAPEPTIDE ARG-GLY-TYR-VAL-TYR-GLN-GLY-LEU 
    2VAA  MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA- 2MICROGLOBULIN AND VESICULAR STOMATITIS VIRUS NUCLEOPROTEIN 
    2VAB  MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA- 2MICROGLOBULIN AND SENDAI VIRUS NUCLEOPROTEIN 
    2VE6  CRYSTAL STRUCTURE OF A MURINE MHC CLASS I H2-DB MOLECULE IN COMPLEX WITH A PHOTOCLEAVABLE PEPTIDE 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    BMA
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    BMA C6 H12 O6
    BETA-D-MANNOSE
    CIS
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    CIS C48 H91 N O11 S
    (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO- BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC- 3-ENYL)TETRACOS-15-ENAMIDE
    CIS:4APQ
    MAN
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    MAN C6 H12 O6
    ALPHA-D-MANNOSE
    NAG
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    NAG C8 H15 N O6
    N-ACETYL-D-GLUCOSAMINE
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
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