2Q86 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE MOUSE INVARIANT NKT CELL RECEPTOR VALPHA14

Authors :   D. M. Zajonc

Date :   08 Jun 07 (Deposition) - 01 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Inkt Cells, Tcr, Glycolipid Recognition, Innate Immunity, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. M. Zajonc, P. B. Savage, A. Bendelac, I. A. Wilson, L. Teyton
Crystal Structures Of Mouse Cd1D-Igb3 Complex And Its Cognate Valpha14 T Cell Receptor Suggest A Model For Dual Recognition Of Foreign And Self Glycolipids.
J. Mol. Biol. V. 377 1104 2008
PubMed-ID: 18295796 | Reference-DOI: 10.1016/J.JMB.2008.01.061

Molecule 1 - VALPHA14 TCR
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Common	:	FRUIT FLY
	Expression System Plasmid	:	PRMHA3
	Expression System Strain	:	SC2 CELLS
	Expression System Taxid	:	7227
	Expression System Vector Type	:	PLASMID
	Fragment	:	EXTRACELLULAR DOMAIN
	Gene	:	VALPHA14
	Mutation	:	YES
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - VBETA8.2
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Common	:	FRUIT FLY
	Expression System Plasmid	:	PRMHA3
	Expression System Strain	:	SC2 CELLS
	Expression System Taxid	:	7227
	Expression System Vector Type	:	PLASMID
	Fragment	:	EXTRACELLULAR DOMAIN
	Gene	:	VBETA8.2
	Mutation	:	YES
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	FUC	2	Ligand/Ion	ALPHA-L-FUCOSE
3	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (4, 6)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
3	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
3	MAN	-1	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:4 , ASN A:23 , TYR A:24 , SER A:25 , HOH A:517 , HOH A:623 , HOH A:625 , GLN C:112	BINDING SITE FOR RESIDUE NAG A 500
2	AC2	SOFTWARE	HOH A:622 , HOH A:624 , HOH A:625 , HOH A:626 , GLN C:14 , GLN C:112 , HOH C:216	BINDING SITE FOR RESIDUE NAG A 501
3	AC4	SOFTWARE	GLN C:14 , LYS C:167	BINDING SITE FOR RESIDUE MAN A 503
4	AC5	SOFTWARE	ALA A:69 , HOH A:623 , HOH A:624	BINDING SITE FOR RESIDUE FUC A 504
5	AC6	SOFTWARE	TRP B:156 , GLN B:203 , GLN B:205 , ASN B:226 , HOH B:593	BINDING SITE FOR RESIDUE NAG B 510
6	AC7	SOFTWARE	GLN A:112 , GLN C:2 , GLU C:4 , ASN C:23 , TYR C:24 , SER C:25 , HOH C:223	BINDING SITE FOR RESIDUE NAG C 500
7	AC8	SOFTWARE	GLN A:14 , TYR A:110 , GLN A:112 , HOH A:536 , HOH A:540	BINDING SITE FOR RESIDUE NAG C 501
8	AC9	SOFTWARE	ALA C:69 , HOH C:308 , HOH C:507	BINDING SITE FOR RESIDUE FUC C 506

Asymmetric Unit

No.	Residues
1	A:22	-	A:89
2	A:132	-	A:182
3	A:157	-	B:167
4	B:23	-	B:91
5	B:141	-	B:202
6	C:22	-	C:89
7	C:157	-	D:167
8	D:23	-	D:91
9	D:141	-	D:202

Asymmetric Unit

No.	Residues
1	Ser A:6	-	Pro A:7
2	Thr A:27	-	Pro A:28
3	Ser B:7	-	Pro B:8
4	Phe B:147	-	Pro B:148
5	Ser C:6	-	Pro C:7
6	Thr C:27	-	Pro C:28
7	Ser D:7	-	Pro D:8
8	Phe D:147	-	Pro D:148

Asymmetric Unit (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TCA_MOUSE_001 *	Y	2	D	TCA_MOUSE	---	---	A/C	Y	110	D
2	UniProt	VAR_TCA_MOUSE_002 *	Y	2	N	TCA_MOUSE	---	---	A/C	Y	110	N
3	UniProt	VAR_TCB2_MOUSE_001 *	K	50	R	TCB2_MOUSE	---	---	B/D	K	160	R
4	UniProt	VAR_TCB2_MOUSE_002 *	Y	70	H	TCB2_MOUSE	---	---	B/D	Y	180	H
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TCA_MOUSE_001 *	Y	2	D	TCA_MOUSE	---	---	A	Y	110	D
2	UniProt	VAR_TCA_MOUSE_002 *	Y	2	N	TCA_MOUSE	---	---	A	Y	110	N
3	UniProt	VAR_TCB2_MOUSE_001 *	K	50	R	TCB2_MOUSE	---	---	B	K	160	R
4	UniProt	VAR_TCB2_MOUSE_002 *	Y	70	H	TCB2_MOUSE	---	---	B	Y	180	H
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TCA_MOUSE_001 *	Y	2	D	TCA_MOUSE	---	---	C	Y	110	D
2	UniProt	VAR_TCA_MOUSE_002 *	Y	2	N	TCA_MOUSE	---	---	C	Y	110	N
3	UniProt	VAR_TCB2_MOUSE_001 *	K	50	R	TCB2_MOUSE	---	---	D	K	160	R
4	UniProt	VAR_TCB2_MOUSE_002 *	Y	70	H	TCB2_MOUSE	---	---	D	Y	180	H
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2Q86)

(no "Exon" information available for 2Q86)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:189
 aligned with TCA_MOUSE | P01849 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:192
                                                                                                                                         1                                                                                  
                                     -         -         -         -         -         -         -         -         -         -         1        11        21        31        41        51        61        71        81  
            TCA_MOUSE     - -------------------------------------------------------------------------------------------------------------PYIQNPEPAVYQLKDPRSQDSTLCLFTDFDSQINVPKTMESGTFITDKTVLDMKAMDSKSNGAIAWSNQTSFTCQDIFKETNA  83
               SCOP domains d2q86a1 A:0-110 automated matches                                                                              d2q86a2 A:111-191 automated matches                                               SCOP domains
               CATH domains 2q86A01 A:0-109 Immunoglobulins                                                                               ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee.....eeeeeee...eeeeee..eeeeee....eeeeee...hhhhheeeeeee.hhhhhee...eeeeee........eeeeee.......eeeeeeee.............eee...eeee..---.eeeeeeeee.....hhhhhh..... Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------------------------------------------------------------------D--------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------N--------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2q86 A   0 KTQVEQSPQSLVVRQGENCVLQCNYSVTPDNHLRWYKQDTGKGLVLLTVLVDQKDKTSNGRYSATLDKDAKHSTLHITATLLDDTATYFCVVGDRGSALFGSGTQLIVIPYIQNPEPAVYQLKDPRSQDSTLCLFTDFDSQINVPKTMESGTFITDKCVLDMK---SKSNGAIAWSNQTSFTCQDIFKETNA 191
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159  |   |169       179       189  
                                                                                                                                                                                            162 166

Chain B from PDB  Type:PROTEIN  Length:233
 aligned with TCB2_MOUSE | P01851 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:233
                                                                                                                                        1                                                                                                                            
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102       112       122   
           TCB2_MOUSE     - ------------------------------------------------------------------------------------------------------------EDLRNVTPPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVSTDPQAYKESNYSYCLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRA 125
               SCOP domains d2q86b1 B:3-111 automated matches                                                                            d2q86b2 B:112-235 T-cell antigen receptor                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeee......ee.......eee.....eeeeee...hhhhheeeeeeeee..eeee...eeeeee.hhhhh...eeeee..hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....eeee..eeeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------R-------------------H------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q86 B   3 AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGGGGTLYFGAGTRLSVLEDLRNVTPPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVCTDPQAYKESNYSYCLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRA 235
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232

Chain C from PDB  Type:PROTEIN  Length:190
 aligned with TCA_MOUSE | P01849 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:193
                                                                                                                                         1                                                                                   
                                     -         -         -         -         -         -         -         -         -         -         1        11        21        31        41        51        61        71        81   
            TCA_MOUSE     - -------------------------------------------------------------------------------------------------------------PYIQNPEPAVYQLKDPRSQDSTLCLFTDFDSQINVPKTMESGTFITDKTVLDMKAMDSKSNGAIAWSNQTSFTCQDIFKETNAT  84
               SCOP domains d2q86c1 C:0-110 automated matches                                                                              d2q86c2 C:111-192 automated matches                                                SCOP domains
               CATH domains 2q86C01 C:0-109 Immunoglobulins                                                                               ----------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------DUF1968-2q86C01 C:116-192                                                     Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------DUF1968-2q86C02 C:116-192                                                     Pfam domains (2)
         Sec.struct. author ...eeee..eeeee....eeeeeee......eeeeeee.....eeeeeee...eeeeee..eeeeee....eeeeee...hhhhheeeeeeee....eee...eeeeee........eeeeee.......eeeeeeee..............ee...eeee..---.eeeeeeee......hhhhhh...... Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------------------------------------------------------------------D---------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------N---------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q86 C   0 KTQVEQSPQSLVVRQGENCVLQCNYSVTPDNHLRWYKQDTGKGLVLLTVLVDQKDKTSNGRYSATLDKDAKHSTLHITATLLDDTATYFCVVGDRGSALFGSGTQLIVIPYIQNPEPAVYQLKDPRSQDSTLCLFTDFDSQINVPKTMESGTFITDKCVLDMK---SKSNGAIAWSNQTSFTCQDIFKETNAT 192
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159  |   |169       179       189   
                                                                                                                                                                                            162 166

Chain D from PDB  Type:PROTEIN  Length:233
 aligned with TCB2_MOUSE | P01851 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:233
                                                                                                                                        1                                                                                                                            
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102       112       122   
           TCB2_MOUSE     - ------------------------------------------------------------------------------------------------------------EDLRNVTPPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVSTDPQAYKESNYSYCLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRA 125
               SCOP domains d2q86d1 D:3-111 automated matches                                                                            d2q86d2 D:112-235 T-cell antigen receptor                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------C1-set-2q86D01 D:125-214                                                                  --------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------C1-set-2q86D02 D:125-214                                                                  --------------------- Pfam domains (2)
         Sec.struct. author .eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeee......ee.......eee.....eeeeee...hhhhheeeeeeeee..eeee...eeeeee.hhhhh...eeeee..hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....eeee..eeeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------R-------------------H------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q86 D   3 AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGGGGTLYFGAGTRLSVLEDLRNVTPPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVCTDPQAYKESNYSYCLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRA 235
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Mouse (Mus musculus) [TaxId: 10090] (360)

1a	d2q86a1	A:0-110
1b	d2q86a2	A:111-191
1c	d2q86b1	B:3-111
1d	d2q86c1	C:0-110
1e	d2q86c2	C:111-192
1f	d2q86d1	D:3-111

Family: C1 set domains (antibody constant domain-like) (3013)

Protein domain: T-cell antigen receptor (81)

Mouse (Mus musculus), beta-chain [TaxId: 10090] (15)

2a	d2q86b2	B:112-235
2b	d2q86d2	D:112-235

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

1a	2q86A01	A:0-109
1b	2q86C01	C:0-109

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: C1-set (338)

Mus musculus (Mouse) (118)

1a	C1-set-2q86D01	D:125-214
1b	C1-set-2q86D02	D:125-214

Clan: no clan defined [family: DUF1968] (16)

Family: DUF1968 (16)

Mus musculus (Mouse) (2)

2a	DUF1968-2q86C01	C:116-192
2b	DUF1968-2q86C02	C:116-192

Asymmetric Unit(hide GO term definitions)

Chain A,C (TCA_MOUSE | P01849)

cellular component
	GO:0016021		integral component of membrane		The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020		membrane		A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain B,D (TCB2_MOUSE | P01851)

cellular component
	GO:0016021		integral component of membrane		The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020		membrane		A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	Cis Peptide Bonds
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		Thr C:27 - Pro C:28	[ RasMol ]

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	2q86
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	TCB2_MOUSE \| P01851
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UniProtKB/Swiss-Prot
	TCA_MOUSE \| P01849	:	1lp9 2j8u 2jcc 3c6l 3mbe
	TCB2_MOUSE \| P01851	:	1l0x 1l0y 1mwa

2cde	STRUCTURE OF THE HUMAN HOMOLOG VA24
2eyr	STRUCTURE OF THE HUMAN HOMOLOG VA24

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (8, 8)

SS Bonds (9, 9)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 8)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 8)

CATH Domains (1, 2)

Pfam Domains (2, 4)

Gene Ontology (2, 4)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File